@article {pmid41381437,
year = {2025},
author = {Hao, C and Dungait, JAJ and Shang, W and Hou, R and Gong, H and Yang, Y and Lambers, H and Yu, P and Delgado-Baquerizo, M and Xu, X and Kumar, A and Deng, Y and Peng, X and Cui, Z and Kuzyakov, Y and Zhou, J and Zhang, F and Tian, J},
title = {Conservation agriculture raises crop nitrogen acquisition by amplifying plant-microbe synergy under climate warming.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11067},
pmid = {41381437},
issn = {2041-1723},
mesh = {*Nitrogen/metabolism ; *Triticum/metabolism/microbiology/growth & development ; Soil Microbiology ; *Crops, Agricultural/metabolism/microbiology ; Plant Roots/metabolism/microbiology ; *Agriculture/methods ; Climate Change ; Soil/chemistry ; Nitrification ; Nitrates/metabolism ; *Conservation of Natural Resources ; Metabolomics ; Microbiota ; Metagenomics ; Bacteria/metabolism/genetics ; },
abstract = {Sustainable crop production in a warming climate requires land management strategies that support plant-soil-microbe interactions to optimize nitrogen (N) availability. Here, we investigate the interacting effects of 10 years' experimental warming and management (conservation vs. conventional agriculture) on wheat N acquisition using in situ [15]N-labeling, root metabolomics and microbial metagenomics. We find that warming amplifies the positive effects on wheat nitrate uptake by 25% in conservation agriculture compared to conventional agriculture, while alleviating microbial competition for N. Additionally, warming increases soil gross N mineralization and nitrification rates by 191% and 159%, but decreases microbial immobilization by 24% in conservation agriculture. Concurrently, microbial genes for mineralization and nitrification are enriched, while those for N immobilization and nitrate reduction are reduced under conservation agriculture with warming. These shifts are driven by alterations in root primary and secondary metabolites, which reshape N-cycling microbial functional niches and optimize multiple microbial N processes beyond mere organic N mining. This reconfiguration increases carbon-nitrogen exchange efficiency, enabling wheat to outcompete soil microorganisms for N. Collectively, our findings suggest that conservation agriculture enhances plant N acquisition by strengthening plant-soil-microbe interactions under climate change, providing a sustainable strategy for future food security.},
}

*Nitrogen/metabolism
*Triticum/metabolism/microbiology/growth & development
Soil Microbiology
*Crops, Agricultural/metabolism/microbiology
Plant Roots/metabolism/microbiology
*Agriculture/methods
Climate Change
Soil/chemistry
Nitrification
Nitrates/metabolism
*Conservation of Natural Resources
Metabolomics
Microbiota
Metagenomics
Bacteria/metabolism/genetics

@article {pmid41381092,
year = {2025},
author = {Lane, KR and Jones, SE and Osborne, TH and Geller-McGrath, D and Nwaobi, BC and Chen, L and Thomas, BC and Hudson-Edwards, KA and Banfield, JF and Santini, JM},
title = {Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70261},
doi = {10.1111/1758-2229.70261},
pmid = {41381092},
issn = {1758-2229},
support = {NE/L002485/1//Natural Environment Research Council/ ; BB/N012674/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //Hellenic Coppers Mines Ltd/ ; },
mesh = {*Copper/metabolism/chemistry ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Archaea/metabolism/genetics/classification/isolation & purification ; *Sulfides/metabolism/chemistry ; *Microbial Consortia ; Metagenomics ; *Minerals/metabolism/chemistry ; *Microbiota ; Plasmids/genetics ; },
abstract = {Copper bioleaching is a green technology for the recovery of copper from chalcopyrite (CuFeS2) and chalcocite (Cu2S) ores. Much remains to be learned about how mineral type and surface chemistry influence microbial community composition. Here, we established a microbial consortium from a copper bioleaching column in Cyprus on chalcopyrite and then sub-cultured it to chalcocite to investigate how the community composition shifts due to changes in mineral structure and the absence of mineral-derived Fe. The solution chemistry was determined and microbial communities characterised by genome-resolved metagenomics after 4 and 8 weeks of cultivation. Acidithiobacillus species and strains, a Rhodospirilales, Leptospirillum ferrodiazotrophum and Thermoplasmatales archaea dominated all enrichments, and trends in abundance patterns were observed with mineralogy and surface-attached versus planktonic conditions. Many bacteria had associated plasmids, some of which encoded metal resistance pathways, sulphur metabolic capacities and CRISPR-Cas loci. CRISPR spacers on an Acidithiobacillus plasmid targeted plasmid-borne conjugal transfer genes found in the same genus, likely belonging to another plasmid, evidence of intra-plasmid competition. We conclude that the structure and composition of metal sulphide minerals select for distinct consortia and associated mobile elements, some of which have the potential to impact microbial activity during sulphide ore dissolution.},
}

*Copper/metabolism/chemistry
*Bacteria/metabolism/genetics/classification/isolation & purification
*Archaea/metabolism/genetics/classification/isolation & purification
*Sulfides/metabolism/chemistry
*Microbial Consortia
Metagenomics
*Minerals/metabolism/chemistry
*Microbiota
Plasmids/genetics

@article {pmid41380668,
year = {2025},
author = {Sumner, JT and Huttelmaier, S and Pickens, CI and Moghadam, AA and Abdala-Valencia, H and Shen, J and , and Hauser, AR and Seed, PC and Wunderink, RG and Hartmann, EM},
title = {Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.},
journal = {Cell host & microbe},
volume = {33},
number = {12},
pages = {2148-2166.e8},
doi = {10.1016/j.chom.2025.11.011},
pmid = {41380668},
issn = {1934-6069},
mesh = {Humans ; *Microbiota/genetics ; *Lung/microbiology ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/pathology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Bacterial Load ; Middle Aged ; Aged ; },
abstract = {The precise microbial determinants driving clinical outcomes in severe pneumonia are unknown. Competing ecological forces produce dynamic microbiota states in health and disease, and a more thorough understanding of these states has the potential to improve pneumonia therapy. Here, we leverage a large collection of bronchoscopic samples from patients with suspected pneumonia to determine lung microbial ecosystem dynamics throughout the course of pneumonia. We combine 16S rRNA gene, metagenomic, and metatranscriptomic sequencing with bacterial-load quantification to reveal clinically relevant drivers of pneumonia progression. Microbiota states are predictive of pneumonia subtypes and exhibit differential stability and pneumonia therapy response. Disruptive forces, such as aspiration, are associated with cohesive changes in gene expression and microbial community structure. In summary, we show that host and microbiota landscapes change in unison with clinical phenotypes and that microbiota state dynamics reflect pneumonia progression. We suggest that distinct pathways of lung microbial community succession mediate pneumonia progression.},
}

Humans
*Microbiota/genetics
*Lung/microbiology
Disease Progression
RNA, Ribosomal, 16S/genetics
*Pneumonia/microbiology/pathology
Metagenomics
Bacteria/classification/genetics/isolation & purification
Male
Female
Bacterial Load
Middle Aged
Aged

@article {pmid41380282,
year = {2025},
author = {Xu, X and Wang, J and Deng, C and Yu, X and Nie, R and Wang, S and Huang, W},
title = {Metagenomic insights into rhizosphere microbiome dynamics of Oenanthe javanica in ecological floating beds under different hydrodynamic regimes.},
journal = {Journal of contaminant hydrology},
volume = {277},
number = {},
pages = {104795},
doi = {10.1016/j.jconhyd.2025.104795},
pmid = {41380282},
issn = {1873-6009},
abstract = {Ecological floating beds (EFBs) are a cost-effective and sustainable technology that utilizes macrophyte to remove nutrients from aquatic ecosystems, where rhizosphere bacterial degradation and assimilation play a key role in nutrient removal. However, the current knowledge about how hydrodynamic regimes impact the rhizosphere bacterial community on EFB systems remains limited. Here, we investigated the effects of different hydrodynamic regimes (i.e., stagnant water, pulsed water, and flowing water conditions) on the rhizosphere bacterial community structure and function of Oenanthe javanica in an experimental EFB system based on metagenomic sequencing. We observed that bacterial community compositions on the roots of O. javanica were significantly differed across the three hydrodynamic regimes, with the highest bacterial biodiversity captured from the flowing water condition. Moreover, a total of 65 nitrogen functional genes (NFGs) were identified in the rhizosphere bacterial community, with nitrate reduction pathways dominating the nitrogen cycling processes. In contrast, totally 139 phosphorus functional genes (PFGs) were detected, primarily involved in purine metabolism, which drove the phosphorus cycling dynamics. We found the distinct nitrogen and phosphorus metabolic strategies of rhizosphere bacterial communities in response to hydrodynamic regime changes. Specifically, the relative abundances of NFGs like nasB, narl, and ansB were significantly increased under the pulsed water condition, whereas gdh_K00262 were relative abundant under the flowing condition. Moreover, pulsed water condition promoted the relative abundances of PFGs such asas phnC, phoD, and pgtP in rhizosphere bacterial communities, in contrast to the stagnant condition, which favored genes like ugpC, purK, phoH, and purA. Our study offers technical support for regulating plant degradation of pollutants to improve EFB's performance in engineering applications.},
}

@article {pmid41379797,
year = {2025},
author = {Vásquez, JN and Doncel, P and Camacho, J and Ruiz, E and Recio, V and Tarragó, D},
title = {Targeted virome deep sequencing reveals frequent herpesvirus detection in intestinal biopsies of inflammatory bowel disease patients.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337322},
doi = {10.1371/journal.pone.0337322},
pmid = {41379797},
issn = {1932-6203},
mesh = {Humans ; *Virome/genetics ; Female ; Male ; *Inflammatory Bowel Diseases/virology/pathology ; Biopsy ; High-Throughput Nucleotide Sequencing ; Adult ; Middle Aged ; *Herpesviridae/genetics/isolation & purification ; Retrospective Studies ; Aged ; Intestinal Mucosa/virology/pathology ; *Intestines/virology/pathology ; Colitis, Ulcerative/virology ; Metagenomics ; Young Adult ; },
abstract = {BACKGROUND: The intestinal virome is increasingly recognized for its impact on intestinal health and disease. Inflammatory bowel disease (IBD) has been linked to microbial dysbiosis, yet most studies rely on fecal samples. Here, we characterized the mucosa-associated virome directly from intestinal biopsies, providing a more localized view of viral activity at the site of pathology.

METHODS: We conducted a retrospective metagenomic study of 56 residual intestinal biopsy samples from IBD patients including ulcerative colitis (n = 37; 66.1%), IBD-Unclassified (n = 9; 16.1%), ulcerative proctitis (n = 7; 12.5%), and Crohn's disease (n = 3; 5.4%), applying high-throughput sequencing after viral nucleic acid enrichment using a probe-based capture approach. Metagenomic data were processed using the Chan Zuckerberg ID (CZ ID) platform.

RESULTS: Viruses were detected in 58.9% (33/56) of the biopsies, primarily members of the Herpesviridae family. EBV was the most frequently detected virus (33.9%), followed by HHV-7 (21.4%), and both CMV and HHV-6 (12.5% each), after decomposing coinfections. Other viruses such as Norovirus and human papillomavirus (HPV) were detected at lower frequencies. Coinfections were also identified. No statistically significant associations were found between viral presence and IBD (ulcerative colitis, Crohn's disease, ulcerative proctitis, and IBD-Unclassified).

CONCLUSIONS: Herpesviruses are rarely detected in healthy intestinal viromes and are generally considered absent, whereas their frequent presence in IBD biopsies suggests possible pathological relevance. Our findings highlight the value of metagenomic sequencing in characterizing the intestinal virome to assess the diagnostic or prognostic value of viral biomarkers in IBD.},
}

Humans
*Virome/genetics
Female
Male
*Inflammatory Bowel Diseases/virology/pathology
Biopsy
High-Throughput Nucleotide Sequencing
Adult
Middle Aged
*Herpesviridae/genetics/isolation & purification
Retrospective Studies
Aged
Intestinal Mucosa/virology/pathology
*Intestines/virology/pathology
Colitis, Ulcerative/virology
Metagenomics
Young Adult

@article {pmid41379255,
year = {2025},
author = {Špiljak, B and Ozretić, P and Brailo, V and Škrinjar, I and Lončar Brzak, B and Andabak Rogulj, A and Butić, I and Tambić Andrašević, A and Vidović Juras, D},
title = {Microbial dysbiosis and host-microbe interactions in proliferative verrucous leukoplakia: insights into carcinogenic potential.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {65},
pmid = {41379255},
issn = {1432-072X},
mesh = {Humans ; *Dysbiosis/microbiology ; *Leukoplakia, Oral/microbiology/pathology ; Microbiota ; *Host Microbial Interactions ; Carcinogenesis ; Mouth Neoplasms/microbiology/pathology ; },
abstract = {Proliferative verrucous leukoplakia (PVL) is a rare and aggressive oral potentially malignant disorder (OPMD) characterized by multifocal keratotic plaques, progressive expansion, high recurrence, and a strong risk of malignant transformation. Although its etiology remains unclear, recent evidence emphasizes the role of the oral microbiome as a key factor in disease progression. Alterations in microbial diversity and ecological balance create a shift toward dysbiosis, supporting a chronic inflammatory microenvironment that favors epithelial transformation. Specific taxa, including Fusobacterium and Porphyromonas, have been implicated in biofilm formation, immune evasion, and modulation of epithelial signaling pathways. These interactions highlight the potential of microbial communities to drive oncogenic processes through host-microbe crosstalk. Advanced methodological approaches such as metagenomics, functional microbiome profiling, and multi-omics integration provide novel opportunities to unravel the mechanisms of dysbiosis in PVL. Beyond pathogenesis, microbiome research opens perspectives for the identification of predictive biomarkers, targeted prevention, and microbiome-based therapeutics. This review synthesizes current insights into the microbial basis of PVL and outlines future directions aimed at improving understanding of host-microbe interactions and their role in oral carcinogenesis. Relevant literature was identified through PubMed and Web of Science searches (1985-2025) using terms related to PVL, oral leukoplakia, OPMD, oral microbiome, and oral squamous cell carcinoma. In conclusion, current evidence suggests that while microbial dysbiosis is not an isolated driver, it likely synergizes with genetic, epigenetic, and immunological factors in PVL progression, offering opportunities for biomarker discovery and novel therapeutic strategies. This study also provides a potential direction for the early diagnosis of PVL and the development of microecologically targeted interventions.},
}

Humans
*Dysbiosis/microbiology
*Leukoplakia, Oral/microbiology/pathology
Microbiota
*Host Microbial Interactions
Carcinogenesis
Mouth Neoplasms/microbiology/pathology

@article {pmid41379245,
year = {2025},
author = {Namadara, S and Pragadeesh, ARU and Uthandi, S and Rangasamy, A and Malaichamy, K and Venkatesan, M and Narayanan, MB and Murugaiyan, S},
title = {Comparative metagenomic analysis of bacterial communities associated with two mealybug species, Phenacoccus saccharifolii and Dysmicoccus carens infesting sugarcane in Tamil Nadu, India.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {504},
pmid = {41379245},
issn = {1573-0972},
support = {DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; },
mesh = {*Saccharum/parasitology ; Animals ; India ; *Bacteria/classification/genetics/isolation & purification ; *Hemiptera/microbiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {This study presents a comparative metagenomic analysis of the gut bacterial communities of two sugarcane-infesting mealybug species, Phenacoccus saccharifolii (WR) and Dysmicoccus carens (RR), from Tamil Nadu, India. Using Oxford Nanopore sequencing of the 16s rRNA gene spanning the hypervariable regions V1 - V9 and predictive metagenomics, differences in microbial diversity, taxonomy, and functional potential were assessed to explore the ecological adaptations of the gut microbiota in mealybugs. The D. carens gut microbiome showed higher species richness than P. saccharifolii (WR) (125 vs. 45 species, p < 0.05) but lower community evenness (0.43 vs. 0.61, p < 0.05), resulting in similar overall Shannon diversity (2.08 vs. 2.30) despite markedly different community structures, which may be influenced by their different feeding niches, including the sugarcane crown region, leaf sheath tissues, and basal stem and root portions. Both mealybug species exhibited contrasting bacterial community structures. D. carens (RR) harbored high abundances of endosymbionts (43.8%), Gilliamella (22.3%), Enterobacter (18.3%), and Candidatus Tremblaya (9.3%), representing a symbiont-dominated microbiome typical of many hemipteran insects. P. saccharifolii (WR) displayed a distinct profile with Serratia as the dominant genus (43.2%), followed by Enterobacter (20.1%), Klebsiella (14.6%), and substantially reduced endosymbiont abundances (14.8%). Beta diversity analysis revealed distinct community clustering of species, highlighting the variation driven by feeding habitat and host genotype. Functional profiling indicated largely conserved metabolic capabilities dominated by amino acid and carbohydrate metabolism, which was a key to compensate the nutrient-poor phloem sap diet. The core microbiome identified several genera that form complex ecological networks, emphasizing their importance in community stability. These findings provide insights into the role of symbiotic bacteria in mealybug adaptation to different ecological niches within the sugarcane agroecosystem. Understanding these host-microbiome interactions may facilitate the development of targeted, microbiome-based biocontrol strategies for sustainable mealybug management in sugarcane cultivation.},
}

*Saccharum/parasitology
Animals
India
*Bacteria/classification/genetics/isolation & purification
*Hemiptera/microbiology
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Phylogeny
DNA, Bacterial/genetics

@article {pmid41379027,
year = {2025},
author = {Esvap, E and Ulgen, KO},
title = {Community Modeling Reveals Disrupted Gut Microbial Secretion in Autism Associated With Redox and Neurometabolic Alterations.},
journal = {Biotechnology journal},
volume = {20},
number = {12},
pages = {e70164},
doi = {10.1002/biot.70164},
pmid = {41379027},
issn = {1860-7314},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Oxidation-Reduction ; Child ; Male ; Feces/microbiology ; *Autism Spectrum Disorder/microbiology/metabolism ; Female ; Child, Preschool ; Metagenomics ; Metabolomics ; Bacteria/metabolism/classification/genetics ; *Autistic Disorder/microbiology/metabolism ; },
abstract = {Emerging evidence suggests that disruptions in the gut microbiome may influence autism spectrum disorder (ASD) through altered microbial metabolism and gut-brain communication. However, the specific metabolic impacts of these microbial changes remain unclear. Community-scale metabolic modeling was applied to shotgun metagenomics data from children with ASD and neurotypical controls to predict secretion of host-impacting metabolites. Modeled ASD-associated communities exhibited altered predicted secretion of metabolites related to redox balance and neurotransmission, including increased 2-ketobutyrate and GABA and reduced riboflavin and inositol, with microbiota transfer therapy (MTT) shifting these profiles toward NT. Empirical fecal metabolomics data showed generally consistent directional trends with model predictions. Reductions in autism severity scores following MTT were associated with increased predicted secretion potentials for inositol and arginine. Taxonomic analysis revealed a depletion of beneficial and an enrichment of pro-inflammatory species, such as Escherichia and Flavonifractor, in ASD. Associations between microbial taxa (e.g., Bacteroides, Bifidobacterium) and neuroactive metabolites highlight microbial modulation as a promising therapeutic strategy in ASD. These results emphasize microbial metabolism as a contributor to ASD traits and a target for therapeutic intervention.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
Oxidation-Reduction
Child
Male
Feces/microbiology
*Autism Spectrum Disorder/microbiology/metabolism
Female
Child, Preschool
Metagenomics
Metabolomics
Bacteria/metabolism/classification/genetics
*Autistic Disorder/microbiology/metabolism

@article {pmid41373884,
year = {2025},
author = {Ahlström, MG and Bjerre, RD and Hu, Y and Seifert, M and Boulund, F and Skov, L and Johansen, JD and Engstrand, L},
title = {Resilience of the Skin Microbiome in Atopic Dermatitis During Short-Term Topical Treatment.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311737},
pmid = {41373884},
issn = {1422-0067},
support = {LF-ST-21-500002//LEO Foundation/ ; },
mesh = {Humans ; *Dermatitis, Atopic/microbiology/drug therapy ; *Microbiota/drug effects ; *Skin/microbiology/drug effects ; Adult ; Female ; Male ; Middle Aged ; Administration, Topical ; Young Adult ; Dysbiosis/microbiology ; Skin Microbiome ; },
abstract = {Atopic dermatitis (AD) is associated with microbial dysbiosis and impaired skin barrier function. Topical therapies, such as moisturisers and antimicrobial fragrance compounds, may modulate the skin microbiome and support disease management. The objective was to evaluate how a moisturiser and a fragrance compound (farnesol) influence skin microbiome composition in individuals with AD and healthy controls. In a randomised, controlled, operator-blinded study, 15 AD patients and 15 healthy controls applied a moisturiser, farnesol, moisturiser + farnesol, or no treatment to defined skin areas over 7 days. Microbiome composition, alpha/beta diversity, and core taxa were analysed using shotgun metagenomics. At baseline, AD patients exhibited distinct microbial profiles, including elevated Staphylococcus aureus and Micrococcus luteus. Neither moisturiser nor farnesol significantly altered richness, beta diversity, or core taxa in either AD patients or controls. However, moisturiser use in healthy individuals modestly increased Shannon diversity, reflecting improved microbial evenness. Despite clear microbiome differences between AD and healthy skin, short-term topical treatment did not markedly shift microbial composition. The observed stability underscores the resilience of the skin microbiome and suggests that longer interventions or more targeted formulations may be necessary to influence microbial dysbiosis in AD.},
}

Humans
*Dermatitis, Atopic/microbiology/drug therapy
*Microbiota/drug effects
*Skin/microbiology/drug effects
Adult
Female
Male
Middle Aged
Administration, Topical
Young Adult
Dysbiosis/microbiology
Skin Microbiome

@article {pmid41373768,
year = {2025},
author = {Sobolev, A and Sibiryakina, D and Chevokina, E and Slonova, D and Yurikova, D and Kozlova, S and Trofimova, A and Zubarev, V and Kiselev, A and Konovalova, O and Sutormin, D and Isaev, A},
title = {Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311616},
pmid = {41373768},
issn = {1422-0067},
support = {075-10-2021-114//Ministry of Science and Higher Education/ ; 22-14-00004//Russian Science Foundation/ ; },
mesh = {*Metagenomics/methods/economics ; Animals ; RNA, Ribosomal, 16S/genetics ; Cost-Benefit Analysis ; Feces/microbiology ; Benchmarking ; *Metagenome ; *DNA, Bacterial/isolation & purification/genetics ; Reproducibility of Results ; Geologic Sediments/microbiology ; *DNA/isolation & purification ; Gastrointestinal Microbiome/genetics ; },
abstract = {Extraction of high-quality microbial DNA remains a critical bottleneck in metagenomic research. Environmental samples often produce fragmented DNA and are prone to contaminations that interfere with downstream sequencing, while widely used commercial kits can be prohibitively expensive. Therefore, systematic evaluation of cost-effective alternatives is essential to support large-scale metagenomic studies. In this work, we benchmarked eight commercial DNA extraction kits from Magen, SkyGen, and Sileks against Qiagen reference kits. Four representative sample types were analyzed: freshwater, seafloor sediments, Pacific oyster (Magallana gigas) gut microbiome, and mammalian feces. DNA yield, integrity, purity, PCR inhibitor content, and eukaryotic DNA admixture were assessed. Microbial community composition, alpha diversity, reproducibility, and contamination ("kitome" and "splashome") were further evaluated using 16S rRNA amplicon sequencing. We revealed that several alternative kits performed comparably or better than the Qiagen reference standard. Magen Soil and Magen Bacterial provided high yields and reproducibility, though the latter produced more fragmented DNA. SkyGen Stool excelled with host-associated samples, while Sileks Soil and Metagenomic kits preserved higher diversity in sediments. Magen Microbiome consistently underperformed. This study identifies multiple cost-effective DNA extraction strategies and provides practical guidance for selecting balanced DNA purification methods for different sample types.},
}

*Metagenomics/methods/economics
Animals
RNA, Ribosomal, 16S/genetics
Cost-Benefit Analysis
Feces/microbiology
Benchmarking
*Metagenome
*DNA, Bacterial/isolation & purification/genetics
Reproducibility of Results
Geologic Sediments/microbiology
*DNA/isolation & purification
Gastrointestinal Microbiome/genetics

@article {pmid41351056,
year = {2025},
author = {Stach, TL and Starke, J and Bouderka, F and Bornemann, TLV and Soares, AR and Wilkins, MJ and Goldman, AE and Stegen, JC and Borton, MA and Probst, AJ},
title = {Conserved environmental adaptations of stream microbiomes in the hyporheic zone across North America.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {253},
pmid = {41351056},
issn = {2049-2618},
support = {426547801//Deutsche Forschungsgemeinschaft/ ; DE-AC05-76RL01830//U.S. Department of Energy/ ; },
mesh = {*Microbiota/genetics ; *Geologic Sediments/microbiology ; *Rivers/microbiology ; North America ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Ecosystem ; Metagenome ; Sulfur/metabolism ; Nitrogen/metabolism ; Nitrogen Cycle ; Adaptation, Physiological ; Metagenomics/methods ; },
abstract = {BACKGROUND: Stream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones-represented by the top sediment layer in this study-are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental factors.

RESULTS: Based on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies.

CONCLUSIONS: The hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems. Video Abstract.},
}

*Microbiota/genetics
*Geologic Sediments/microbiology
*Rivers/microbiology
North America
*Bacteria/classification/genetics/metabolism/isolation & purification
Ecosystem
Metagenome
Sulfur/metabolism
Nitrogen/metabolism
Nitrogen Cycle
Adaptation, Physiological
Metagenomics/methods

@article {pmid41330099,
year = {2025},
author = {Barman, P and Paul, A and Sinha, S and Saha, T and Mondal, N and Dutta, S and Chatterjee, S and Ghosh, W and Chakraborty, R},
title = {Microbial-viral synergy in Eisenia fetida gut supports earthworm survival, detoxification, and functional resilience.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181101},
doi = {10.1016/j.scitotenv.2025.181101},
pmid = {41330099},
issn = {1879-1026},
mesh = {Animals ; *Oligochaeta/physiology/virology/microbiology ; *Gastrointestinal Microbiome ; Soil Pollutants/metabolism ; Inactivation, Metabolic ; RNA, Ribosomal, 16S ; Biodegradation, Environmental ; Bacteria ; Metagenome ; },
abstract = {The ecological success of Eisenia fetida within decomposer food webs is closely linked to the functional diversity of its gut microbiome. This study integrates 16S rRNA gene profiling, whole-metagenome sequencing, and virome analysis to elucidate how microbial and viral communities within the earthworm gut contribute to nutrient biosynthesis, xenobiotic degradation, and environmental adaptation. Earthworms reared on compost feed enriched with Quisqualis indica plant matter showed selective enrichment of bacterial genera such as Ohtaekwangia, Nocardioides, and Steroidobacter, which are associated with hydrocarbon degradation and aromatic compound detoxification. Functional annotation of the gut metagenome revealed complete biosynthetic pathways for riboflavin, lysine, and methionine, and degradation routes for 3-nitropropionic acid (3-NPA) and aromatic pollutants. The gut virome, dominated by Siphoviridae and Myoviridae, carried auxiliary metabolic genes (AMGs) related to redox and xenobiotic metabolism, highlighting viral contributions to microbial adaptability. Reconstruction of metagenome-assembled genomes (MAGs), including a high-quality Flavobacterium MAG encoding both riboflavin biosynthesis and denitrification genes, underscored metabolic specialization within the gut. Collectively, these findings demonstrate that bacterial-viral metabolic synergy underpins E. fetida survival and ecological resilience, suggesting new microbiome-informed strategies for biowaste valorization and soil health restoration through vermicomposting.},
}

Animals
*Oligochaeta/physiology/virology/microbiology
*Gastrointestinal Microbiome
Soil Pollutants/metabolism
Inactivation, Metabolic
RNA, Ribosomal, 16S
Biodegradation, Environmental
Bacteria
Metagenome

@article {pmid41270896,
year = {2026},
author = {Diakité, MT and Sun, S and Somboro, AM and Diakité, B and Koné, A and Kassogué, Y and Fofana, D and Balam, S and Traoré, CB and Maiga, A and Kamaté, B and Ba, D and Diarra, M and Boré, S and Maiga, AI and Dai, Q and Nannini, DR and Holl, J and Murphy, R and Hou, L and Fodor, A and Maiga, M},
title = {Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study.},
journal = {Gene},
volume = {978},
number = {},
pages = {149913},
doi = {10.1016/j.gene.2025.149913},
pmid = {41270896},
issn = {1879-0038},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/pathology ; Case-Control Studies ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Pilot Projects ; Neoplasm Staging ; Adult ; Bacteria/genetics/classification ; },
abstract = {AIM: To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.

METHODS: Shotgun sequencing was performed to characterize participants' fecal microbiota using Illumina's HiSeq platform. This case-control study involved newly diagnosed CRC patients (n = 23) prior to any treatment initiation, and unrelated healthy controls (n = 24) to elucidate their microbial diversity and relative abundance.

RESULTS: The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R[2] = 0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy. Levels of Pseudomonadota, Escherichia, Citrobacter freundii, Klebsiella sp. LTGPAF-6F, Escherichia albertii, Escherichia coli, Caudovirales, Apicomplexa, and Verrucomicrobiota populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to HEMESYN2-PWY: heme biosynthesis II (anaerobic), PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline), FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation, ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis, and AEROBACTINSYN-PWY: aerobactin biosynthesis.

CONCLUSION: Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Colorectal Neoplasms/microbiology/pathology
Case-Control Studies
Male
Female
Middle Aged
Aged
Feces/microbiology
High-Throughput Nucleotide Sequencing/methods
Pilot Projects
Neoplasm Staging
Adult
Bacteria/genetics/classification

@article {pmid41270835,
year = {2025},
author = {Gao, W and Yao, Y and Sun, Y and Pu, W and Xu, L},
title = {Metatranscriptomic characterization of the canine fecal virome from pooled samples in Gansu, China.},
journal = {Virus research},
volume = {362},
number = {},
pages = {199666},
pmid = {41270835},
issn = {1872-7492},
mesh = {Animals ; Dogs ; *Feces/virology ; China ; *Virome ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; Dog Diseases/virology ; Phylogeny ; Pooled Testing ; },
abstract = {As popular companion animals, dogs present a potential risk for zoonotic viral transmission through close contact with humans. To characterize the fecal virome of dogs in Pingliang City, Gansu Province, China, we performed metatranscriptomic sequencing on 30 fecal samples pooled into three libraries, representing three distinct living environments. A total of 112,900,200 clean reads were obtained, revealing 16 viral genera spanning 15 families and highlighting a diverse viral community comprising animal viruses, bacteriophages, and plant viruses. Notably, we identified five known pathogenic viruses: canine astrovirus (3708 reads), canine dicipivirus (6578 reads), canine norovirus (16 reads), canine vesivirus (74 reads), and canine rotavirus (128 reads). Their presence suggests possible exposure events at the human-animal interface, although the infectivity and transmission risk require further experimental validation. These findings significantly expand our understanding of the canine virome and underscore the importance of "One Health" surveillance in companion animals. However, the actual zoonotic potential of the detected viruses, remains to be elucidated through further targeted investigation.},
}

Animals
Dogs
*Feces/virology
China
*Virome
*Viruses/classification/genetics/isolation & purification
Metagenomics
Dog Diseases/virology
Phylogeny
Pooled Testing

@article {pmid41224035,
year = {2026},
author = {Wu, X and Wang, C and Wang, D and Yu, Z and Meng, F},
title = {Microbiota ecology upon moderate concentrations of total ammoniacal nitrogen enhances methane production of anaerobic membrane bioreactor.},
journal = {Bioresource technology},
volume = {441},
number = {},
pages = {133630},
doi = {10.1016/j.biortech.2025.133630},
pmid = {41224035},
issn = {1873-2976},
mesh = {*Bioreactors/microbiology ; *Methane/biosynthesis ; Anaerobiosis ; *Nitrogen/pharmacology ; *Microbiota/drug effects/genetics ; *Ammonia/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Membranes, Artificial ; Sewage/microbiology ; Biofuels ; },
abstract = {In this study, the ecological responses of microbial community of anaerobic membrane bioreactor (AnMBR) upon exposure to moderate concentration total ammoniacal nitrogen (TAN) were studied to unveil the underlying mechanisms of reactor performance variation. The 16S rRNA gene and community assembly analysis indicated that the moderate ammonia concentration imposed limited selection pressure on the methanogenic community. Instead, the community assembly was governed by the random birth, death, and reproduction of community members. Network analysis further suggested that the moderate concentration of TAN established strong cooperative linkage between hydrogenotrophic methanogens (HM) and syntrophic acetate oxidizing bacteria (SAOB) in AnMBR. Metagenome sequencing analysis provided convergent evidence that there were enriched genes responsible for the SAOB-HM pathway as well as direct interspecific electron transfer. Moreover, the morphology of anaerobic granular sludge (AnGS) suggested that the decreased particle size enhanced substrate mass transfer efficiency among community members and the methanogens in inner layer of AnGS received more protection from its neighbors in moderate TAN phases. Consequently, the biogas production, methane yield and specific methanogenic activity (SMA) of granular sludge in moderate TAN phases were significantly increased compared to the low TAN phase. Together, this study has expanded our understanding of facilitation of moderate concentration TAN-containing wastewater treatment on AnMBR process.},
}

*Bioreactors/microbiology
*Methane/biosynthesis
Anaerobiosis
*Nitrogen/pharmacology
*Microbiota/drug effects/genetics
*Ammonia/pharmacology
RNA, Ribosomal, 16S/genetics
*Membranes, Artificial
Sewage/microbiology
Biofuels

@article {pmid41197330,
year = {2025},
author = {Ke, T and Jiang, T and Li, H and Dong, X and Khoo, HE},
title = {Probiotic-fermented milk alleviates hypertension in preeclampsia rats and is associated with increases in branched fatty acid esters of hydroxy fatty acids.},
journal = {Nutrition research (New York, N.Y.)},
volume = {144},
number = {},
pages = {1-15},
doi = {10.1016/j.nutres.2025.10.004},
pmid = {41197330},
issn = {1879-0739},
mesh = {Animals ; Female ; *Probiotics/pharmacology/therapeutic use ; Pregnancy ; *Hypertension ; *Pre-Eclampsia ; Rats ; *Fatty Acids/blood/metabolism ; *Cultured Milk Products ; Gastrointestinal Microbiome ; Blood Pressure/drug effects ; Rats, Sprague-Dawley ; Fermentation ; Esters ; *Milk ; Disease Models, Animal ; Antihypertensive Agents ; },
abstract = {Branched fatty acid esters of hydroxy fatty acids (FAHFAs), a newly-discovered class of endogenous lipids closely associated with obesity, cardiovascular disease, and aging, are potential drug candidates or targets for the prevention and treatment of related conditions. The antihypertensive potential of probiotic-fermented milk has been recognized, but its relevance to preeclampsia (PE) is unclear. It was hypothesized that probiotic-fermented milk could reduce blood pressure in PE rats and influence the contents of FAHFAs, with FAHFAs potentially playing a critical role in this process. To test this hypothesis, the PE rat model was constructed using L-NAME (125 mg/kg), and probiotic-fermented milk (20 mg/kg) was administered for a total of 21 d. Metagenomic sequencing and LC-MS/MS based metabolomics were used. Probiotic-fermented milk substantially attenuated hypertension in PE rats, with an efficacy comparable to that of labetalol (4 mg/kg). Probiotic-fermented milk significantly increased the contents of specific FAHFAs (e.g., 18:0/20:2, 16:0/18:2) in the gut and serum (P < .05) and FAHFAs was negatively correlated with blood pressure (P < .05). Probiotic-fermented milk regulated the composition of gut microbiota (increasing Lactiplantibacillus and Staphylococcus and decreasing Methanobrevibacter and Limosilactobacillus), and down-regulated purine, glyoxylate/dicarboxylate, and amino metabolism, and the one-carbon pool produced by folate. These metabolic shifts were strongly correlated with the gut microbiota and FAHFAs. These results indicate that probiotic-fermented milk alleviates hypertension in PE rats, potentially mediated by FAHFAs. This study provides foundational evidence for the antihypertensive mechanism of probiotic-fermented milk in preeclampsia and supports the development of novel strategies for its prevention and treatment.},
}

Animals
Female
*Probiotics/pharmacology/therapeutic use
Pregnancy
*Hypertension
*Pre-Eclampsia
Rats
*Fatty Acids/blood/metabolism
*Cultured Milk Products
Gastrointestinal Microbiome
Blood Pressure/drug effects
Rats, Sprague-Dawley
Fermentation
Esters
*Milk
Disease Models, Animal
Antihypertensive Agents

@article {pmid41192168,
year = {2025},
author = {Skalny, AV and Korobeinikova, TV and Morozova, G and Menshikova, IV and Gritsenko, VA and Zhang, F and Mak, DV and Guo, X and Sotnikova, TI and Aschner, M and Tinkov, AA},
title = {Serum trace element and mineral levels and fecal microbiota in relation to cartilage damage in rheumatoid arthritis patients.},
journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)},
volume = {92},
number = {},
pages = {127787},
doi = {10.1016/j.jtemb.2025.127787},
pmid = {41192168},
issn = {1878-3252},
mesh = {Humans ; *Arthritis, Rheumatoid/blood/microbiology/pathology ; Male ; Female ; Middle Aged ; *Feces/microbiology ; *Trace Elements/blood ; *Minerals/blood ; *Cartilage/pathology ; *Gastrointestinal Microbiome ; Adult ; Aged ; },
abstract = {UNLABELLED: The objective of the present study was to evaluate serum trace element and mineral levels as well as taxonomic characteristics of gut microbiota and their association with cartilage damage in patients with rheumatoid arthritis (RA).

MATERIALS AND METHODS: Serum trace element and mineral levels in 41 healthy controls and 41 RA patients were assessed using inductively-coupled plasma mass-spectrometry. Taxonomic characteristics of fecal microbiota were assessed using 16S metagenomic sequencing. RA patients were characterized by increased cartilage oligomeric matrix protein (COMP) and complement component 3 (C3) levels, indicative of cartilage damage and inflammation.

RESULTS: Serum Ca, Fe, Se, and Zn levels in RA patients were lower, whereas circulating Cr, Cu, and Mo concentrations exceeded the respective control values. 16S metagenomic sequencing of fecal samples revealed lower relative abundance of Firmicutes and Actinomycetota with a reduction in Firmicutes-to-Bacteroidetes ratio in RA patients. At the class level, the relative abundance of Bacilli, Coriobacteria, and Clostridia in RA patients was lower, whereas that of Bacteroidia and Negativicutes was higher compared to the control group. Tight negative association between serum Zn levels and the abundance of Bacteroidetes and Bacteroidia was observed, whereas correlation between Zn and Firmicutes-to-Bacteroidetes ratio was positive. Multiple linear regression analysis demonstrated that serum COMP level was inversely associated with serum Fe and Se levels, as well as relative abundance of Bacilli and Clostridia, being positively associated with serum Ca and C3 levels.

CONCLUSION: These novel findings demonstrate a multilateral relationship between trace element metabolism, gut microbiota, and cartilage damage in RA.},
}

Humans
*Arthritis, Rheumatoid/blood/microbiology/pathology
Male
Female
Middle Aged
*Feces/microbiology
*Trace Elements/blood
*Minerals/blood
*Cartilage/pathology
*Gastrointestinal Microbiome
Adult
Aged

@article {pmid40985325,
year = {2025},
author = {He, J and Xiao, J and Shen, X and Zhao, K and Lei, X and Zhang, H and Sun, C and Lu, H and Shao, Y},
title = {Multi-Habitat Landscape Promotes Microbial Diversity: Insights from the Traditional Agricultural Heritage and the Global Trend.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {46},
pages = {e06402},
pmid = {40985325},
issn = {2198-3844},
support = {518000-523500922002//Scientific Pre-research Fund of Zhejiang University/ ; CARS-18//Agriculture Research System of China/ ; 32022081//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; 31970483//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; },
mesh = {*Ecosystem ; *Microbiota/genetics ; *Agriculture/methods ; Biodiversity ; Bacteria/genetics/classification ; Fungi/genetics ; Metagenomics ; },
abstract = {Ecosystems are interconnected networks of diverse habitat types, rather than isolated patches. However, the role of the multi-habitat landscape in influencing microbial diversity remains poorly understood. This study investigates bacterial and fungal communities within a 2500-year agricultural heritage system, the Mulberry-dyke and Fish-pond (MF), which integrates various terrestrial and aquatic habitats. Using amplicon sequencing, metagenomics, metatranscriptomics, and genomic analyses, these findings reveal a significant proportion of unclassified microbial taxa, underscoring the importance of MF systems as an untapped reservoir of microbial genetic resources. Moreover, single-nucleotide-level analyses demonstrate that a multi-habitat landscape enhances microbial diversity through ecosystem-wide assembly, facilitated by cross-habitat microbial dispersal. Taxa found across multiple habitats exhibit convergence in microdiversity and adaptive genetic traits, indicating both ecological and functional mechanisms underlying their adaptability. A global analysis of public microbiome datasets furthermore confirms that regions with higher habitat heterogeneity support significantly higher taxonomic and functional diversity of microbiomes. Overall, this study sheds new light on the overlooked microbial diversity in traditional agricultural heritages and emphasizes the value of ancestral ecological wisdom underlying multi-habitat integration for ecosystem management. These insights offer valuable guidance for developing sustainable agricultural strategies, enhancing microbial diversity, and reinforcing ecosystem resilience in the face of global change.},
}

*Ecosystem
*Microbiota/genetics
*Agriculture/methods
Biodiversity
Bacteria/genetics/classification
Fungi/genetics
Metagenomics

@article {pmid40971838,
year = {2025},
author = {Guo, X and Liang, A},
title = {Rhizosphere-derived microbiome of Ailanthus altissima drives gut microbiome composition in Lycorma delicatula (Hemiptera: Fulgoridae).},
journal = {Journal of economic entomology},
volume = {118},
number = {6},
pages = {2771-2782},
doi = {10.1093/jee/toaf217},
pmid = {40971838},
issn = {1938-291X},
support = {32470469//National Natural Science Foundation of China/ ; 32070470//National Natural Science Foundation of China/ ; 31561163003//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Rhizosphere ; *Hemiptera/microbiology ; *Ailanthus/microbiology ; Bacteria/classification/isolation & purification/genetics ; Soil Microbiology ; },
abstract = {The spotted lanternfly (SLF), Lycorma delicatula (White) (Hemiptera: Fulgoridae), a highly polyphagous invasive pest, preferentially feeds on tree-of-heaven (TOH), Ailanthus altissima (Mill.) Swingle (Sapindales: Simaroubaceae). However, the bacterial interactions between this pest and its host plant remain poorly understood. In this study, we investigated the bacterial community composition and functional profiles in the SLF gut, TOH leaves, and TOH rhizosphere soil using amplicon and metagenomic sequencing. This study showed that the bacterial alpha-diversity differed significantly among the 3 sample types (P < 0.05). Venn analysis identified 4 shared amplicon sequence variants (ASVs) between the TOH rhizosphere soil and SLF gut, suggesting potential bacterial interactions or transfer. Further source-tracking analysis indicated that most gut bacteria originated from the rhizosphere soil. However, the dominant taxa varied across compartments: Proteobacteria dominated both the SLF gut and TOH leaves, while Acidobacteria predominated in the TOH rhizosphere soil. Network analysis revealed significant correlations between gut and rhizosphere microbes, notably Candidatus Vidania and Fastidiosipila (P < 0.05, r = 1). Functional profiling showed that the rhizosphere microbiome was enriched in nitrogen cycling and carbon fixation pathways, whereas the gut microbiome was associated with carbohydrate metabolism and nutrient assimilation. These results provide new insights into the potential roles of microbiomes in mediating plant-insect interactions and underscore the rhizosphere as a critical microbial source for SLF. Understanding these microbial connections may support the development of innovative and sustainable pest management strategies.},
}

Animals
*Gastrointestinal Microbiome
*Rhizosphere
*Hemiptera/microbiology
*Ailanthus/microbiology
Bacteria/classification/isolation & purification/genetics
Soil Microbiology

@article {pmid40967406,
year = {2026},
author = {Harwood, M and South, J and Dunn, AM and Stebbing, PD and Burgess, A and Bojko, J},
title = {Pathogen diversity of the non-native narrow-clawed crayfish (Pontastacus leptodactylus) in a UK water body.},
journal = {Journal of invertebrate pathology},
volume = {214},
number = {},
pages = {108458},
doi = {10.1016/j.jip.2025.108458},
pmid = {40967406},
issn = {1096-0805},
mesh = {Animals ; *Astacoidea/microbiology/parasitology/virology ; Introduced Species ; United Kingdom ; Symbiosis ; },
abstract = {Biological invasions are intrinsically linked to introducing associated symbiotic organisms, some of which can be parasitic or pathogenic. The pathogenic risk of an 'invasive parasite' (aka. exotic pathogen) stems from its potential to infect native hosts and induce behavioural change or mortality, with the pathogen potentially presenting a greater risk than the host. Conversely, parasites translocated by invasive hosts may also reduce the impact of their host, indirectly curbing the hosts impact on the invaded ecosystem. In this study, we develop a pathogen profile for the narrow-clawed crayfish, Pontastacus leptodactylus. This is a non-native species in the United Kingdom, and poses a possible risk as a sink for invasive parasites. We use histopathology, metagenomics and metratranscriptomics to outline the symbiotic diversity harboured by a P. leptodactylus population from West Yorkshire, England. We discovered several protozoan and bacterial species that appear to be putatively commensal with this invader, as well as several RNA viruses (Hepelivirales; Picornavirales; Nodaviridae, and others) that may be more pathogenic in nature. Microsporidia and Nudiviridae were absent in our population sample set, as were all metazoan obligate parasites, such as trematodes and acanthocephalans. Using the novel genomic and pathological data available to us, we have explored the evolutionary history of each symbiotic species and provided an initial assessment on the putative risk to native species.},
}

Animals
*Astacoidea/microbiology/parasitology/virology
Introduced Species
United Kingdom
Symbiosis

@article {pmid40885432,
year = {2026},
author = {Kwon, M and Kwon, SH and Jang, H and Oh, H and Sun, S and Jung, C and Kil, EJ},
title = {Landscape-scale virome analysis uncovers endemic and emerging honey bee viruses in the Silk-Road hub of Uzbekistan.},
journal = {Journal of invertebrate pathology},
volume = {214},
number = {},
pages = {108436},
doi = {10.1016/j.jip.2025.108436},
pmid = {40885432},
issn = {1096-0805},
mesh = {Animals ; Bees/virology ; *Virome ; Uzbekistan ; *RNA Viruses/isolation & purification/genetics ; Phylogeny ; *Insect Viruses/genetics/isolation & purification ; Genome, Viral ; },
abstract = {Honey bee health is increasingly threatened worldwide by a complex and evolving viral landscape; however, this aspect in Central Asia remains understudied despite the region being strategically positioned along historic and modern trade routes. In 2024, we conducted a nationwide virome survey of Apis mellifera across 32 cities in 11 regions of Uzbekistan, combining the metagenomic data of 14 pooled RNA-seq libraries with RT-PCR validation and phylogenetic analyses. High-quality sequencing yielded an average of approximately 60 million reads per pool. We recovered 30 viral species from 162 genomic sequences (131 complete sequences), including 11 honey bee-associated and 19 plant-infecting viruses. All samples harbored deformed wing virus type A (DWV-A), and co-infection with DWV-B predominated. Our findings provided the first full-length DWV-B genomes from Central Asia, revealing that it had > 97 % identity to European strains. New variants of the Sacbrood virus (partial sequence, approximately 4.7 kb) and Lake Sinai virus UZB were also detected. The chronic bee paralysis virus was sequenced in full for the first time in Uzbekistan, and varroa orthomyxovirus-1 exhibited segment-specific divergence. Additionally, we identified two novel plant viruses: Gulistan nepovirus 1 and Arpa carmo-like virus 1. Phylogenetic patterns of the identified viruses indicate that Uzbekistan serves as a genetic corridor connecting European and Asian virus populations. These findings fill critical geographical gaps, underscore the need for transboundary surveillance, and provide a genomic baseline for future diagnostics, epidemiology, and control strategies aimed at safeguarding pollinator and ecosystem health.},
}

Animals
Bees/virology
*Virome
Uzbekistan
*RNA Viruses/isolation & purification/genetics
Phylogeny
*Insect Viruses/genetics/isolation & purification
Genome, Viral

@article {pmid41370178,
year = {2025},
author = {Peto, L and Fawcett, N and Kamfose, MM and Scarborough, C and Peniket, A and Danby, R and Peto, TEA and Crook, DW and Llewelyn, MJ and Walker, AS},
title = {The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.97751},
pmid = {41370178},
issn = {2050-084X},
support = {NIHR200915//National Institute for Health and Care Research/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Adult ; Cross-Sectional Studies ; Middle Aged ; Aged ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Feces/microbiology ; Metagenomics ; United Kingdom ; *Bacteria/drug effects/classification/genetics ; Young Adult ; },
abstract = {Better metrics to compare the impact of different antimicrobials on the gut microbiome would aid efforts to control antimicrobial resistance (AMR). The Antibiotic Resistance in the Microbiome - Oxford (ARMORD) study recruited inpatients, outpatients, and healthy volunteers in Oxfordshire, UK, who provided stool samples for metagenomic sequencing. Data on previous antimicrobial use and potential confounders were recorded. Exposures to each antimicrobial were considered as factors in a multivariable linear regression, also adjusted for demographics, with separate analyses for those contributing samples cross-sectionally or longitudinally. Outcomes were Shannon diversity and relative abundance of specific bacterial taxa (Enterobacteriaceae, Enterococcus, and major anaerobic groups) and antimicrobial resistance genes (targeting beta-lactams, tetracyclines, aminoglycosides, macrolides, and glycopeptides). 225 adults were included in the cross-sectional analysis, and a subset of 79 patients undergoing haematopoietic cell transplant provided serial samples for longitudinal analysis. Results were largely consistent between the two sampling frames. Recent use of piperacillin-tazobactam, meropenem, intravenous co-amoxiclav, and clindamycin was associated with large reductions in microbiome diversity and reduced abundance of anaerobes. Exposure to piperacillin-tazobactam and meropenem was associated with a decreased abundance of Enterobacteriaceae and an increased abundance of Enterococcus and major AMR genes, but there was no evidence that these antibiotics had a greater impact on microbiome diversity than iv co-amoxiclav or oral clindamycin. In contrast, co-trimoxazole, doxycycline, antifungals, and antivirals had less impact on microbiome diversity and selection of AMR genes. Simultaneous estimation of the impact of over 20 antimicrobials on the gut microbiome and AMR gene abundance highlighted important differences between individual drugs. Some drugs in the WHO Access group (co-amoxiclav, clindamycin) had similar magnitude impact on microbiome diversity to those in the Watch group (meropenem, piperacillin-tazobactam) with potential implications for acquisition of resistant organisms. Metagenomic sequencing can be used to compare the impact of different antimicrobial agents and treatment strategies on the commensal flora.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Male
Female
Adult
Cross-Sectional Studies
Middle Aged
Aged
*Anti-Bacterial Agents/pharmacology
*Anti-Infective Agents/pharmacology
Feces/microbiology
Metagenomics
United Kingdom
*Bacteria/drug effects/classification/genetics
Young Adult

@article {pmid41369685,
year = {2025},
author = {Mohammadi, R and Morovati, H and Safari, F},
title = {The human mycobiome: a critical yet understudied component of health and disease.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {12},
pages = {},
doi = {10.1099/mic.0.001631},
pmid = {41369685},
issn = {1465-2080},
mesh = {Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation & purification/physiology ; COVID-19/microbiology/complications ; Dysbiosis/microbiology ; SARS-CoV-2 ; Metagenomics ; Neoplasms/microbiology ; },
abstract = {The human body hosts a complex and dynamic microbial community that is crucial for maintaining health. While bacteria dominate this system, fungal communities, collectively called the mycobiome, are increasingly recognized as vital contributors. However, fungi remain understudied due to challenges in culturing many species, limiting our understanding of their roles, interactions and effects on human biology. Advances in next-generation sequencing have transformed mycobiome research, revealing fungal diversity and its impact on health and disease. This review examines the mycobiome's composition and function across major body sites, including the gut, mouth, lungs, reproductive tract and skin. It also explores connections between fungal imbalances (dysbiosis) and diseases such as neurological disorders, cancer and post-COVID-19 complications. Despite progress, challenges persist, including the need for better culture-independent diagnostic tools and standardized research methods. Combining culturomics and metagenomics could help overcome these limitations and identify new treatment targets. By summarizing current knowledge and highlighting research gaps, this review aims to guide future studies on the mycobiome's role in human health.},
}

Humans
*Mycobiome
*Fungi/genetics/classification/isolation & purification/physiology
COVID-19/microbiology/complications
Dysbiosis/microbiology
SARS-CoV-2
Metagenomics
Neoplasms/microbiology

@article {pmid41369187,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Jimenez, K},
title = {Depth-driven decline in viral diversity unveils potential novel viruses in global deep-sea ecosystems.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {12},
pages = {},
doi = {10.1099/mic.0.001632},
pmid = {41369187},
issn = {1465-2080},
mesh = {*Seawater/virology ; *Viruses/genetics/classification/isolation & purification ; *Biodiversity ; Ecosystem ; Metagenomics ; Phylogeny ; Microbiota ; Oceans and Seas ; Metagenome ; },
abstract = {Deep-sea ecosystems remain poorly understood due to exploration challenges. Despite the advancements metagenomics have brought to the understanding of the ocean microbiome, the diversity of marine viruses, particularly in the deep sea, is still not well characterized. In this study, we analysed the impact of depth on the composition and diversity of marine viruses in deep-sea waters at a global scale. Raw reads from deep-sea shotgun DNA sequences were retrieved from the Tara and Malaspina expeditions, encompassing depths from 270 to 4,005 m. A total of 80 samples containing viral reads were identified and analysed through a comprehensive bioinformatics pipeline, including quality assessment, taxonomic classification and metabolic annotation. The analysis reveals that microbial viral diversity significantly decreases with depth, with shallower waters exhibiting higher species richness. We determined that a substantial proportion of deep-sea viral sequences remains unclassified - up to 31.9% at depths of 270-1,000 m and 9.6% at 2,400-4,005 m. Additionally, a higher abundance of auxiliary metabolic genes was observed at shallower depths, indicating potential roles in host metabolism and adaptation. Our findings reveal the deep ocean as a vast, largely unexplored source of microbial viral diversity. This research emphasizes how depth influences viral diversity and community makeup in deep-sea environments, underscoring the need for further exploration to fully grasp their complexity and ecological roles.},
}

*Seawater/virology
*Viruses/genetics/classification/isolation & purification
*Biodiversity
Ecosystem
Metagenomics
Phylogeny
Microbiota
Oceans and Seas
Metagenome

@article {pmid41368641,
year = {2025},
author = {He, J and Jia, J and Qu, W and Zhang, S and Fan, K and Lin, R and Zhao, W and Niu, Y and Huang, Y and Jia, L},
title = {Bacteroides ovatus-derived N-methylserotonin inhibit colorectal cancer via the HTR1D-mediated cAMP-PKA-NF-κB signaling axis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1696701},
pmid = {41368641},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/metabolism/pathology/drug therapy/microbiology ; Animals ; NF-kappa B/metabolism ; Mice ; Signal Transduction/drug effects ; Cyclic AMP/metabolism ; Gastrointestinal Microbiome ; Male ; *Serotonin/analogs & derivatives/pharmacology/metabolism ; Female ; *Bacteroides/metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Middle Aged ; Cell Line, Tumor ; Aged ; Disease Models, Animal ; },
abstract = {OBJECTIVE: To analyze differences in gut microbiota composition, metabolites, and metabolic pathways between healthy individuals and colorectal cancer (CRC) patients, and to investigate the inhibitory effects of N-methylserotonin (NMS) produced by Bacteroides ovatus (B.o) from orange fiber on CRC progression and its underlying mechanisms.

METHODS: (1) Fecal samples from CRC patients (n=26) and healthy controls (n=20) were collected for metagenomic sequencing and untargeted metabolomics analysis; (2) The ability of B.o to produce NMS from orange fiber was validated in vitro; (3) A CRC mouse model was established using azoxymethane (AOM)/dextran sulfate sodium (DSS) induction, followed by evaluation of body weight, rectal bleeding, colorectal length, tumor number, and intestinal barrier function; (4) Network pharmacology, molecular docking, and western blot analysis were combined to verify the mechanism of action; (5) 16S rRNA sequencing was performed to analyze gut microbiota changes.

RESULTS: (1) CRC patients showed significantly increased metabolic pathways including glycolysis, methane metabolism, beneficial amino acid degradation, and linoleic acid degradation, along with significantly decreased B.o abundance and NMS levels, which were positively correlated; (2) NMS significantly inhibited CRC cell proliferation, migration, and invasion, while promoting apoptosis; (3) Combined treatment with B.o and orange fiber or NMS alone reduced tumorigenesis and improved intestinal barrier function; (4) Mechanistic studies revealed that these effects could be mediated through downregulation of 5-hydroxytryptamine receptor 1D (HTR1D) expression and inhibition of the cAMP/PKA/IκBα/NF-κB pathway; (5) The treatments optimized gut microbiota structure and metabolite composition.

CONCLUSION: B.o and its metabolite NMS possibly inhibit CRC progression by modulating the HTR1D-mediated cAMP/PKA/NF-κB signaling pathway, while improving gut microbiota structure, providing a novel therapeutic target for CRC prevention and treatment.},
}

Humans
*Colorectal Neoplasms/metabolism/pathology/drug therapy/microbiology
Animals
NF-kappa B/metabolism
Mice
Signal Transduction/drug effects
Cyclic AMP/metabolism
Gastrointestinal Microbiome
Male
*Serotonin/analogs & derivatives/pharmacology/metabolism
Female
*Bacteroides/metabolism
Cyclic AMP-Dependent Protein Kinases/metabolism
Middle Aged
Cell Line, Tumor
Aged
Disease Models, Animal

@article {pmid41338072,
year = {2025},
author = {Jose, S and Lohith Kumar, DH and Malla, MA and Featherston, J and Bux, F and Kumari, S},
title = {Insights into microbial community, nitrogen‑phosphorus metabolism from metagenomic and metabolomic analysis of microalgal-cyanobacterial consortium-based bioinoculants.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181092},
doi = {10.1016/j.scitotenv.2025.181092},
pmid = {41338072},
issn = {1879-1026},
mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Microalgae/physiology ; *Soil Microbiology ; Fertilizers ; *Cyanobacteria/physiology ; *Microbiota ; Metagenomics ; *Microbial Consortia ; Metabolomics ; Agriculture ; },
abstract = {The intensification of agriculture through chemical fertilizers has led to severe environmental consequences. This study provides a comprehensive investigation on chemical fertilizer, vermiculite and on microalgal-cyanobacterial consortia (bioinoculants) influencing soil microbial community. Chemical fertilizer application significantly altered the microbial community, suppressing the dominant phylum Proteobacteria to 48.3 % abundance from 60.9 % in the control soil. The bioinoculant treatments maintained a high Proteobacteria abundance (58.9 %-59.7 %) and fostered a growth-oriented, anabolic strategy. The 50:50 mix treatment uniquely promoted the fungal phylum Basidiomycota to 18.2 % abundance and showed the highest investment in the Glycolysis/Gluconeogenesis pathway (23.0 %). Chemical fertilizer treatment upregulated genes for rapid nitrogen assimilation (glnA, Log2FC = 0.60) and phosphorus starvation response (phoB, Log2FC = 0.65; pstS, Log2FC = 0.83). The enhanced energy production and conversion (11.83 %), amino acid transport and metabolism (11.20 %), and fatty acid biosynthesis (45.3 %) was observed in bioinoculant treatment. Unlike chemical fertilizer treatment, bioinoculant treatment led to the accumulation of the osmoprotectant trehalose and structural membrane lipids, while the 50:50 mix was uniquely characterized by a higher abundance of xylose. These findings demonstrate that the microalgal-cyanobacterial consortium can enhance nutrient recycling, and potentially boost soil health by reshaping the soil microbiome and metabolic functions, offering a promising strategy for sustainable agriculture.},
}

*Phosphorus/metabolism
*Nitrogen/metabolism
*Microalgae/physiology
*Soil Microbiology
Fertilizers
*Cyanobacteria/physiology
*Microbiota
Metagenomics
*Microbial Consortia
Metabolomics
Agriculture

@article {pmid41314069,
year = {2025},
author = {Kumari, SP and Hooda, S and Diwan, P and Gupta, RK},
title = {Seasonal variations and functional insights into the urban air microbiome across public transit environments at railway stations in Delhi, India.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181062},
doi = {10.1016/j.scitotenv.2025.181062},
pmid = {41314069},
issn = {1879-1026},
mesh = {India ; Seasons ; *Microbiota ; *Railroads ; *Air Microbiology ; *Environmental Monitoring ; Cities ; Bacteria/classification ; },
abstract = {Airborne microbial communities play an underappreciated yet critical role in shaping urban environmental health, particularly in densely crowded public transit systems. This study aimed to explore the taxonomic and functional landscape of airborne bacteria, highlighting the seasonal disparities across summer and autumn seasons, in the public transit air (railway stations) of Delhi, a populated megacity characterized by extreme pollution levels and one of the world's busiest railway networks. Metagenomic analyses revealed distinct seasonal signatures in microbial community composition and diversity. Alpha diversity was higher during autumn, though not statistically significant, while beta diversity differed significantly between seasons. LEfSe analysis identified season-specific indicator taxa, including Moraxella, Barrientosiimonas, Methylobacterium, for autumn and Stutzerimonas, Caulobacter, Pseudomonas for summer, representing a mix of opportunistic pathogens and environmentally significant taxa. Correlation networks highlighted distinct seasonal clustering patterns. Resistome and virulome profiling revealed the presence of different resistance gene classes and virulence factor categories in abundance. Correlation networks uncovered significant associations between specific genes and bacterial genera, suggesting ecological partitioning in gene carriage. Temperature and air quality index explained a part of the variance observed in the taxonomic and functional dynamics. Metagenome-assembled genomes captured seasonally distinct taxa, and biosynthetic gene cluster screening identified 317 gene clusters, including terpene, RiPP-like, and hserlactone clusters. The findings underscore the ecological complexity and public health relevance of airborne bacteria and raise concerns about their potential role in microbial transmission and long-term respiratory health risks. These insights are crucial for public health surveillance, urban air quality management, and guiding future investigations into the microbial safety of urban environments.},
}

India
Seasons
*Microbiota
*Railroads
*Air Microbiology
*Environmental Monitoring
Cities
Bacteria/classification

@article {pmid41308447,
year = {2025},
author = {Yang, Z and Chen, B and Zhang, Q and Hu, X and Sun, L and Lu, T and Zhu, L and Ma, Y and Zhong, H and Ni, Y and Qian, H},
title = {Potential of traditional Chinese medicine as an antibiotic alternative for mitigating antibiotic resistance: A case study of Tetrastigma hemsleyanum.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140613},
doi = {10.1016/j.jhazmat.2025.140613},
pmid = {41308447},
issn = {1873-3336},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; Mice ; *Drug Resistance, Microbial/drug effects/genetics ; Medicine, Chinese Traditional ; *Drugs, Chinese Herbal/pharmacology ; *Anti-Inflammatory Agents/pharmacology ; Lipopolysaccharides ; Male ; },
abstract = {The overuse of antibiotics in livestock production has accelerated the spread of antibiotic resistance genes (ARGs), posing a serious global public health threat. Identification of safe and effective alternatives to antibiotics has therefore become a research priority. Tetrastigma hemsleyanum (TH), a traditional Chinese medicine, modulates the intestinal microbiota; however, the mechanisms underlying its antibiotic-like effects are not fully understood. In this study, we investigated the anti-inflammatory effects of TH in a lipopolysaccharide-induced mouse model of intestinal inflammation. Metagenomic sequencing was used to evaluate its effects on intestinal microbiota composition and ARG abundance. TH effectively alleviated intestinal inflammation, significantly increased the abundance of beneficial microbes such as Lactobacillus, and suppressed the proliferation of major ARG-carrying pathogens, including Proteus and Shigella. Functional analysis revealed that TH treatment markedly enhanced the Wnt and TGF-β signaling pathways, which are associated with intestinal barrier repair and immune response regulation, respectively. Furthermore, TH supplementation restored ARG diversity, reduced the abundance of high-risk ARGs, and suppressed the spread of multidrug resistance genes, underscoring its potential for mitigating antibiotic resistance risks. These findings highlight the potential of TH as an alternative antibiotic and may be used as a feed additive to reduce antibiotic usage while enhancing animal health.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/pharmacology
Mice
*Drug Resistance, Microbial/drug effects/genetics
Medicine, Chinese Traditional
*Drugs, Chinese Herbal/pharmacology
*Anti-Inflammatory Agents/pharmacology
Lipopolysaccharides
Male

@article {pmid41297255,
year = {2025},
author = {Lindstedt, K and Osińska, A and Bargheet, A and Sørum, H and Wick, RR and Holt, KE and Pettersen, VK and Sundsfjord, A and Wasteson, Y},
title = {Microbiota and resistome dynamics in untreated and treated wastewater: A ten-month study leveraging RNA-probe capture and subspecies-level metagenomics.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140566},
doi = {10.1016/j.jhazmat.2025.140566},
pmid = {41297255},
issn = {1873-3336},
mesh = {*Wastewater/microbiology ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; *Microbiota ; Humans ; Norway ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; },
abstract = {Wastewater is regarded as a hotspot for the acquisition and dissemination of antimicrobial resistance genes (ARGs) in bacteria, and wastewater treatment plants are key sites for studying and monitoring these phenomena. This study employed metagenomic approaches, with and without targeted ARG enrichment, to investigate the composition and dynamics of the microbiota, resistome, and mobilome in untreated (UWW) and treated (TWW) wastewater from a full-scale treatment plant serving municipal and hospital wastewater in Oslo, Norway. Over a ten-month period, we observed that wastewater treatment led to a significant reduction in the relative abundance of human gut-associated bacterial species and total load of coliform bacteria, alongside an increase in environmental bacterial taxa. This shift correlated with a significant reduction in the relative abundance and richness of ARGs and mobile genetic elements. Despite this, the effect of treatment on the relative abundance of key AMR-associated pathogens was highly inconsistent. Further subspecies analysis revealed several Escherichia coli and Klebsiella pneumoniae lineages persisted in UWW and TWW over multiple months, suggesting stable colonization and survival despite treatment processes. Targeted RNA probe-hybridisation enrichment detected clinically important ARGs in both UWW and TWW samples, including genes encoding extended-spectrum β-lactamases, carbapenemases, glycopeptide resistance, and colistin resistance. Most of these were undetectable by shotgun metagenomics alone, demonstrating the strength of this technique in high-sensitivity ARG surveillance. These findings highlight the value of combined metagenomic methods in wastewater AMR surveillance, the potential for monitoring high-risk bacterial lineages, and high-sensitivity detection of clinically important ARGs, in a low AMR prevalence setting.},
}

*Wastewater/microbiology
Metagenomics
*Drug Resistance, Bacterial/genetics
*Microbiota
Humans
Norway
Anti-Bacterial Agents/pharmacology
Bacteria/genetics/drug effects

@article {pmid41297254,
year = {2025},
author = {Hatwar, N and Qureshi, A},
title = {Biodegradation of PVC by novel bacterial consortia isolated from municipal solid waste dumpsite.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140589},
doi = {10.1016/j.jhazmat.2025.140589},
pmid = {41297254},
issn = {1873-3336},
mesh = {*Polyvinyl Chloride/metabolism ; Biodegradation, Environmental ; Waste Disposal Facilities ; *Bacteria/metabolism/genetics/isolation & purification ; *Microbial Consortia ; Solid Waste ; Soil Microbiology ; Refuse Disposal ; },
abstract = {In view of environmental issues related to Polyvinyl chloride (PVC), attempts have been made in the present study, to enrich and isolate novel bacteria from landfill dumpsites, capable of degrading PVC with reduced emissions. A potential bacterial consortium (NH_AQ) was designed, which comprised of Lysinibacillus spp., Bacillus spp., Staphylococcus spp., Exiguobacterium spp., and Arthrobacter spp. Metagenomic analysis of landfill soils indicated predominance of these bacterial species, which ensured that the culturable bacteria could be isolated from landfill sites for PVC degradation. This study was carried out at three temperatures (ambient, 37°C and 50°C). The percentage weight reduction of PVC films was 31.45 % ± 2 at 37°C. SEM-EDX showed external erosion and changes in chemical element composition, due to growth of bacteria as biofilms on PVC films at 37 °C. FTIR study confirmed oxidation and dechlorination happening during PVC utilization. TGA analysis indicated PVC thermal shifts in presence of consortia and ion chromatography too showed a significant reduction in chlorine content. Overall findings demonstrated that the designed NH_AQ consortium could degrade PVC effectively, offering a promising and sustainable approach to mitigate PVC pollution through microbial action in future.},
}

*Polyvinyl Chloride/metabolism
Biodegradation, Environmental
Waste Disposal Facilities
*Bacteria/metabolism/genetics/isolation & purification
*Microbial Consortia
Solid Waste
Soil Microbiology
Refuse Disposal

@article {pmid41273973,
year = {2025},
author = {Peng, L and Yang, F and Zhang, J and Shang, J and Xu, W and Sheng, S and Li, Q and Zou, Y and Yue, Z},
title = {Ecological drivers and functional roles of phage communities in the Yangtze River's freshwater ecosystems.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140564},
doi = {10.1016/j.jhazmat.2025.140564},
pmid = {41273973},
issn = {1873-3336},
mesh = {*Rivers/virology ; China ; *Bacteriophages/genetics/physiology ; *Ecosystem ; Fresh Water/virology ; Virome ; Geologic Sediments ; },
abstract = {The Yangtze River, China's largest and most significant freshwater system, is facing increasing pollution pressures due to rapid urbanization. While bacterial-mediated antibiotic resistance has been extensively studied, the functional roles and ecological risks of phage communities remain poorly understood. Here, we conducted a comprehensive virome analysis across four habitats (free-living setting, particle-associated setting, sediment, and bank soil) using 204 samples from the Yangtze River. We identified 18,865 viral operational taxonomic units (vOTUs) and observed significant correlations between viral communities and metagenome-assembled genomes (MAGs) across all habitats. Notably, the virus-to-host ratio (VHR) decreased significantly with increased elevation. Functional annotation revealed 1367 viruses contigs carrying genes associated with six functional categories, each showing distinct habitat-specific patterns. Carbohydrate-degrading enzymes (CAZy) were abundant in free-living setting water. Among phage-borne ARGs, vancomycin resistance was predominated, especially in sediment and bulk soil, while mercury resistance were most prevalent in sediments. Chitinase genes constituted the most abundant group among phage-encoded genes for plastic degradation. We identified 84 high-confidence virus-host pairs, predominantly infecting Proteobacteria. Random forest modeling identified elevation as the dominant driver of viral community abundance across habitats. Higher elevations were correlated with increased pH and reduced NH4[+]-N concentrations, suggesting nutrient limitation may weaken virus-host interactions. This study provides the first systematic assessment of viral diversity and functional potential in the Yangtze River, offering novel insights into phage ecology in freshwater.},
}

*Rivers/virology
China
*Bacteriophages/genetics/physiology
*Ecosystem
Fresh Water/virology
Virome
Geologic Sediments

@article {pmid41237940,
year = {2026},
author = {Borroni, D and Lo Monaco, F and Ferraro, S and Mazzotta, C and Settino, M and Gabrielli, F and Papa, FT and Alfonsi, C and Di Pietro, F and Rizzuto, V and Stroffolini, G and Bonzano, C and Laganovska, G and Vanags, J and Rechichi, M and Rocha-de-Lossada, C and Ballesteros-Sánchez, A and Zeppieri, M and Gagliano, C},
title = {Ocular surface microbiota in primary open angle glaucoma.},
journal = {Experimental eye research},
volume = {262},
number = {},
pages = {110734},
doi = {10.1016/j.exer.2025.110734},
pmid = {41237940},
issn = {1096-0007},
mesh = {Humans ; *Glaucoma, Open-Angle/microbiology/drug therapy ; Cross-Sectional Studies ; Male ; Female ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Aged ; *Bacteria/genetics/isolation & purification ; Intraocular Pressure/physiology ; DNA, Bacterial/genetics ; *Conjunctiva/microbiology ; *Dysbiosis/microbiology ; },
abstract = {Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness, yet the contribution of the ocular-surface (OS) microbiota remains poorly defined. We conducted a cross-sectional study including 27 POAG patients on chronic hypotensive therapy and 119 healthy Italian controls, profiled by 16S rRNA amplicon sequencing (Ion GeneStudio S5) and analyzed with QIIME2/phyloseq. POAG samples showed higher α-diversity (Shannon 4.23 vs 2.77; Observed richness 407 vs 154; Wilcoxon q < 1 × 10[-9]) and a distinct β-diversity profile (PERMANOVA p = 0.001; R[2] = 0.104). Compositional shifts included depletion of Firmicutes with loss of Staphylococcus in controls' place, and enrichment of Proteobacteria (e.g., Pseudomonas) together with unclassified Enterobacterales and a larger unclassified fraction. Differential-abundance testing identified numerous significant taxa separating groups, consistent with a more diverse yet less defined microbiota in POAG. These findings indicate an ocular-surface dysbiosis associated with POAG in a treatment-exposed cohort, supporting the relevance of host-microbe interactions and motivating longitudinal, treatment-naïve and functional studies before causal or translational inferences.},
}

Humans
*Glaucoma, Open-Angle/microbiology/drug therapy
Cross-Sectional Studies
Male
Female
*Microbiota
Middle Aged
RNA, Ribosomal, 16S/genetics
Aged
*Bacteria/genetics/isolation & purification
Intraocular Pressure/physiology
DNA, Bacterial/genetics
*Conjunctiva/microbiology
*Dysbiosis/microbiology

@article {pmid41237630,
year = {2025},
author = {Hemmat-Jou, MH and Li, F and Wang, D and Gao, R and Xiao-Xia, Z and Chen, Y and Fang, L},
title = {Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140469},
doi = {10.1016/j.jhazmat.2025.140469},
pmid = {41237630},
issn = {1873-3336},
mesh = {*Wetlands ; *Soil Microbiology ; Metagenomics ; *Drug Resistance, Microbial/genetics ; *Viruses/genetics ; Metagenome ; Microbiota ; },
abstract = {Paddy soils and wetlands form a critical soil-water interface that supports global crop production and biogeochemical cycling. Understanding the role of viruses in these ecosystems is vital for predicting ecosystem resilience. Considering the significance of viruses in microbial community structure and environmental pollution, we analyzed 163 metagenomes from 18 countries in Asia, Europe, America, and Australia. We characterized the global distribution and potential ecological functions of viruses through viral auxiliary metabolic genes (vAMGs), antibiotic resistance genes (vARGs), and metal(loid) resistance genes (vMRGs). We found viruses with globally consistent compositions and host profiles, characterized by high richness and a dominance of lysogenic families. We identified 497 vAMGs associated with carbon, phosphorus, nitrogen, and sulfur cycling, and detected 279 vARGs (conferring resistance to 10 antibiotic) and 141 vMRGs (against 7 metal(loids)). These genes exhibited strong co-localization and co-selection patterns, and their transduction can promote the emergence of multi-resistant microbes, reshaping microbial communities. Therefore, viruses are key mobile vectors for the environmental spread of these genes. By quantifying these pathways, we provide a crucial advancement for ecological risk identification and assessment. This meta-analysis provides a comprehensive overview of virus-mediated biogeochemical processes and resistance gene propagation. We demonstrate that viruses can disseminate antibiotic and metal(loid) resistance, a pollution-driven process that poses potential health risks. Furthermore, by regulating key metabolic pathways, viruses can influence greenhouse gas fluxes. Our findings underscore the necessity of integrating viruses into climate models, pollution mitigation strategies, and One Health policies to assess ecological risks and to protect ecosystem and public health.},
}

*Wetlands
*Soil Microbiology
Metagenomics
*Drug Resistance, Microbial/genetics
*Viruses/genetics
Metagenome
Microbiota

@article {pmid41237622,
year = {2025},
author = {Liu, B and Wang, S and Ren, J and Zhang, Z and Ma, J and Li, T and Zhou, Q and Sun, J},
title = {Impacts of non-spherical polyethylene nanoplastics on microbial communities and antibiotic resistance genes in the rhizosphere of pea (Pisum sativum L.): An integrated metagenomic and metabolomic analysis.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140425},
doi = {10.1016/j.jhazmat.2025.140425},
pmid = {41237622},
issn = {1873-3336},
mesh = {*Pisum sativum/microbiology/growth & development/drug effects/metabolism ; *Rhizosphere ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Metabolomics ; *Polyethylene/toxicity ; Soil Microbiology ; *Microbiota/drug effects ; *Microplastics/toxicity ; *Soil Pollutants/toxicity ; Genes, Bacterial ; Bacteria/genetics/drug effects ; },
abstract = {The ecological effects of nanoplastics (NPs) has become a growing concern; however, the influence of non-spherical NPs-which better represent real-world morphologies-remains poorly understood. This study investigated the impact of non-spherical polyethylene (PE) NPs on the growth of pea (Pisum sativum L.) and its rhizosphere microenvironment across different concentration levels (0, 20, and 200 mg/kg) using integrated metagenomics and metabolomics. Results showed that high-dose (200 mg/kg) exposure significantly inhibited plant growth. Although soil physicochemical properties remained unchanged, the rhizosphere microbial communities experienced significant restructuring, characterized by a marked enrichment of Pseudomonas and a reduction in beneficial Rhizobium populations. Metagenomic analysis revealed a concurrent increase in the abundance and diversity of antibiotic resistance genes (ARGs) under non-spherical PE-NP stress. This was accompanied by a shift in bacterial host composition, with a trend toward a higher prevalence of potentially pathogenic taxa such as Pseudomonas aeruginosa. Metabolomics analysis further revealed that non-spherical PE-NPs altered the rhizosphere metabolite profile, thereby significantly driving the succession of ARG hosts. Our integrated analysis enhances the understanding of how non-spherical PE-NPs disrupt microbial communities and elevate the risks of ARGs in rhizosphere soil, highlighting the significance of incorporating environmentally relevant NPs into environmental risk assessments.},
}

*Pisum sativum/microbiology/growth & development/drug effects/metabolism
*Rhizosphere
Metagenomics
*Drug Resistance, Microbial/genetics
Metabolomics
*Polyethylene/toxicity
Soil Microbiology
*Microbiota/drug effects
*Microplastics/toxicity
*Soil Pollutants/toxicity
Genes, Bacterial
Bacteria/genetics/drug effects

@article {pmid41223471,
year = {2025},
author = {Zhang, Y and Gao, M and Zhang, X and Tang, A and Wang, S and Wang, X},
title = {How microalgae-bacteria consortia adapt sulfamethoxazole pressure: Insights from physiological and genetic responses.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140406},
doi = {10.1016/j.jhazmat.2025.140406},
pmid = {41223471},
issn = {1873-3336},
mesh = {*Sulfamethoxazole/pharmacology/toxicity ; *Microalgae/drug effects/genetics/physiology/metabolism ; *Water Pollutants, Chemical/toxicity ; Adaptation, Physiological ; *Bacteria/drug effects/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Microbial Consortia/drug effects ; Reactive Oxygen Species/metabolism ; Photosynthesis/drug effects ; },
abstract = {Microalgae-bacteria consortia (MBC) are regarded as an energy-saving alternative for wastewater treatment process, while their reliability is challenged under long-term antibiotic pressure. Unfortunately, the underlying physiological and genetic mechanisms enabling adaptation to such prolonged antibiotic pressure remain largely unknown. This study systematically investigates the adaptive responses of MBC systems to sulfamethoxazole (SMX) pressure during two exposure stages (100 and 200 μg/L). While the system remained stable at 100 μg/L SMX (stage I), its performance declined at 200 μg/L (stage II), with COD and ammonium removal decreasing by 7.5 % and 8.8 %, respectively. This was accompanied by adverse physiological responses, including a 36.3 ± 3.2 % decrease in photosynthetic oxygen production, a 96.2 ± 9.7 % increase in ROS levels, and a 49.0 ± 5.3 % reduction in EPS content. Remarkably, both pollutant removal and physiological state were fully restored following a 100-day recovery period. This resilience may be attributed to the enrichment of microbial communities such as Chlorophyta and Bacillariophyta, whose presence strongly correlated with reduced antibiotic resistance gene (ARG) dissemination. Genetic analysis further indicated that suppressed ATP synthase and electron transfer within the oxidative phosphorylation pathway may represent important adaptive costs. Fortunately, the response regulators within the two-component system functioned as central mediators, coordinating both extracellular EPS secretion and intracellular antioxidant activity. Overall, this study advances current understandings of adaptive mechanism and offers insights for facilitating stable operation under long-term antibiotic pressure.},
}

*Sulfamethoxazole/pharmacology/toxicity
*Microalgae/drug effects/genetics/physiology/metabolism
*Water Pollutants, Chemical/toxicity
Adaptation, Physiological
*Bacteria/drug effects/genetics/metabolism
*Anti-Bacterial Agents/pharmacology
*Microbial Consortia/drug effects
Reactive Oxygen Species/metabolism
Photosynthesis/drug effects

@article {pmid41222145,
year = {2025},
author = {Koo, H and Heber, K and Tian, S and Connolly, ST and Hao, F and Zhao, J and Swencki-Underwood, B and Patterson, AD and Townsend, GE and Bisanz, JE},
title = {A synthetic gut microbiota provides an understanding of the maintenance and functional impact of phage.},
journal = {mBio},
volume = {16},
number = {12},
pages = {e0234125},
doi = {10.1128/mbio.02341-25},
pmid = {41222145},
issn = {2150-7511},
support = {R35 GM151045/GM/NIGMS NIH HHS/United States ; T32 GM156692/GM/NIGMS NIH HHS/United States ; R01 GM147178/GM/NIGMS NIH HHS/United States ; R00 AI147165/AI/NIAID NIH HHS/United States ; T32 DK120509/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Bacteriophages/physiology/isolation & purification/genetics ; *Bacteroides/virology/genetics ; Germ-Free Life ; },
abstract = {UNLABELLED: Phages are under intense study as therapeutics and mediators of microbial community behavior; however, tractable models are needed to study phages in the context of the mammalian gut. To address this gap, we isolated phages against members of a synthetic gut microbial community (sFMT), identifying the Bacteroides uniformis JEB00023 (DSM 6597) phage HKP09. While resistance to HKP09 was observable within hours of infection in monoculture, high titers of HKP09 were maintained in vitro and in gnotobiotic mouse models over extended periods. Sequencing of resistant B. uniformis lines revealed phase variation upstream of a capsular polysaccharide locus driving the generation of resistant and sensitive subpopulations, thus demonstrating a mechanism allowing stable coexistence of both virus and bacterial host. Communities infected in vitro and in vivo with HKP09 showed transiently reduced loads of B. uniformis DSM 6597. Its impact in the gut was distinct from communities constructed without its host B. uniformis strain (sFMT∆JEB00023). Rather than a compensatory increase in closely related Bacteroides strains, the most significant impacts were observed on distantly related strains, demonstrating that phage perturbations more broadly impact community structure in ways not easily predicted by phylogeny or simple strain exclusion. Metabolomic analyses of the feces of HKP09-infected sFMT-colonized gnotobiotic animals demonstrated altered abundances of amino acids and microbial fermentation products compared to uninfected mice and those colonized with sFMT∆JEB00023. Taken together, these data provide a controlled model for studying phages in the context of the mammalian gut, providing mechanistic insights into phage-host dynamics and their consequences on the function of microbial communities.

IMPORTANCE: Phages are key members of the gut microbiome, but the understanding of their biological significance for host health lags behind their bacterial hosts. In this study, we demonstrate the use of a phage-infection model using defined, synthetic microbial communities that colonize the intestinal tract of mice. We uncovered that spontaneous inversions in the genome of Bacteroides uniformis perpetually generate subpopulations, which are either sensitive or resistant to phage infection, allowing for the coexistence of predator and prey in this species. Phage infection demonstrated broad impacts on community structure and metabolism in animals, which are not easily predicted by the exclusion of the viral host. This research demonstrates a tractable approach through which the impacts of phage on both the microbiome and mammalian host can be deciphered.},
}

Animals
*Gastrointestinal Microbiome
Mice
*Bacteriophages/physiology/isolation & purification/genetics
*Bacteroides/virology/genetics
Germ-Free Life

@article {pmid41192191,
year = {2026},
author = {Zhou, G and Wang, YS and Zhang, GF and Zhang, SY and Wen, X and Cui, ZB and Shi, QS and Xie, XB},
title = {Gut microbiota composition and antibiotic resistance ontology landscape in Micropterus salmoides: Insights from metagenomic and metabolomic analyses.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {57},
number = {},
pages = {101666},
doi = {10.1016/j.cbd.2025.101666},
pmid = {41192191},
issn = {1878-0407},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Metabolomics ; *Metagenomics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/classification/metabolism ; Anti-Bacterial Agents/pharmacology ; *Fishes/microbiology/metabolism ; Metagenome ; },
abstract = {Micropterus salmoides, a pivotal aquaculture species in China, faces critical challenges including high disease susceptibility and insufficient characterization of gut microbiota-associated antibiotic resistance ontology (ARO). This study integrated metagenomic and metabolomic approaches to systematically characterize the compositional dynamics, diversity patterns, and spatiotemporal distribution of gut microbiota and AROs in M. salmoides across four developmental stages, while clarifying their interactions with metabolic pathways. Metagenomic profiling identified Proteobacteria, Firmicutes, and Fusobacteria as the dominant bacterial phyla, with Acinetobacter baumannii and Alcanivorax profundi exhibiting stage-specific abundance patterns. A total of 150 distinct ARO subtypes were identified, among which tetracycline- and glycopeptide-resistance genes (e.g., tetA and vanR) showing high abundance, with their resistance primarily mediated by efflux-driven mechanisms. Untargeted metabolomics uncovered 4459 metabolites, with robust correlations observed between core microbial genera (e.g., Flavobacterium and Herbaspirillum) and lipid/amino acid metabolic pathways. Co-occurrence network analysis further demonstrated significant interconnections between ARO subtypes and lineages of Proteobacteria/Firmicutes. Our multi-omics framework provides comprehensive insights into the gut microbiota-ARO-metabolism nexus in M. salmoides, thereby establishing a correlative framework for developing precision interventions to control the dissemination of antimicrobial resistance and improve disease management in sustainable aquaculture systems.},
}

*Gastrointestinal Microbiome
Animals
*Metabolomics
*Metagenomics
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/classification/metabolism
Anti-Bacterial Agents/pharmacology
*Fishes/microbiology/metabolism
Metagenome

@article {pmid41192179,
year = {2025},
author = {Wu, GG and Jin, JA and Han, NN and Guo, WL and Fan, NS and Jin, RC},
title = {Multiomic insights into the regulatory mechanism of anammox consortia: Interspecies cooperation, degradation and self-adaptation to plasticizer stress.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140319},
doi = {10.1016/j.jhazmat.2025.140319},
pmid = {41192179},
issn = {1873-3336},
mesh = {*Diethylhexyl Phthalate/toxicity/metabolism ; Biodegradation, Environmental ; *Plasticizers/toxicity/metabolism ; *Microbial Consortia ; Oxidation-Reduction ; *Water Pollutants, Chemical/metabolism/toxicity ; Anaerobiosis ; Bacteria/metabolism/genetics ; *Ammonium Compounds/metabolism ; },
abstract = {Phthalates are prevalent in wastewater treatment systems and pose a potential threat to microbial communities. In this study, it was found that the nitrogen removal efficiency of anaerobic ammonium oxidation (anammox) process remained at 92.5 ± 2.4 % after the long-term exposure to di-(2-ethylhexyl) phthalate (DEHP). Although the relative abundance of Candidatus Kuenenia decreased by 5.5 %, that of other denitrifying functional bacteria increased to maintain the system stability. The adaptation of anammox consortia to DEHP mainly depended on microbial cooperation and molecular regulation. Combined with metagenomic and metatranscriptomic analyses, Bacillus subtilis functioned as the DEHP-degrading species and exhibited a collaborative relationship with other degrading microorganisms. The expression levels of carbon metabolism, two-component system and quorum sensing related genes were significantly (p < 0.05) upregulated by 0.4-6.6 folds. The structural equation model further proved that biodegradation was the main contributor to mitigating DEHP inhibition. Notably, Ca. Kuenenia and transposons were the host of most antibiotic resistance genes (ARGs) and the main mobile genes elements, respectively. DEHP also triggered oxidative stress and resistance dissemination in anammox consortia. These findings provide molecular insights into the microbial regulatory mechanism in responding to plasticizer stress and drive the expansion of anammox process application.},
}

*Diethylhexyl Phthalate/toxicity/metabolism
Biodegradation, Environmental
*Plasticizers/toxicity/metabolism
*Microbial Consortia
Oxidation-Reduction
*Water Pollutants, Chemical/metabolism/toxicity
Anaerobiosis
Bacteria/metabolism/genetics
*Ammonium Compounds/metabolism

@article {pmid41175632,
year = {2026},
author = {Patel, AB and Jain, KR and Gupta, V and Lal, R and Madamwar, D},
title = {Structural and functional responses of microbial communities in coastal sediments towards anthropogenic pollution caused by ship breaking activities.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107665},
doi = {10.1016/j.marenvres.2025.107665},
pmid = {41175632},
issn = {1879-0291},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Microbiota ; *Ships ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring ; Bacteria/classification ; India ; Metals, Heavy/analysis ; Metagenome ; Biodiversity ; },
abstract = {Coastal ecosystems, like many others on the planet, face chronic threats from anthropogenic activities. The Alang-Sosiya Ship Breaking Yard (ASSBY) located near Bhavnagar in Gujarat, India, represents one such ecosystem impacted by decades of ship-breaking activities. This study aimed to assess the differences in microbial community composition between polluted coastal samples and pristine samples through high-throughput sequencing. Additionally, microbial co-occurrence networks and genes related to antibiotic and heavy metal resistance were predicted using metagenome mining. The analysis confirmed elevated heavy metal concentrations, particularly iron, in polluted samples. In non-polluted sites, alpha diversity indices showed a high microbial diversity compared to polluted sites. The bacterial communities from Deltaproteobacteria at non-polluted sites noticeably shifted to Gammaproteobacteria at polluted sites. Unclassified reads constituted a significant portion of the bacterial diversity. LEfSe (Linear discriminant analysis Effect Size) analysis identified potential bacterial biomarkers, including Pseudomonas, Halomonas and Rhodovulum, which were differentially abundant at polluted sites and may play roles in the biodegradation of xenobiotic compounds. Moreover, Co-occurrence network analysis validated these bacterial biomarkers from polluted sites and revealed their habitat-specific nature. Polluted metagenomes were enriched with genes related to aromatic compound degradation and stress responses, particularly genes for heavy metal and antibiotic resistance. These findings suggest that chronic pollution from ship-breaking activities has led to a shift in microbial communities, leading to an increased presence of resistance mechanisms in the polluted coastal environment to adapt to prolonged heavy pollution.},
}

*Geologic Sediments/microbiology/chemistry
*Microbiota
*Ships
*Water Pollutants, Chemical/analysis
*Environmental Monitoring
Bacteria/classification
India
Metals, Heavy/analysis
Metagenome
Biodiversity

@article {pmid41086610,
year = {2026},
author = {Li, H and Gao, H and Chen, S and Li, X and Zhou, J},
title = {Intensive mariculture shifts microbial communities and life-history strategies in the semi-enclosed bay: Case study in Sansha Bay, China.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107607},
doi = {10.1016/j.marenvres.2025.107607},
pmid = {41086610},
issn = {1879-0291},
mesh = {China ; *Bays/microbiology ; *Microbiota ; *Aquaculture ; Eutrophication ; RNA, Ribosomal, 16S ; *Environmental Monitoring ; Animals ; },
abstract = {Coastal bays often experience significant disturbances from various mariculture activities, frequently leading to severe eutrophication. Yet, the ecological consequences of nutrient inputs derived from mariculture on bay-associated microbial communities remain insufficiently understood. Sansha Bay, known as the world's largest cage mariculture site for Larimichthys crocea, represents a characteristic semi-enclosed bay commonly utilized for studying the environmental impacts of intensive mariculture. In this study, we compared the highly eutrophic Sansha Bay with the relatively undisturbed natural East China Sea to investigate how intensive mariculture influences the bay microbial biosphere, focusing on community composition, assembly mechanisms, functional profiles, and life-history strategies. Amplicon sequencing and metagenomic analyses showed that Sansha Bay had a greater proportion of fast-growing microorganisms, nitrogen and carbon cycling microbes, and antibiotic-resistant bacteria. Null model analysis indicated that while natural coastal microbial assemblages were predominantly shaped by stochastic processes, deterministic selection became increasingly prominent as mariculture activities intensified. Correspondingly, microbial life-history traits, including 16S rRNA gene copy number, codon usage bias, predicted maximum growth rates, genome size, guanine-cytosine content, transposase abundance, and niche breadth, were consistently elevated in the eutrophic bay. These results suggest that eutrophication associated with mariculture drives a shift in life-history strategies from oligotrophs (K-strategists) to copiotrophs (r-strategists). Collectively, this study yields novel mechanistic understanding of how intensive mariculture reshapes microbial community structures, laying the groundwork for forecasting changes in coastal ecosystems subjected to ongoing human disturbances.},
}

China
*Bays/microbiology
*Microbiota
*Aquaculture
Eutrophication
RNA, Ribosomal, 16S
*Environmental Monitoring
Animals

@article {pmid40915974,
year = {2026},
author = {Ribeiro, MC and Colombo, APV and de Oliveira, AM and Lourenço, TGB and Honório, HM and de Freitas, EC and Messora, MR and Furlaneto, FAC},
title = {The Interplay Between Lifestyle and Oral/Faecal Microbial Profiles Among Periodontal Disease Patients: A Cross-Sectional Study.},
journal = {Journal of clinical periodontology},
volume = {53},
number = {1},
pages = {82-97},
doi = {10.1111/jcpe.70029},
pmid = {40915974},
issn = {1600-051X},
mesh = {Humans ; Cross-Sectional Studies ; *Feces/microbiology ; Male ; Female ; Middle Aged ; *Life Style ; Adult ; *Periodontal Diseases/microbiology ; *Mouth/microbiology ; *Microbiota ; *Periodontitis/microbiology ; Biofilms ; Gingivitis/microbiology ; Aged ; RNA, Ribosomal, 16S ; Diet ; },
abstract = {AIM: To characterise periodontal and faecal microbiomes of individuals with periodontal health (PH) and diseases, and evaluate associations with periodontal, sociodemographic, anthropometric, nutritional and lifestyle factors.

MATERIALS AND METHODS: Dental biofilm and faecal samples from individuals (n = 24/group) with PH, gingivitis (GG) and periodontitis (PE) were sequenced (16S rRNA). Anthropometric data and questionnaires on demographics, lifestyle, diet and intestinal habits were collected. Data were statistically analysed (p < 0.05).

RESULTS: GG and PE groups showed higher age, BMI, waist/abdominal circumferences and trans-fat intake and lower selenium and vitamin E intake compared to PH. Individuals with PE had higher hip circumference and lower income, education and intake of iron as well as vitamins A and B9. PE microbiomes (oral and faecal) showed distinct compositions, with the highest number of unique oral species. Faecal richness was lower in PE and GG compared to PH. Specific microbial taxa correlated with periodontal status and host factors.

CONCLUSION: Periodontal and faecal microbiomes vary across periodontal conditions. Discriminant analysis classified 77% of individuals by periodontal status, with key markers for PE including older age, poor dietary quality and distinct microbial oral and faecal signatures. These findings highlight the role of clinical, dietary and microbial factors in periodontal disease profiling.},
}

Humans
Cross-Sectional Studies
*Feces/microbiology
Male
Female
Middle Aged
*Life Style
Adult
*Periodontal Diseases/microbiology
*Mouth/microbiology
*Microbiota
*Periodontitis/microbiology
Biofilms
Gingivitis/microbiology
Aged
RNA, Ribosomal, 16S
Diet

@article {pmid41366428,
year = {2025},
author = {Xiong, Z and Dodson, BP and Rogers, MB and Sneiderman, CT and Janesko-Feldman, K and Vagni, V and Manole, M and Li, X and Rajasundaram, D and Clark, RSB and Raphael, I and Morowitz, MJ and Mariño, E and Kochanek, PM and Jha, RM and Kohanbash, G and Simon, DW},
title = {Microbial production of short-chain fatty acids attenuates long-term neurologic impairment after traumatic brain injury.},
journal = {Journal of neuroinflammation},
volume = {22},
number = {1},
pages = {285},
pmid = {41366428},
issn = {1742-2094},
support = {R21 NS131689/NS/NINDS NIH HHS/United States ; R21 NS131689/NS/NINDS NIH HHS/United States ; R01NS 127372/NH/NIH HHS/United States ; },
mesh = {Animals ; *Brain Injuries, Traumatic/metabolism/complications ; Mice ; Mice, Inbred C57BL ; *Fatty Acids, Volatile/metabolism/biosynthesis ; *Gastrointestinal Microbiome/physiology ; Male ; },
abstract = {BACKGROUND: Traumatic brain injury (TBI) triggers persistent gut microbiome dysbiosis characterized by depletion of short-chain fatty acid (SCFA)-producing bacteria. However, the link between SCFA depletion and long-term neurologic impairment (LTNI) after TBI remains unclear. Previously, we and others noted the involvement of metabolite-sensing receptors and SCFA ligands in mouse models of neurodegenerative diseases, including Alzheimer's. Here, we further investigated SCFA-mediated neuroprotection in LTNI at both microbiome and single-cell resolution using the controlled cortical impact (CCI) model of TBI with a high-yielding SCFA diet to examine their mechanistic role in pathogenesis.

METHODS: C57BL6/J mice were randomized to CCI (6 m/s, 2 mm) or sham surgery. Following surgery, mice were randomized to a study diet based on a balanced modification of the AIN93-G diet containing either 15% high amylose maize starch (HAMS) control diet or acetylated and butyrylated HAMS (HAMSAB) for 6 months to model increased SCFA production by bacterial fermentation in the gut. Morris water maze test and nesting assessment were performed at 1, 3, and 6 months after injury. The longitudinal gut microbiome changes were investigated by 16 S rRNA amplicon and metagenomic sequencing of fecal pellets at baseline, 1 month, and 6 months post-injury. At 6 months, pericontusional tissue was collected for single-cell RNA-sequencing following the 10X Genomics protocol or histologic analysis.

RESULTS: Compared to the HAMS control diet, HAMSAB diet remodeled the CCI murine gut microbiome at an early phase, increased various SCFA-producing taxa, and attenuated neurologic deficits up to 6 months after CCI. In mice fed HAMSAB diet, single-cell transcriptomics and pathway analysis identified the promotion of neurogenesis, including increased doublecortin-positive immature neurons. In myeloid cells, HAMSAB induced an anti-inflammatory phenotype, inhibiting pro-inflammatory signaling interaction such as midkine signaling, and promoted differentiation to disease-associated microglia (DAM). Simultaneously, SCFAs reduced neurodegenerative pathway activity in neurons and glial cells and reduced phosphorylated tau deposition in pericontusional cortex.

CONCLUSIONS: Diet-facilitated microbial production of acetate and butyrate attenuates behavioral deficits of LTNI after TBI and produces enduring benefits at the single-cell level on the neuro-inflammatory and neuro-progenitor responses. This therapeutic approach could have a broader potential to prevent neurodegenerative disease.},
}

Animals
*Brain Injuries, Traumatic/metabolism/complications
Mice
Mice, Inbred C57BL
*Fatty Acids, Volatile/metabolism/biosynthesis
*Gastrointestinal Microbiome/physiology
Male

@article {pmid41365917,
year = {2025},
author = {Duarte, VDS and Franklin, FV and Krysmann, A and Porcellato, D},
title = {Longitudinal study of the udder microbiome using genome-centric metagenomics uncovers pathogen-driven adaptation and succession.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {227},
pmid = {41365917},
issn = {2055-5008},
support = {314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; },
mesh = {Animals ; Female ; *Mammary Glands, Animal/microbiology ; Cattle ; *Mastitis, Bovine/microbiology ; Longitudinal Studies ; *Metagenomics/methods ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification/pathogenicity ; Lactation ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; },
abstract = {Bovine mastitis remains a major disease affecting dairy herds globally due to its complex and multi-etiological nature. To address gaps in microbial and immunological understanding, this longitudinal study examined the udder microbiome across lactation in 24 Norwegian Red cows. Somatic cell count (SCC) and microbiota composition varied by lactation stage, with low SCC (< 100,000 cells/mL) more frequent in early (80%) and middle (78.9%) than late lactation (53%) and dry-off (53.1%). Microbial diversity was shaped by SCC, lactation stage, and individual variability. Temporal profiling identified persistent infections involving Staphylococcus aureus and Staphylococcus chromogenes, while samples with low SCC were enriched in beneficial genera including Corynebacterium, Bradyrhizobium, and Lactococcus. Shotgun metagenomics revealed pathogen-specific metabolic traits, and genome-centric analysis recovered 142 MAGs characterized via sequence typing, virulence, and resistance profiling. These findings offer valuable insights into microbial adaptation and succession, informing strategies to better manage and prevent mastitis.},
}

Animals
Female
*Mammary Glands, Animal/microbiology
Cattle
*Mastitis, Bovine/microbiology
Longitudinal Studies
*Metagenomics/methods
*Microbiota
*Bacteria/genetics/classification/isolation & purification/pathogenicity
Lactation
RNA, Ribosomal, 16S/genetics
Genome, Bacterial

@article {pmid41365804,
year = {2025},
author = {Thompson, AR and Adams, BJ and Hogg, ID and Yooseph, S},
title = {Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70249},
doi = {10.1111/1758-2229.70249},
pmid = {41365804},
issn = {1758-2229},
support = {ANT 2133685//National Science Foundation/ ; OPP-2224760//National Science Foundation/ ; DBI-2400009//National Science Foundation/ ; OAC-2408259//National Science Foundation/ ; OPP-1043681//National Science Foundation/ ; OPP-1559691//National Science Foundation/ ; OPP-2129685//National Science Foundation/ ; //Antarctica New Zealand (Event K024)/ ; //New Zealand Antarctic Research Institute (Event K024)/ ; //Monte L. Bean Life Science Museum, the Department of Biology, Brigham Young University/ ; //Kravis Department of Integrated Sciences, Claremont McKenna College/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenome ; *Anti-Bacterial Agents/biosynthesis ; Ecosystem ; Soil/chemistry ; *Gases/metabolism ; },
abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.},
}

Antarctic Regions
*Soil Microbiology
*Bacteria/metabolism/genetics/classification/isolation & purification
Metagenome
*Anti-Bacterial Agents/biosynthesis
Ecosystem
Soil/chemistry
*Gases/metabolism

@article {pmid41361579,
year = {2025},
author = {Anunobi, OO and Abiola, RB and Ogah, CF},
title = {In silico pathogenomics of draft metagenome-assembled genome of gut Enterobacter cloacae from a gastroenteritis patient exhibiting potential determinants of multi-drug resistance and virulence.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {6},
pmid = {41361579},
issn = {1572-9699},
mesh = {*Enterobacter cloacae/genetics/pathogenicity/drug effects/isolation & purification ; Humans ; *Gastroenteritis/microbiology ; *Genome, Bacterial ; *Drug Resistance, Multiple, Bacterial/genetics ; Virulence/genetics ; Enterobacteriaceae Infections/microbiology ; *Metagenome ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Computer Simulation ; Computational Biology ; Gastrointestinal Microbiome ; Phylogeny ; },
abstract = {Antimicrobial resistance (AMR) is considered one of the top 10 threats to global public health and development. Opportunistic bacteria such as Enterobacter cloacae have been reported to acquire resistance determinants, making them pathogenic reservoirs and a threat to health and most are on the path of becoming superbugs. These bacteria are commonly isolated along with pathogens from the stool and urine of patients diagnosed with typhoid fever, paratyphoid fever, gastroenteritis, urinary tract infection, and bloodstream infection or sepsis. The E. cloacae strain EC78 studied here is a metagenomic-assembled genome that was binned from sequenced data of a mixed bacterial culture taken from a patient diagnosed with gastroenteritis. The isolate was sequenced with Illumina Novaseq 6000 platform and analysed with various bioinformatics tools. EC78 origin strain contained antibiotics resistance genes, insertion sequences, phages, and virulence factors. Notable virulence genes responsible for immune modulation, efflux of drugs, invasion and nutritional virulence previously reported in Klebsiella pneumoniae., Escherichia coli, Shigella sp., and Salmonella sp. etc., were identified in EC78. Genetic characteristics that could contribute to pathogenicity, virulence, and antibiotic resistance, not commonly associated with E. cloacae, were identified in gut-domiciled EC78, suggesting the evolution of counter-therapy in the bacteria, probably driven by its quest for survival in an otherwise competitive biome.},
}

*Enterobacter cloacae/genetics/pathogenicity/drug effects/isolation & purification
Humans
*Gastroenteritis/microbiology
*Genome, Bacterial
*Drug Resistance, Multiple, Bacterial/genetics
Virulence/genetics
Enterobacteriaceae Infections/microbiology
*Metagenome
Anti-Bacterial Agents/pharmacology
Virulence Factors/genetics
Computer Simulation
Computational Biology
Gastrointestinal Microbiome
Phylogeny

@article {pmid41354993,
year = {2025},
author = {Zhang, W and Zhang, M and Xie, J and Huang, H and Schmitz-Esser, S and Li, W and Liu, H and Li, D},
title = {Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43425},
pmid = {41354993},
issn = {2045-2322},
support = {2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; QD2023A46//Mianyang Teachers' College/ ; 2022 CPB-B09//the grants from the independent project of Chengdu Research Base of Giant Panda Breeding/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; *Ursidae/microbiology ; *Anti-Bacterial Agents/pharmacology/administration & dosage/therapeutic use ; *Antibiotic Prophylaxis ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Cefotaxime/pharmacology/administration & dosage ; Feces/microbiology ; Metagenome ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects/classification ; },
abstract = {For giant pandas, the ecological impact of prophylactic postoperative antibiotics on their gut microbial communities and resistome is not well characterized. Here, we assessed the impact of intravenous cefotaxime administration by analyzing longitudinal fecal samples from five giant pandas via 16 S rRNA sequencing (n = 304 samples) and shotgun metagenomics (n = 22 samples). 16 S-based analysis revealed that antibiotic exposure significantly altered bacterial community structure, resulting in a pronounced increase in the abundance of Pseudomonadota (from 50% ± 24% to 60% ± 38%; P < 0.001) and a reduction in Shannon diversity (from 2.8 ± 0.4 to 2.4 ± 1.3; P < 0.05). In contrast, metagenomic analysis indicated that cefotaxime exposure did not significantly increase the overall diversity of antimicrobial resistance genes (ARGs) or virulence factor genes (VFGs). However, we observed a marked expansion in the diversity of the CTX-M β-lactamase family (blaCTX-M), which persisted into the recovery phase. We also recovered 10 metagenome-assembled genomes (MAGs) harboring both ARGs and VFGs, identifying them as potential antibiotic-resistant pathogens (ARPs). Their abundance, however, remained unchanged throughout treatment. These findings provide new insights into the effects of short-term antibiotic exposure in giant pandas, highlighting its transient effect on microbial community structure and a limited effect on resistome diversity.},
}

Animals
*Gastrointestinal Microbiome/drug effects/genetics
*Ursidae/microbiology
*Anti-Bacterial Agents/pharmacology/administration & dosage/therapeutic use
*Antibiotic Prophylaxis
Metagenomics
RNA, Ribosomal, 16S/genetics
Cefotaxime/pharmacology/administration & dosage
Feces/microbiology
Metagenome
*Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects/classification

@article {pmid41093042,
year = {2025},
author = {Noordzij, HT and Wortel, MT and Heintz-Buschart, A and Petrikonyte, P and de Muinck, EJ and Trosvik, P},
title = {Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids.},
journal = {Plasmid},
volume = {134},
number = {},
pages = {102761},
doi = {10.1016/j.plasmid.2025.102761},
pmid = {41093042},
issn = {1095-9890},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Plasmids/genetics ; Infant ; Feces/microbiology ; Infant, Newborn ; Bacteroides/genetics ; Longitudinal Studies ; Female ; Computational Biology/methods ; Male ; Clostridium/genetics ; },
abstract = {Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant Bacteroides plasmid pBI143. Overall, the genus Bacteroides had the highest plasmid carriage, while the highest plasmid diversity was observed in Clostridium, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Plasmids/genetics
Infant
Feces/microbiology
Infant, Newborn
Bacteroides/genetics
Longitudinal Studies
Female
Computational Biology/methods
Male
Clostridium/genetics

@article {pmid40972220,
year = {2026},
author = {Saha, S and Mondal, A and Bag, S and Ghosh, S and Mandal, AH and Saha, NC and Chatterjee, S and Sopjani, M and Multisanti, CR and Faggio, C},
title = {Are biopesticides really safe? Impacts on gut microbiota and intestinal health in freshwater fish.},
journal = {Journal of contaminant hydrology},
volume = {276},
number = {},
pages = {104727},
doi = {10.1016/j.jconhyd.2025.104727},
pmid = {40972220},
issn = {1873-6009},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Fishes/microbiology ; Fresh Water ; *Biological Control Agents/toxicity ; *Water Pollutants, Chemical/toxicity ; Aquaculture ; *Intestines/drug effects ; Pesticides/toxicity ; },
abstract = {The growing use of biopesticides as eco-friendly alternatives to chemical pesticides is reshaping pest control in agriculture and aquaculture. However, their potential effects on non-target aquatic species, particularly freshwater fish, remain underexplored. This review investigates how different biopesticides, such as microbial agents, biochemical compounds, and plant-incorporated protectants, affect the gut microbiota and intestinal health of freshwater fish. The gut microbiome plays a vital role in digestion, nutrient absorption, immunity, and overall fish health. Biopesticide exposure may disrupt microbial balance, leading to reduced diversity, changes in community composition, inflammation, and dysbiosis. These alterations can impair digestive efficiency, immune function, growth, and reproduction. Promising mitigation strategies include the use of probiotics, prebiotics, symbiotics, insect-based feeds and other non-bacterial dietary interventions to restore gut homeostasis and improve fish resilience. In addition, advanced techniques like metagenomics and metabolomics are enhancing our understanding of host-microbiome interactions under biopesticide exposure. This review emphasizes the importance of including gut microbiota health in environmental risk assessments for biopesticide use in aquaculture. Future studies should adopt a multidisciplinary approach combining toxicology, microbiology, nutrition, and environmental science to develop species-specific, long-term strategies that safeguard fish health in increasingly pesticide-influenced aquatic environments.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Fishes/microbiology
Fresh Water
*Biological Control Agents/toxicity
*Water Pollutants, Chemical/toxicity
Aquaculture
*Intestines/drug effects
Pesticides/toxicity

@article {pmid40407188,
year = {2025},
author = {Batarseh, TN and Koskella, B},
title = {Distinguishing among evolutionary and ecological processes shaping microbiome dynamics.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf107},
pmid = {40407188},
issn = {1751-7370},
support = {//San Francisco Chan-Zuckerberg Biohub. BK is the San Francisco Chan-Zuckerberg Biohub Investigator/ ; #2209111//National Science Foundation Postdoctoral Research Fellowship in Biology/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification ; *Biological Evolution ; Genetic Variation ; Genome, Bacterial ; },
abstract = {Evolution is defined as the change in allele frequency over time as a result of either neutral processes, such as genetic drift, or as an adaptive process in response to selection. In contrast, ecological dynamics describe changes in population densities, species distributions, species interactions, and/or relative abundances within communities, all of which can also be the result of either stochastic or deterministic processes. Although the distinction between these patterns has long held for plants and animals, microbial community dynamics can blur the line between ecological and evolutionary processes, especially as they can occur on very similar timescales. Despite the importance of differentiating changes occurring within a population or strain from those occurring among populations, many common methodologies used to study microbiomes are not able to differentiate among them. In this review, we summarize the forces known to generate genetic diversity in bacterial genomes and describe the approaches used to study bacterial evolution from simple to more complex systems. We then explore how current methodologies and conceptual understanding can be applied to both understand and differentiate between the ecological and evolutionary processes in microbial communities. By highlighting lessons from longitudinal microbiome studies and experimental evolution, we explore the unique opportunities afforded by newer sequencing approaches and better sequencing resolution. Throughout, we identify the unique and outstanding challenges in studying these processes in microbiome systems and emphasize the great benefits in doing so to move forward our ability to better predict and manipulate microbiomes.},
}

*Microbiota/genetics
*Bacteria/genetics/classification
*Biological Evolution
Genetic Variation
Genome, Bacterial

@article {pmid41360540,
year = {2026},
author = {Zhang, M and Jiang, Z and Li, J and Marie-Colette, AK and Liu, Q and Hao, N and Wang, J},
title = {Analyzing the contribution of functional microorganism to volatile flavor compounds in Semillon wine and predicting their metabolic roles during natural fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117842},
doi = {10.1016/j.foodres.2025.117842},
pmid = {41360540},
issn = {1873-7145},
mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Volatile Organic Compounds/analysis/metabolism ; *Vitis/microbiology ; Gas Chromatography-Mass Spectrometry ; Taste ; Odorants/analysis ; China ; Microbiota ; Food Microbiology ; *Flavoring Agents/analysis ; *Bacteria/metabolism/classification ; Solid Phase Microextraction ; Hanseniaspora/metabolism ; },
abstract = {Indigenous microorganism plays a pivotal role in natural wine fermenting and its distinctive qualities shaping. However, the contributions of functional microbial taxa to wine flavor formation remain underexplored. This study focuses on the natural fermentation systems of Semillon grapes from Wuwei and Zhangye Gansu sub-regions within the Hexi Corridor of China. We characterized the dynamics of microbial community succession during fermentation using a combination of metagenomic sequence and culture-dependent analysis. Concurrently, volatile compounds were quantified using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. The mechanistic of functional microorganisms in wine flavor formation were unveiled by constructing KEGG metabolic network. The results revealed distinct microbial succession patterns between the two regions. In Zhangye, Hanseniaspora dominated the early fermentation stage, succeeded by Saccharomyces, Fructobacillus, and Brachyspira in middle and late stages. Conversely, in Wuwei, Pichia prevailed initially, with Brachyspira becoming stably enriched. Volatile esters and higher alcohols were identified as the major flavor components, contributing aroma notes of flowers, fresh greens, and stone fruits to the Semillon wine. Correlation analysis indicated positive associations between most key volatile aroma compounds and Saccharomyces, Brachyspira, Hanseniaspora, and Acetobacter. Metagenomic functional prediction highlighted carbohydrate and amino acid metabolic as the predominant pathways, with key processes involving glycolysis, fatty acid biosynthesis, and esterification. Core microbial taxa (Saccharomyces, Hanseniaspora, Starmerella, etc.) regulated flavor compound synthesis through a synergistic metabolic network. This study elucidates the succession of functional microorganisms and the development of flavor profiles during the natural fermentation of Semillon in the Hexi Corridor providing a reference for the development and application of functional microorganisms.},
}

*Fermentation
*Wine/analysis/microbiology
*Volatile Organic Compounds/analysis/metabolism
*Vitis/microbiology
Gas Chromatography-Mass Spectrometry
Taste
Odorants/analysis
China
Microbiota
Food Microbiology
*Flavoring Agents/analysis
*Bacteria/metabolism/classification
Solid Phase Microextraction
Hanseniaspora/metabolism

@article {pmid41358671,
year = {2025},
author = {Ngwese, MM and Adegbite, BR and Zinsou, JF and Fitzstevens, JL and Schmidt, VT and Moure, PAN and Maloum, MN and Tyakht, AV and Huus, KE and Youngblut, ND and Kremsner, PG and Adegnika, AA and Ley, RE},
title = {Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587966},
doi = {10.1080/19490976.2025.2587966},
pmid = {41358671},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/parasitology/microbiology ; Animals ; Gabon/epidemiology ; Female ; Male ; Child ; *Helminthiasis/parasitology/epidemiology/microbiology ; Metagenomics ; *Helminths/isolation & purification/classification/genetics ; Child, Preschool ; Rural Population ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Ascaris lumbricoides/isolation & purification ; Strongyloides stercoralis/isolation & purification ; Necator americanus/isolation & purification ; Trichuris/isolation & purification ; Biodiversity ; },
abstract = {Soil-transmitted helminths (STH) are common in (sub)tropical regions and primarily affect impoverished populations. These parasites reside in the gut, where they interact with both the microbiota and host immunity. Clinical STH detection is laborious and often not performed within the context of gut microbiome studies. Here, we present a proof-of-concept study assessing whether fecal metagenome data could be used to assess STH infection, and to relate STH infection to microbiome features. We leveraged 310 gut metagenomes obtained from mother-child pairs in two different locations in Gabon: one rural and one semi-urban, and assessed the presence of four STH species (Ascaris lumbricoides, Strongyloides stercoralis, Trichuris trichiura, and Necator americanus) using qPCR. Sequence data were used to characterize the microbiomes and to detect these parasites. Metagenomic read mapping and genome coverage metrics closely matched qPCR detection patterns. Within-location analyses revealed that parasite species richness was associated with microbiome diversity and taxonomic composition, with the strongest associations observed in children from the rural site. Applying this approach to published data from five additional African cohorts identified context-specific parasite-microbiome associations, as well as a modest but reproducible association between microbiome alpha diversity and parasite infection. These findings highlight the potential of shotgun metagenomics for concurrent parasite detection and microbiome profiling across diverse geographic and demographic contexts.},
}

Humans
*Gastrointestinal Microbiome/genetics
Feces/parasitology/microbiology
Animals
Gabon/epidemiology
Female
Male
Child
*Helminthiasis/parasitology/epidemiology/microbiology
Metagenomics
*Helminths/isolation & purification/classification/genetics
Child, Preschool
Rural Population
Bacteria/classification/genetics/isolation & purification
Metagenome
Ascaris lumbricoides/isolation & purification
Strongyloides stercoralis/isolation & purification
Necator americanus/isolation & purification
Trichuris/isolation & purification
Biodiversity

@article {pmid41355553,
year = {2025},
author = {Kim, MJ and Park, JH and Eom, YB},
title = {The Transmissibility of the Human Skin Virome: Potential Forensic Implications.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70197},
doi = {10.1002/mbo3.70197},
pmid = {41355553},
issn = {2045-8827},
support = {//Soonchunhyang University (SCH-20130328), Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; //Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; },
mesh = {Humans ; *Virome ; *Skin/virology ; Adult ; *Viruses/classification/genetics/isolation & purification ; Male ; Female ; Young Adult ; Republic of Korea ; Metagenome ; },
abstract = {The objective of this study was to evaluate the temporal stability and object-to-skin transferability of the skin virome in a Korean population. Skin virus metagenomes were collected from the anatomical locations (forehead, left hand, and right hand) of eight healthy adults and monitored over 3 months at intervals of 6 weeks. To assess the potential transfer of virome between skin and objects, subjects were instructed to contact four types of objects (cell phones, door handles, fabric, and plastic). Virome samples were then collected from the surfaces of these objects. Viruses were identified using databases and viral annotation bioinformatics tools. Fifteen viral families were consistently found to be stable and well-transmissible across anatomical locations and four types of objects. Furthermore, the presence/absence profiles of 54 viral species belonging to these 15 viral families exhibited significant individual specificity on both the skin (p < 0.01) and the objects handled by each subject (p < 0.05). We confirmed that these 54 viral markers remain stable over time within individuals and are transferable to contacted surfaces. Additionally, we explored the potential of using the virome as an individual identification marker, which may suggest new approaches for forensic applications.},
}

Humans
*Virome
*Skin/virology
Adult
*Viruses/classification/genetics/isolation & purification
Male
Female
Young Adult
Republic of Korea
Metagenome

@article {pmid41355481,
year = {2025},
author = {Becerra, D and Rodríguez-Caballero, G and Marhuenda-Egea, FC and Olaya-Abril, A and Moreno-Vivián, C and Sáez, LP and Luque-Almagro, VM and Roldán, MD},
title = {Microbial Diversity of the Surface of Polypropylene and Low Density Polyethylene-Based Materials (Plastisphere) From an Area Subjected to Intensive Agriculture.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70121},
doi = {10.1002/mbo3.70121},
pmid = {41355481},
issn = {2045-8827},
support = {//This study was supported by Ministerio de Ciencia e Innovación, Spain (grant PID2021-124174OB-I00)./ ; },
mesh = {*Polypropylenes/metabolism ; *Polyethylene/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Agriculture ; *Biodiversity ; Biodegradation, Environmental ; Phylogeny ; },
abstract = {Accumulation of synthetic plastics in the biosphere has led to global pollution, provoking serious consequences for the environment and human health. Uncontrolled agricultural plastic landfills have the risk of becoming a source of agrochemicals and microplastics. Biotechnological approaches to solve plastic pollution include the removal of these polymers through biological degradation, which is a friendly environmental method. The microbial communities colonizing plastic debris (plastisphere) are considered as a potential source of plastic-degrading microorganisms. In this study, a bacterial biodiversity analysis, based on 16S rRNA gene-targeted metagenomic sequencing, was achieved in the plastisphere of low-density polyethylene (LDPE) and polypropylene (PP) polymers from an agricultural landfill. The α-diversity analysis did not show significant differences between LDPE and PP plastispheres and the plastic-free bulk soil, while LDPE and PP bacterial communities clustered close, but separately from the bulk soil in a β-diversity analysis. Although the taxonomic composition of both plastispheres was different, they shared a significantly higher proportion of Cyanobacteria and Deinococcota than the bulk soil. Additional analyses showed different indicator families, genera and species that can be associated with plastispheres. A predictive functional analysis suggests that degradation of plastic additives in both plastispheres is probably occurring. In addition, the existence of degradation processes for specific herbicides in each plastisphere is highlighted, and the possible exposure of LDPE to both physical and biological degradation processes is also described. These results will contribute to characterize the soil plastisphere exposed to different environmental conditions, and to understand the specific biological niches where plastic-degrading microorganisms could survive.},
}

*Polypropylenes/metabolism
*Polyethylene/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
*Soil Microbiology
RNA, Ribosomal, 16S/genetics
Agriculture
*Biodiversity
Biodegradation, Environmental
Phylogeny

@article {pmid41270588,
year = {2025},
author = {Pramanick, A and Saikh, SR and Mushtaque, MA and Karri, D and Gandhi, N and Das, SK},
title = {Long-range transported bacteria perturbing airborne bacterial diversity and pathogenicity over Eastern Himalayas, India.},
journal = {The Science of the total environment},
volume = {1008},
number = {},
pages = {180981},
doi = {10.1016/j.scitotenv.2025.180981},
pmid = {41270588},
issn = {1879-1026},
mesh = {India ; *Air Microbiology ; *Bacteria/pathogenicity/classification ; *Environmental Monitoring ; *Air Pollutants/analysis ; Biodiversity ; *Microbiota ; Himalayas ; },
abstract = {Long-range transported bacteria have a significant impact on hill-top airborne bacterial diversity and pathogenicity. Present study investigates airborne bacterial community structure over a hill-top region of the Eastern Himalayas, based on two years (2022--23) of investigations on culture-independent metagenomic analysis. Winter-time hill-top microbial loading is found to be a minimum of about 21,401.5 ± 2791.0 × 10[5] m[-3], representing background Himalayan airborne bacterial concentration, and a maximum of 6.7 ± 1.2 × 10[5] m[-3] on dusty summer days. 80 % of the total Himalayan bacterial population is due to long-range transport via horizontal and vertical movement of atmosphere, causing about 60 % perturbation in Himalayan bacterial diversity. Space-borne observations with 3-days back-trajectories analysis reveal a thick dust layer between 2 and 3 km over Eastern Himalayas, coming from the Thar Desert. Long-range transported dust-attached bacteria cause a 40 % enhancement in unique bacterial loading, while 6 % unique genera are noticed in upwelling of foothill pollution, and 8 % unique bacterial genera are found in downwelling from free troposphere to the hill-top atmosphere. Desert dust-attached long-range transported bacteria contain one-third skin-infecting pathogens, while upwelling pollutants carry mainly respiratory-infecting bacteria (45 %), and downwelling transport is dominated by gastrointestinal tract-infecting bacteria (50 %). Interestingly, local Himalayan bacteria (20 %) are consistently loaded with pathogens, predominantly causing respiratory (36 %) and skin (31 %) infections throughout the study period. Present results highlight the profound impact of atmospheric transport processes on regional bacterial diversity and public health in hill-top region, highlighting Himalayan atmosphere as a dynamic and global conveyor of life, including pathogens across long distances.},
}

India
*Air Microbiology
*Bacteria/pathogenicity/classification
*Environmental Monitoring
*Air Pollutants/analysis
Biodiversity
*Microbiota
Himalayas

@article {pmid41260397,
year = {2026},
author = {Abbasi, E},
title = {Metagenomic surveillance of emerging viruses in mosquito populations from high-risk regions of Iran.},
journal = {Journal of virological methods},
volume = {340},
number = {},
pages = {115301},
doi = {10.1016/j.jviromet.2025.115301},
pmid = {41260397},
issn = {1879-0984},
mesh = {Animals ; Iran/epidemiology ; *Culicidae/virology ; *Metagenomics ; Phylogeny ; *Arboviruses/genetics/classification/isolation & purification ; *Mosquito Vectors/virology ; *Virome ; High-Throughput Nucleotide Sequencing ; Epidemiological Monitoring ; Computational Biology ; RNA, Viral/genetics ; },
abstract = {BACKGROUND: Mosquito-borne arboviruses pose a growing threat to public health, particularly in ecologically vulnerable and climatically dynamic regions. This study aimed to investigate the diversity of emerging arboviruses in mosquito populations from high-risk provinces in southern and southeastern Iran using a metagenomic surveillance approach.

METHODS: Adult mosquitoes were collected from 36 sites across Hormozgan, Sistan and Baluchestan, and Khuzestan provinces. Specimens were pooled by species and location, followed by RNA extraction and high-throughput sequencing. Bioinformatics analysis was performed to identify viral taxa and assess phylogenetic relationships.

RESULTS: A total of 4275 mosquitoes representing six species were analyzed. Virome analysis revealed 43 viral taxa, including medically important arboviruses such as dengue virus serotype 2 (DENV-2), chikungunya virus (CHIKV), and West Nile virus (WNV). Multiple novel viral sequences were also detected, including putative members of Phenuiviridae and Orthomyxoviridae. Viral diversity was highest in Hormozgan province and positively correlated with ambient temperature.

CONCLUSION: This study provides the first comprehensive metagenomic insight into mosquito viromes in Iran, revealing both endemic and potentially novel arboviruses. These findings underscore the need for integrated genomic surveillance and regional vector-borne disease preparedness.},
}

Animals
Iran/epidemiology
*Culicidae/virology
*Metagenomics
Phylogeny
*Arboviruses/genetics/classification/isolation & purification
*Mosquito Vectors/virology
*Virome
High-Throughput Nucleotide Sequencing
Epidemiological Monitoring
Computational Biology
RNA, Viral/genetics

@article {pmid41077176,
year = {2025},
author = {Agrawal, K and Hong, ASY and Cifuentes-González, C and Kumar, VS and Rojas-Carabali, W and Zhang, S and Wang, Q and de-la-Torre, A and Gijs, M and Gill, T and Rosenbaum, JT and Rajagopala, SV and Gangaputra, S and Conforti, A and Ross, RP and Yang, P and Wong, S and Agrawal, R},
title = {Microbiome signatures and their role in uveitis: Pathogenesis, diagnostics, and therapeutic perspectives.},
journal = {Progress in retinal and eye research},
volume = {109},
number = {},
pages = {101409},
doi = {10.1016/j.preteyeres.2025.101409},
pmid = {41077176},
issn = {1873-1635},
mesh = {Humans ; *Uveitis/microbiology/diagnosis/therapy/immunology ; Animals ; Dysbiosis ; *Microbiota/physiology ; *Gastrointestinal Microbiome/physiology ; },
abstract = {Non-infectious uveitis is a group of complex inflammatory eye diseases shaped by genetic susceptibility, immune dysregulation, and environmental cues. Among these, the mucosal microbiome-including gut, oral, and ocular surface microbial communities-has emerged as a key player in modulating systemic and ocular immune responses. Recent evidence supports a gut-eye axis wherein microbial dysbiosis alters intestinal barrier function, perturbs T cell homeostasis, and drives systemic immune activation that can breach ocular immune privilege. Specific taxa, such as Prevotella and Faecalibacterium, as well as microbial metabolites including short-chain fatty acids, have been implicated in promoting or mitigating ocular inflammation. Human leukocyte antigen (HLA) alleles, notably HLA-B27 and HLA-A29, influence both microbiome composition and disease phenotype, suggesting a gene-microbiome-immunity triad of interaction in uveitis pathogenesis. Drawing on insights from metagenomics, metabolomics, in vitro and in vivo experimental and murine models, this review delineates four key mechanisms-immune imbalance, antigenic mimicry, epithelial barrier disruption, and bacterial translocation-that underpin the key roles of microbiome in uveitis. We combine current literature and integrate findings from our research programs to highlight diagnostic and therapeutic opportunities. Microbiome-informed strategies, such as rational probiotic design, dietary modulation, and targeted microbial therapies, hold promise for complementing existing immunosuppressive regimens. Translating these insights into clinical practice requires robust multi-omic studies, longitudinal cohorts, mechanistic studies, and precision-guided intervention trials. By framing uveitis within a mucosal immunological context, this review proposes a future precision medicine roadmap for integrating microbiome science into ocular inflammatory disease management.},
}

Humans
*Uveitis/microbiology/diagnosis/therapy/immunology
Animals
Dysbiosis
*Microbiota/physiology
*Gastrointestinal Microbiome/physiology

@article {pmid41353034,
year = {2025},
author = {McCone, N and Hosokawa, M},
title = {Recovering genomes from uncultured fungi with single-cell genomics.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2025.11.004},
pmid = {41353034},
issn = {1347-4421},
abstract = {Single-cell genomics (SCG) complements culture-independent metagenomics for accessing fungal genomes, particularly from lineages that remain uncultured. We contrast metagenomics, which excels when profiling community composition and metabolic potential but often underrepresents low-abundance fungi, with SCG, which first isolates individual cells or nuclei to generate single-amplified genomes (SAGs) and can recover rare or microdiverse taxa. We then organize existing fungal SCG applications into three subgroups: spore-level sequencing from host-enriched or environmental material; single-nucleus genomics for multinucleate fungi; and single-spore sequencing of haploid progeny for diploid linkage and chromosome phasing. Across studies, pooling and co-assembly of cognate cells improves completeness; key hurdles persist in wall lysis, whole-genome amplification bias, and contamination control. Practical advances include shallow sequencing for QC triage, nuclei pooling with normalized co-assembly, and hybrid long- and short-read assembly. SCG adds unique value where strain resolution and genotypic context matter, including host-to-mobile-element linkage, recovery of large biosynthetic gene clusters, and karyotype validation against telomere-to-telomere references. Used alongside metagenomics, SCG enables a strain-resolved view of fungal biodiversity and function, with incremental improvements across the SCG pipeline promising routine access to genomes from early-diverging and other environmentally embedded fungi.},
}

@article {pmid41351142,
year = {2025},
author = {Sharko, F and Busova, V and Boulygina, E and Burakova, A and Pankova, S and Nedoluzhko, A},
title = {Ancient DNA sheds light on the historical distribution of the rare and ephemeral plant Coleanthus subtilis in Southern Siberia.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12365-4},
pmid = {41351142},
issn = {1471-2164},
abstract = {BACKGROUND: Ancient DNA is a valuable source of information about the distant past of our planet. Reconstructing the past ecosystems is essential for understanding many aspects of life in the steppes of southern Siberia and Central Asia, where numerous human societies representing different archaeological cultures have lived. The remains of their activities, revealed by archaeological excavations, provide a wide range of sources for the cultural and natural/biological history of the region. One of the most enigmatic Iron Age archaeological cultures in southern Siberia is the Tashtyk culture, which dates back to the 1st - 7th centuries AD. The people of this culture inhabited the Minusinsk Basin and practiced different burial rites, including cremation. Thanks to the exceptional preservation of organic remains in individual Tashtyk burials we know of quite an unusual phenomenon: the placement of cremains into the human-like mannequins made from animal skin and filled with herbaceous plants. This study analyses ancient DNA extracted from the grass stuffing of a mannequin found in 2023 at the Oglakhty cemetery, which dates back to 250-300 AD. Our aim is to identify the plant species that were used to stuff the mannequin approximately 1,700 years ago, and to compare their diversity with that of modern-day plant species. This is particularly significant given that the Oglakhty region is part of the Khakassky State Nature Reserve, which was added to the UNESCO Tentative List in 2016 due to its biodiversity and concentration of archaeological sites.

RESULTS: We sequenced the ancient DNA of a dried historical grass mixture in order to reconstruct the nearly complete chloroplast genomes of several apparent Poaceae species. Our analysis showed that, 1,700 years ago, the diversity of plant species in the Oglakhty area was similar to the modern meadow flora of the Minusinsk Basin. These included typical steppe and forest-steppe zone plant genera of Siberia, such as Holcus, Phleum, Poa, and Stipa. Interestingly, alongside the species commonly found in modern southern Siberian steppes and meadows, we discovered the rare, ephemeral, and protected moss grass, Coleanthus subtilis (Tratt.) Seidel ex Roem. et Schult. whose current distribution range spans highly fragmented areas of northern Eurasia and North America but not the Minusinsk Basin.

CONCLUSION: The herbaceous plant C. subtilis, whose DNA fragments were obtained through the metagenomic profiling of the human-like mannequin's stuffing at the Oglakhty cemetery, provides new insights into the cultural and natural history of Siberia. Firstly, we identified several grass taxa in the mannequin's stuffing. Most of them are characteristic for the steppe zone; the only exception is C. subtilis, which usually inhabits riverbanks. Therefore, we assume that, despite being primarily stuffed with the steppe plants, the Oglakhty mannequin was crafted on a riverbank, where C. subtilis might have got inside likely by chance. It is important to note that the stuffing process apparently took place after the vegetation season of C. subtilis in second half of summer and the beginning of autumn. Secondly, our research suggests that a population of C. subtilis, which is currently absent from the documented flora of southern Siberia, previously grew in the Minusinsk Basin wetlands. Our study highlights the need for field expeditions aimed to identify endemic populations of C. subtilis in the Yenisei River valley.},
}

@article {pmid41297753,
year = {2026},
author = {Zhong, Z and Ye, W and Li, B and Al-Dhabi, NA and Zhao, J and Li, S and Sun, Y and Zhang, H and Tang, W and Chen, S},
title = {Phosphate-iron modified Enteromorpha Prolifera hydrochar enhances dry anaerobic digestion of food waste: Synergistic mechanisms of electron transfer network, microbial consortia remodeling, and metagenomic insights.},
journal = {Environmental research},
volume = {289},
number = {},
pages = {123385},
doi = {10.1016/j.envres.2025.123385},
pmid = {41297753},
issn = {1096-0953},
mesh = {Anaerobiosis ; Iron/chemistry ; *Microbial Consortia ; Phosphates/chemistry ; *Ulva ; *Refuse Disposal/methods ; Electron Transport ; Metagenomics ; Solid Waste ; Food Loss and Waste ; Edible Seaweeds ; },
abstract = {The dual pressures of marine ecological disasters and urban solid waste treatment pose severe challenges to sustainable development. However, current research mostly focuses on single waste treatment, lacking coordinated governance strategies. This study innovatively proposes a "marine-urban" solid waste collaborative treatment strategy, converting Enteromorpha Prolifera into phosphate - iron composite modified hydrothermal carbon (P-MEPHC) via hydrothermal carbonization technology, and systematically analyzes its enhancement mechanisms in dry anaerobic digestion of food waste. Characterization results indicate that P-MEPHC possesses high electrical conductivity (488 S/m), a hierarchical mesoporous structure (BET specific surface area of 15.15 m[2]/g, average pore size of 10.57 nm), and abundant Fe-P-O active sites. Engineering verification showed that the addition of 52 mg/g VSS (volatile suspended solids) P-MEPHC increased the cumulative methane production to 99.25 mL/g VS (volatile solids), representing a 50.6 % improvement over the control group. Concurrently, the peak value of soluble chemical oxygen demand (SCOD) was elevated to 111.53 g/L, while the inhibition intensity of ammonia nitrogen was reduced by 32 %. Metagenomics indicated that it achieves process enhancement through dual regulatory mechanisms: at the community structure level, it enriches syntrophic acid-producing bacteria Sporanaerobacter (+7.9 %) and hydrogenotrophic methanogens Methanoculleus (+17.7 %); at the metabolic function level, it significantly upregulates the expression of core methanogenic metabolic genes such as acetyl-CoA synthase (ACSS1_2, +255 %), thereby activating the direct interspecies electron transfer pathway. This research provides a technically feasible paradigm with both environmental and economic benefits for the coordinated resource utilization of near - shore algal bloom biomass and organic solid waste, and promotes the closed - loop integration of blue carbon sinks and urban metabolic systems.},
}

Anaerobiosis
Iron/chemistry
*Microbial Consortia
Phosphates/chemistry
*Ulva
*Refuse Disposal/methods
Electron Transport
Metagenomics
Solid Waste
Food Loss and Waste
Edible Seaweeds

@article {pmid41275679,
year = {2026},
author = {Matu, A and Valverde, A and Cason, E and Gomez-Arias, A and Maleke, M and Castillo, J},
title = {Microbial consortia in mine water bioremediation: principles, design and practical applications.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124956},
doi = {10.1016/j.watres.2025.124956},
pmid = {41275679},
issn = {1879-2448},
mesh = {*Biodegradation, Environmental ; *Mining ; *Microbial Consortia ; Bioreactors ; },
abstract = {The impact of mining activities on water sources is a global concern, especially in water-scarce countries such as Southern Africa, Mediterranean region, western Asia, and South America. Bioremediation emerges as a feasible and attractive alternative to address this environmental issue. However, while biological sulfate reduction and the emerging use of using microbially induced carbonate precipitation (MICP) for remediating polluted mine water have gained attention, strategies for designing effective microbial consortia have seen little advancement. The performance of microbial consortia in these treatments can be quite variable. Most improvement strategies have focused mainly on bioreactor design and selecting suitable carbon sources, addressing technical aspects while neglecting the central players in this process: the microbes themselves. Enhancing consortium effectiveness requires revisiting foundational concepts such as monoculture, co-culture, division of labor, and bottom-up versus top-down approaches. While these concepts offer significant theoretical potential to improve consortium performance, they have seldom been applied in practice for mine water bioremediation. In this literature review, we revisit these principles and explore the integration of novel tools such as metagenomics and bioinformatics. These approaches can deepen our understanding of indigenous microbial diversity, uncover dynamic interactions among microbial species, and identify keystone species as potential candidates for bioremediation. By leveraging their genomic potential, it becomes possible to design consortia that are more efficient and better suited to support the recovery of contaminated water sources.},
}

*Biodegradation, Environmental
*Mining
*Microbial Consortia
Bioreactors

@article {pmid41218435,
year = {2026},
author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y},
title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124889},
doi = {10.1016/j.watres.2025.124889},
pmid = {41218435},
issn = {1879-2448},
mesh = {RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology/chemistry ; *Microbiota ; Metagenomics ; Ecosystem ; Nitrates ; Bacteria/genetics ; },
abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.},
}

RNA, Ribosomal, 16S/genetics
Geologic Sediments/microbiology/chemistry
*Microbiota
Metagenomics
Ecosystem
Nitrates
Bacteria/genetics

@article {pmid40912476,
year = {2025},
author = {Lu, Z and Petersen, C and Dai, R and Reyna, ME and Ahmadiankalati, M and Sifuentes, E and Dai, DLY and Hoskinson, C and Del Bel, KL and Miliku, K and Moraes, TJ and Mandhane, PJ and Becker, AB and Azad, MB and Simons, E and Lou, W and Ambalavanan, A and Duan, Q and Turvey, SE and Subbarao, P},
title = {Early-preschool wheeze trajectories are predominantly nonallergic with distinct biologic and microbiome traits.},
journal = {The Journal of allergy and clinical immunology},
volume = {156},
number = {6},
pages = {1556-1572},
doi = {10.1016/j.jaci.2025.07.034},
pmid = {40912476},
issn = {1097-6825},
mesh = {Humans ; *Respiratory Sounds/immunology ; Infant ; Female ; Male ; Child, Preschool ; *Asthma/diagnosis/epidemiology/microbiology/immunology ; Phenotype ; *Microbiota ; Cohort Studies ; Hypersensitivity ; },
abstract = {BACKGROUND: Disentangling preschool wheezing heterogeneity in terms of clinical traits, temporal patterns, and collective health care burden is critical for precise and effective interventions.

OBJECTIVE: We aimed to collectively define contributions and distinct characteristics of respiratory phenotypes based on longitudinal wheeze and atopic sensitization patterns in the first 5 years of life.

METHODS: Group-based trajectory analysis was performed in the CHILD Cohort Study to identify distinct wheeze and allergic sensitization trajectories. Trajectories were evaluated for associated risk factors, health care utilization, biologic determinants, and clinical outcomes. Stool samples for shotgun metagenomic sequencing profiles of infant microbiomes collected at ages 3 months and 1 year were assessed for phenotype-specific biomarkers.

RESULTS: A total of 6 distinct respiratory phenotypes were identified on the basis of samples from 2902 children; the phenotypes differed by temporal wheeze and allergic sensitization patterns. Although allergic wheeze phenotypes (found in 11.6% of participants) carried the highest risk of asthma diagnosis, the more common nonallergic phenotypes (in 88.3% of participants) contributed to the majority of 5-year asthma diagnoses (61.4% of diagnoses). Most importantly, nonallergic phenotypes accounted for more than two-thirds of health care utilization in this age group. Phenotypes differed by lung function, blood eosinophil counts, allergic comorbidities, and weight-for-age z score. Moreover, microbiome profiles developed from 1439 infants revealed that largely nonoverlapping microbial signatures at age 1 year are associated with each phenotype.

CONCLUSION: We identified novel early-childhood respiratory phenotypes to disentangle nonoverlapping paths to preschool wheezing. Our findings highlight the continued clinical relevance of nonatopic wheeze phenotypes, which remain undertreated despite accounting for a substantial proportion of health care utilization and asthma diagnoses.},
}

Humans
*Respiratory Sounds/immunology
Infant
Female
Male
Child, Preschool
*Asthma/diagnosis/epidemiology/microbiology/immunology
Phenotype
*Microbiota
Cohort Studies
Hypersensitivity

@article {pmid40691354,
year = {2026},
author = {Roux, S and Coclet, C},
title = {Viromics approaches for the study of viral diversity and ecology in microbiomes.},
journal = {Nature reviews. Genetics},
volume = {27},
number = {1},
pages = {32-46},
pmid = {40691354},
issn = {1471-0064},
mesh = {*Microbiota/genetics ; *Viruses/genetics/classification ; *Virome/genetics ; Humans ; Metagenomics/methods ; Ecosystem ; Genetic Variation ; Biodiversity ; Animals ; Genome, Viral ; },
abstract = {Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.},
}

*Microbiota/genetics
*Viruses/genetics/classification
*Virome/genetics
Humans
Metagenomics/methods
Ecosystem
Genetic Variation
Biodiversity
Animals
Genome, Viral

@article {pmid41350543,
year = {2025},
author = {Nickodem, CA and Tran, PQ and Neeno-Eckwall, E and Congdon, AG and Sanford, GR and Silva, EM and Hite, JL},
title = {Soil management strategies drive divergent impacts on pathogens and environmental resistomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43215},
pmid = {41350543},
issn = {2045-2322},
support = {AD00001395//U.S. Department of Agriculture/ ; 58-5090-2-035//U.S. Department of Agriculture/ ; AD00001395//U.S. Department of Agriculture/ ; },
mesh = {*Soil Microbiology ; Manure/microbiology ; Fertilizers ; *Soil/chemistry ; Animals ; Agriculture/methods ; Poultry ; Microbiota ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Humans ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) is a growing global health threat, and the genes that confer drug resistance are increasingly recognized as widespread environmental contaminants. Livestock manure, widely used as a non-synthetic fertilizer, is a potential source of AMR contamination in the environment. Manure fertilizers are well-documented reservoirs of AMR genes (ARGs) and drug-resistant pathogens. However, the role of soil management practices in shaping the persistence and spread of these genes after manure application remains poorly understood. We conducted a large-scale field experiment to evaluate how soil management practices influence the resistome (the genomic content involved in resistance to antimicrobial agents) and the overall microbiome of agricultural soils. Specifically, we ask: Does the use of composted poultry manure in organic soil management practices increase the risk of transmitting ARGs and drug-resistant pathogens? We integrated metagenomic sequencing with risk score analyses to assess the abundance, diversity, and mobility of resistance genes. Contrary to expectations, our results indicate that non-organic practices, despite not applying poultry manure, posed greater risks for transmitting AMR genes and human pathogens - due to significantly higher co-occurrence of ARGs with mobile genetic elements (MGEs), which facilitate horizontal gene transfer. In contrast, organic practices, that applied composted poultry manure, increased overall ARG and metal resistance gene (MRG) abundance, but the genes were less diverse and less mobile. These findings show that focusing solely on ARG and MRG abundance can misrepresent AMR risks and underscore the importance of evaluating gene mobility and management context when assessing AMR hazards. Our study highlights how soil management can be strategically leveraged to mitigate AMR transmission, offering actionable insights for sustainable agriculture, environmental stewardship, and public health protection.},
}

*Soil Microbiology
Manure/microbiology
Fertilizers
*Soil/chemistry
Animals
Agriculture/methods
Poultry
Microbiota
Metagenomics
*Drug Resistance, Bacterial/genetics
Humans
Gene Transfer, Horizontal

@article {pmid41350329,
year = {2025},
author = {Sato, Y and Kumagai, H and Hirooka, H and Yoshida, T},
title = {Differences in prokaryotic and viral community between rumen and feces.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43232},
pmid = {41350329},
issn = {2045-2322},
mesh = {*Feces/microbiology/virology ; Animals ; *Rumen/microbiology/virology ; Metagenomics/methods ; *Viruses/genetics/classification ; Metagenome ; Bacteria/genetics ; Virome ; *Prokaryotic Cells/virology ; Genome, Viral ; Gastrointestinal Microbiome ; },
abstract = {Ruminants harbor diverse microbial communities, including prokaryotes and viruses, across their digestive tract. Rumen viruses contribute to carbohydrate metabolism; however, their persistence and host interactions in the lower gastrointestinal tract remain unclear. In this study, we investigated the prokaryotic and viral communities in the rumen and feces of the same wethers using whole-metagenomic and virus-like particle metagenomic sequencing. For prokaryotic community analysis, we reconstructed over 300 metagenome-assembled genomes, most of which were novel. These revealed strong site specificity, with distinct prokaryotic community compositions between the rumen and feces. Virome analysis recovered more than 6,000 viral genomes, including many novel viruses. Unlike prokaryotes, several viruses were found to be shared between the rumen and feces. Auxiliary metabolic genes encoding glycoside hydrolases were identified in several rumen-associated viral genomes, whereas fecal-associated viral genomes did not harbor such genes. Host-virus interaction analysis predicted that viruses predominantly infect dominant bacterial taxa and methanogens within each gastrointestinal site, although some viruses may interact with hosts across different sites. These findings highlight the strong site specificity of the prokaryotic communities and the comparatively broader distribution of viruses within the ruminant gastrointestinal tract. These insights advance understanding of virus-prokaryote-host interactions with implications for animal productivity.},
}

*Feces/microbiology/virology
Animals
*Rumen/microbiology/virology
Metagenomics/methods
*Viruses/genetics/classification
Metagenome
Bacteria/genetics
Virome
*Prokaryotic Cells/virology
Genome, Viral
Gastrointestinal Microbiome

@article {pmid41348832,
year = {2025},
author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A},
title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337760},
doi = {10.1371/journal.pone.0337760},
pmid = {41348832},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; },
abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.},
}

Animals
*Gastrointestinal Microbiome
Humans
Mice
*Fecal Microbiota Transplantation/methods
*Virome
Male
Diet, High-Fat/adverse effects
Obesity/therapy/microbiology
*Feces/virology
Mice, Inbred C57BL
*Glucose/metabolism
Metabolic Syndrome/therapy/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/genetics

@article {pmid41348596,
year = {2025},
author = {Hernández-Velázquez, R and Ziemski, M and Bokulich, NA},
title = {ViromeXplore: integrative workflows for complete and reproducible virome characterization.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf638},
pmid = {41348596},
issn = {1477-4054},
support = {22.00210//Swiss State Secretariat for Education, Research and Innovation/ ; //European Union nor European Research Executive Agency/ ; },
mesh = {*Virome ; *Workflow ; *Metagenomics/methods ; *Software ; High-Throughput Nucleotide Sequencing ; *Computational Biology/methods ; *Viruses/genetics/classification ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results ; },
abstract = {Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.},
}

*Virome
*Workflow
*Metagenomics/methods
*Software
High-Throughput Nucleotide Sequencing
*Computational Biology/methods
*Viruses/genetics/classification
Metagenome
Microbiota
Genome, Viral
Reproducibility of Results

@article {pmid41348453,
year = {2025},
author = {Li, C and Ge, H and Huang, W and Zilda, DS and Radjasa, OK and Zhao, L and Cong, B and Liu, S and Zhang, Z},
title = {Vertically stratified microbial diversity and keystone species driving element cycling in the Magellan seamount sediments.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001493},
pmid = {41348453},
issn = {2057-5858},
mesh = {*Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Archaea/genetics/classification ; Phylogeny ; Biodiversity ; Microbiota ; },
abstract = {Deep-sea polymetallic nodules, rich in cobalt, nickel and titanium, are valuable for electronics, aerospace and energy industries. However, the vertical distribution and ecological functions of prokaryotic communities in sediments beneath nodules from the Magellan seamounts, a unique microbial habitat characterized by ultra-slow sedimentation rates (0.4-4 mm ky[-1]) and heterogeneous metal gradients, remain poorly characterized. In our research, 16S rRNA gene amplicon sequencing and metagenomic analyses of sediment cores (0-20 cm) from the western Pacific polymetallic nodule province revealed statistically significant decreases in prokaryotic diversity (Shannon index: 9.446 to 2.288; P<0.001). Proteobacteria, Crenarchaeota, Chloroflexi and Bacteroidota were the dominant taxa. The microbial co-occurrence network in the surface layer had a longer mean path length (2.11 vs 1 in the bottom layer) and a larger network diameter (11 vs 1), indicating a loose community structure and greater resistance to disturbance, while the bottom microbial network had a higher density (0.037 vs 0.01) and clustering coefficient (0.32 vs 1), suggesting tight microbial interactions. The concentrations of MnO (6.96-9.41 µg g[-1]) and P2O5 (2.55-3.89 µg g[-1]) gradually decreased with increasing depth. The concentrations of Co and Pb were relatively high in the surface sediments (0-8 cm) but decreased significantly below 8 cm. In contrast, the concentrations of Fe2O3 and As increased with depth. The environmental factors depth, MnO, Fe2O3 and heavy metals (Cr, Zn and Cu) were found to be the main drivers of the microbial community structure. We assembled 122 metagenome-assembled genomes from the metagenomic data. Gene abundance analysis revealed that sox genes (soxB/C/D/X/Y/Z) and assimilatory sulphate reduction genes (cysC and cysH) were highly abundant in the surface sediment, whereas the abundance of dissimilatory sulphate reduction genes (dsrA and dsrB) was enhanced in the bottom layer, reflecting a hierarchical adaptive strategy for sulphur metabolism. Our study expands current knowledge on the vertical variations of microbial diversity and microbially driven biogeochemical cycling in deep-sea settings underneath polymetallic nodules. Characterizing the microbial community underneath those nodules may provide insights into microbial resilience in extreme oligotrophic environments and valuable insights for future deep-sea mining activities.},
}

*Geologic Sediments/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/metabolism
Metagenomics/methods
Archaea/genetics/classification
Phylogeny
Biodiversity
Microbiota

@article {pmid41348443,
year = {2025},
author = {Luu, LDW and Bryant, C and Brown, J and Turner, M and Pham, TH and Mazraani, R and Burke, C and Jury, B and Shrestha, M and Fleming, K and Bateson, D and Russell, D and Bassett, F and Ong, E and Hocking, JS and Sweeney, S and Huston, WM},
title = {Cervicovaginal microbiome composition and absolute quantity are associated with pelvic inflammatory disease.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001574},
pmid = {41348443},
issn = {2057-5858},
mesh = {Humans ; Female ; *Pelvic Inflammatory Disease/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Case-Control Studies ; *Vagina/microbiology ; Adult ; *Cervix Uteri/microbiology ; Vaginosis, Bacterial/microbiology ; Gardnerella vaginalis/genetics ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; Young Adult ; },
abstract = {Pelvic inflammatory disease (PID), which involves infection and inflammation of the female reproductive tract, can lead to sequelae including chronic pelvic pain, ectopic pregnancy and tubal factor infertility. A causative pathogen is not identified in many PID cases (idiopathic PID) and does not develop in all women with a sexually transmitted infection or bacterial vaginosis. Therefore, there is a need to better understand the pathogenesis of PID. A case-control study was conducted to explore microbiome, antibiotic resistance and immune gene expression in PID. Microbial profiling using both 16S rRNA gene amplicon and metagenomic approaches revealed that bacterial vaginosis-associated bacteria such as Gardnerella vaginalis, Fannyhessea vaginae, Ureaplasma parvum and members of the Prevotella spp. were significantly enriched in PID cases, while healthy controls were associated with Lactobacillus (L.) crispatus. Quantitative analysis with species-specific quantitative real-time PCR (qPCR) indicated that a high copy number of L. crispatus (measured using calibrated copy estimates by qPCR) was strongly associated with cervical samples from women in the control group, whereas PID cases with this organism had low copies when measured using qPCR. Antibiotic resistance to tetracyclines was more frequently predicted in metagenome-assembled genomes from PID cases, and corresponding isolates cultured from cases were less susceptible to doxycycline (L. iners). Overall, this study supports that PID is associated with cervicovaginal dysbiosis and an absence or low quantity of L. crispatus.},
}

Humans
Female
*Pelvic Inflammatory Disease/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Case-Control Studies
*Vagina/microbiology
Adult
*Cervix Uteri/microbiology
Vaginosis, Bacterial/microbiology
Gardnerella vaginalis/genetics
Metagenomics
*Bacteria/genetics/classification/isolation & purification
Young Adult

@article {pmid41346331,
year = {2025},
author = {Preenanka, R and Sivam, V and Sasikala, R and Koombankallil, R and Raveendran, K and Jacob, J and Devadas, AL and Ravikumar, NK and Anbalakan, M and Chigilipalli, H and Thangaraj, RS and Basha, AK and Joseph, TC and Badireddy, MR and Vaiyapuri, M},
title = {Muscle Microbiome Analysis of Indian Mackerel (Rastrelliger kanagurta) Delineated Classical and Novel Spoilage Bacteria.},
journal = {Journal of food science},
volume = {90},
number = {12},
pages = {e70751},
doi = {10.1111/1750-3841.70751},
pmid = {41346331},
issn = {1750-3841},
support = {BT/PR46349/AAQ/3/1063/2022// Department of Biotechnology/ ; // Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; *Perciformes/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Seafood/microbiology ; Food Packaging/methods ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; *Muscles/microbiology ; Vacuum ; Metagenomics ; Food Storage ; },
abstract = {Metagenomics allows a comprehensive insight into the spoilage-associated muscle microbiome shifts in the air-packed and vacuum-packed Indian mackerel. This study explored the microbial composition and diversity of spoilage flora in air-packed (T1M, T2M, and T3M) and vacuum-packed (T4M, T5M, and T6M) Indian mackerel (Rastrelliger kanagurta) stored at 0 ± 2°C (iced), 5 ± 2°C (chilled), and 30 ± 2°C (abused) temperatures through metagenomics, targeting the V1-V9 region of 16s rRNA. Total Volatile Base Nitrogen and Thiobarbituric Acid were analyzed to confirm the spoilage threshold limit, and accordingly, the fish muscle tissue on the spoilage day was selected for microbiome analysis. Metagenomic analysis revealed distinct variation in the relative abundance and spoilage microbiome between the air-packed and vacuum-packed Indian mackerel stored at iced, chilled, and abused temperatures. The predominant bacterial species responsible for spoilage were Cetobacterium ceti, Clostridium polyendosporum, and Gilliamella apicola in vacuum-packed mackerel, whereas Shewanella arctica, S. aquimarina, S. baltica, Staphylococcus xylosus, and Burkholderia cepacia played a major role in the spoilage of air-packed samples. The observed bacterial population dynamics across different temperatures and packaging significantly influenced the microbiome diversity in Indian mackerel. Summing up, this study emphasizes the unique and diverse microbes contributing to spoilage and provides a valuable guide for the flora that need to be controlled for extending the shelf life of Indian mackerel.},
}

Animals
*Perciformes/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Seafood/microbiology
Food Packaging/methods
Food Microbiology
RNA, Ribosomal, 16S/genetics
*Muscles/microbiology
Vacuum
Metagenomics
Food Storage

@article {pmid41346299,
year = {2025},
author = {Zhang, C and Zhao, Z and Zhou, F and Shi, C and Zhai, X and Sha, Z and Chu, Q and Liu, H and Liu, S and Pan, Z and Wang, X and Pan, X and Fang, M and Rillig, MC and Wang, Z},
title = {Conventional and Biodegradable Microplastics Both Impair Soil Phosphorus Cycling and Availability via Microbial Suppression.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11806},
pmid = {41346299},
issn = {1520-5851},
abstract = {Microplastics (MPs) are emerging soil pollutants that can disrupt essential biogeochemical processes, yet their effects on phosphorus (P) cycling remain underexplored. Here, we conducted a 150-day incubation experiment using agricultural soil amended with either polyethylene (PE, conventional) or polylactic acid (PLA, biodegradable) MPs to investigate their impact on microbially mediated P cycling. MPs altered soil P cycling and decreased available phosphorus (AP) by ∼15% after 90 days. Fourier transform infrared spectroscopy revealed weakened AP-associated functional groups (P-O-P, P-O, and P═O), most pronounced under PLA treatment. These shifts were accompanied by reduced abundances of key P-cycling taxa (Bacillus, Paenibacillus, and Sphingomonas) and downregulation of phosphatase gene abundance (phoA/D/X: -65.4% in PE, -59.8% in PLA). Correspondingly, the activities of acid, neutral, and alkaline phosphatases were all suppressed, with alkaline phosphatase in PE-treated soil reduced by 34.1%. Together, these results demonstrate that MPs disturb biotic transformation pathways, leading to subsequent alterations in the chemical speciation of soil P and decreased AP content. Notably, significant disruption was observed for both conventional and biodegradable types. Our findings challenge the prevailing assumption of environmental benignity for biodegradable plastics and underscore the urgent need for mechanistic assessments of their byproducts. Such disruption may hinder microbial P mobilization and decrease fertilizer use efficiency, ultimately threatening soil health and agricultural sustainability.},
}

@article {pmid41253025,
year = {2025},
author = {Tian, R and Chen, N and Liu, Z and Yan, YG and Wang, YW and Zhao, P and Bo Zhao, C and Zhang, L and Zhang, Q and Tang, YP},
title = {Lactobacillus johnsonii alleviates rhubarb-induced diarrhoea by regulating the gut microbiota and TLR4/NF-κB signalling pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {149},
number = {},
pages = {157550},
doi = {10.1016/j.phymed.2025.157550},
pmid = {41253025},
issn = {1618-095X},
mesh = {*Rheum/chemistry/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Toll-Like Receptor 4/metabolism ; *Diarrhea/chemically induced/therapy/microbiology ; Animals ; NF-kappa B/metabolism ; Signal Transduction/drug effects ; Male ; *Lactobacillus ; Wine ; Mice ; },
abstract = {BACKGROUND: Rhubarb (RH) is a commonly used traditional Chinese medicine (TCM) for treating digestive system diseases. However, long-term or excessive use of RH can cause gastrointestinal adverse reactions, such as diarrhoea. RH steaming with wine (PRH) can affect gut microbiota (GM) and alleviate diarrhoea caused by rhubarb. Nevertheless, the causal relationship between differential strains and wine steaming in alleviating RH-induced diarrhoea remains unclear.

PURPOSE: This study aimed to further elucidate the mechanism of wine steaming in alleviating the RH-induced diarrhoea through establishing a causal relationship.

METHODS: The components of RH and PRH were detected using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) technology. Differential strains were screened using metagenomic sequencing technology. To evaluate the alleviating effect of Lactobacillus johnsonii (L. john) on RH-induced diarrhoea, the faecal water rate, intestinal propulsion rate, intestinal transit time, and six-hour defecation volume were measured. Histopathological observations of the duodenum, jejunum, and ileum were conducted using the hematoxylin-eosin (HE) staining method. Meanwhile, the levels of inflammatory factors and immunoglobulins (IgG and IgA) in the ileum were detected by enzyme-linked immunosorbent assay (ELISA). The counts of CD4[+], CD8[+], and T regulatory cells (Treg) in peripheral blood were measured using flow cytometry. The protein expression of toll-like receptor 4 (TLR4), nuclear factor kappa-B (NF-κB), zonula occludens-1 (ZO-1), and occludin in the ileum tissue was detected using immunohistochemistry and Western blotting. Faecal samples were analysed using 16S rRNA sequencing technology, and the levels of short-chain fatty acids (SCFAs) were detected using gas chromatography-mass spectrometry (GC-MS). Endogenous metabolites were analysed using UPLC-MS.

RESULTS: Thirty-seven chemical ingredients in RH and PRH were identified, mainly containing anthraquinones, phenolic acids, and flavonoids. The relative peak areas of anthraquinone components decreased in PRH. Screened from RH and PRH, the differential strain L. john alleviated diarrhoea induced by RH, decreased faecal water rate and intestinal propulsion rate, and improved the degree of pathological damage in the small intestine. L. john can downregulate the levels of inflammatory factors (IL-6, TNF-α, IL-17, and IFN-γ), inhibit the expression of TLR4/NF-κB, upregulate the expression of ZO-1 and Occludin, increase the contents of IgG and IgA, CD4[+]/CD8[+] ratio, and Treg cell percentage. The supplementation of L. john can regulate the composition of GM, with decreased Streptococcus and increased norank_f_Muribaculaceae, and elevate the levels of SCFAs, including acetic acid, propionic acid, and butyric acid mediated by GM. Metabolic analysis showed that L. john alleviated the disorder in the glycerophospholipid metabolic pathway.

CONCLUSION: L. john can alleviate diarrhoea and intestinal pathological damage caused by RH by improving GM dysbiosis and SCFAs level abnormalities, restoring cellular immune function and intestinal barrier function, and regulating abnormal expression of TLR4/NF-κB and release of inflammatory factors. The findings have revealed the causal relationship between GM and the alleviation of RH-induced diarrhoea by steaming with wine and contributed to the understanding of the mechanism of wine steaming in alleviating the RH-induced diarrhoea.},
}

*Rheum/chemistry/adverse effects
*Gastrointestinal Microbiome/drug effects
*Toll-Like Receptor 4/metabolism
*Diarrhea/chemically induced/therapy/microbiology
Animals
NF-kappa B/metabolism
Signal Transduction/drug effects
Male
*Lactobacillus
Wine
Mice

@article {pmid40300566,
year = {2025},
author = {Komijani, M and Mahdi, ES and Komijani, M and Alaghmand, A},
title = {Metagenomics Study Suggests the Role of Vitamins and Gut Microbiome in Autism Spectrum Disorder.},
journal = {Digestion},
volume = {106},
number = {6},
pages = {515-529},
doi = {10.1159/000545483},
pmid = {40300566},
issn = {1421-9867},
mesh = {Humans ; *Autism Spectrum Disorder/microbiology/blood ; *Gastrointestinal Microbiome/genetics/physiology ; Metagenomics ; Male ; Feces/microbiology ; Female ; Folic Acid/blood ; Case-Control Studies ; Child, Preschool ; Child ; *Vitamin B 12/blood ; RNA, Ribosomal, 16S/genetics ; *Cholecalciferol/blood ; *Vitamins/blood ; },
abstract = {INTRODUCTION: Autism is a neurological disability that often appears after the age of three in children, also known as an autism spectrum disorder (ASD). Several studies have examined the influence of some environmental factors, and many parameters related to the behavior of autistic patients have been measured in order to find ways to reduce ASD. This study investigates the relationship between ASD and serum levels of vitamin D3, B12, folic acid, and the gut microbiome.

METHODS: The serum levels of vitamin D3, B12, and folic acid in ASD patients were measured by the ELISA method and compared to healthy groups. DNA was extracted from stool samples of ASD patients and the control group, and then the gut microbiome was investigated via a metagenomics approach. Metagenomics sequencing was performed to analyze the 16S rRNA gene sequencing for phylum and sub phylum level microbiome.

RESULT: The result showed no significant change in the VitD3 and folate levels of ASD patients compared to the control group (p = 0.157 and p = 0.0505, respectively). There was a significant difference in the VitB12 level between control healthy individuals and ASD patients, in which the serum VitB12 concentration was significantly lower than the control group (p = 0.0001). Our results regarding gut metagenomics showed that the abundance of the Actinobacteria by the phylum level was significantly higher in the ASD patients compared to the control group (p = 0.0013). The abundance of the Firmicutes by the phylum level was significantly lower in the ASD patients compared to the control group (p = 0.0016). The abundance of Bifidobacteriaceae, and Ruminococcaceae by the family level was significantly higher in the ASD patients compared to the control group (p = 0.0004 and p = 0.0489, respectively). Our results indicated less species richness in the ASD patients compared to the control group.

CONCLUSION: Patients with ASD have lower serum levels of vitamin B12 and different gut microbiome compared to healthy controls. Low vitamin B12 levels and altered gut microbiome are significantly associated with ASD in this study. However, further research is needed to determine whether these factors could serve as predictors of severe outcomes in ASD.},
}

Humans
*Autism Spectrum Disorder/microbiology/blood
*Gastrointestinal Microbiome/genetics/physiology
Metagenomics
Male
Feces/microbiology
Female
Folic Acid/blood
Case-Control Studies
Child, Preschool
Child
*Vitamin B 12/blood
RNA, Ribosomal, 16S/genetics
*Cholecalciferol/blood
*Vitamins/blood

@article {pmid39827989,
year = {2025},
author = {Cheng, CK and Ye, L and Wang, Y and Wang, YL and Xia, Y and Wong, SH and Chen, S and Huang, Y},
title = {Exercised gut microbiota improves vascular and metabolic abnormalities in sedentary diabetic mice through gut‒vascular connection.},
journal = {Journal of sport and health science},
volume = {14},
number = {},
pages = {101026},
pmid = {39827989},
issn = {2213-2961},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Physical Conditioning, Animal/physiology ; *Fecal Microbiota Transplantation ; *Diabetes Mellitus, Type 2/therapy/metabolism/physiopathology ; Mice ; Male ; Sedentary Behavior ; Oxidative Stress ; Mice, Inbred C57BL ; Endoplasmic Reticulum Stress ; MicroRNAs/metabolism ; Endothelium, Vascular ; Receptors, Leptin ; },
abstract = {BACKGROUND: Exercise elicits cardiometabolic benefits, reducing the risks of cardiovascular diseases and type 2 diabetes. This study aimed to investigate the vascular and metabolic effects of gut microbiota from exercise-trained donors on sedentary mice with type 2 diabetes and the potential mechanism.

METHODS: Leptin receptor-deficient diabetic (db/db) and nondiabetic (db/m[+]) mice underwent running treadmill exercise for 8 weeks, during which fecal microbiota transplantation (FMT) was parallelly performed from exercise-trained to sedentary diabetic (db/db) mice. Endothelial function, glucose homeostasis, physical performance, and vascular signaling of recipient mice were assessed. Vascular and intestinal stresses, including inflammation, oxidative stress, and endoplasmic reticulum (ER) stress, were investigated. RNA sequencing analysis on mouse aortic and intestinal tissues was performed. Gut microbiota profiles of recipient mice were evaluated by metagenomic sequencing.

RESULTS: Chronic exercise improved vascular and metabolic abnormalities in donor mice. Likewise, FMT from exercised donors retarded body weight gain and slightly improved grip strength and rotarod performance in recipient mice. Exercise-associated FMT enhanced endothelial function in different arteries, suppressed vascular and intestinal stresses, and improved glucose homeostasis in recipient mice, with noted microRNA-181b upregulation in aortas and intestines. Altered gut microbiota profiles and gut-derived factors (e.g., short-chain fatty acids and glucagon-like peptide-1) as well as improved intestinal integrity shall contribute to the cardiometabolic benefits, implying a gut‒vascular connection.

CONCLUSION: This proof-of-concept study indicates that exercised microbiota confers cardiometabolic benefits on sedentary db/db mice, extending the beneficial mechanism of exercise through gut‒vascular communication. The findings open up new therapeutic opportunities for cardiometabolic diseases and shed light on the development of exercise mimetics by targeting the gut microbiota.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Physical Conditioning, Animal/physiology
*Fecal Microbiota Transplantation
*Diabetes Mellitus, Type 2/therapy/metabolism/physiopathology
Mice
Male
Sedentary Behavior
Oxidative Stress
Mice, Inbred C57BL
Endoplasmic Reticulum Stress
MicroRNAs/metabolism
Endothelium, Vascular
Receptors, Leptin

@article {pmid41345123,
year = {2025},
author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM},
title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1913},
pmid = {41345123},
issn = {2052-4463},
support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; },
mesh = {*Metagenome ; Pacific Ocean ; *Transcriptome ; *RNA, Transfer/genetics ; *Seawater/microbiology ; Ecosystem ; Microbiota ; },
abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.},
}

*Metagenome
Pacific Ocean
*Transcriptome
*RNA, Transfer/genetics
*Seawater/microbiology
Ecosystem
Microbiota

@article {pmid41345120,
year = {2025},
author = {Abad-Recio, IL and Rubel, V and Filker, S and Garate, L and Stoeck, T and Logares, R and Lanzén, A},
title = {The Basque Coast Estuarine Sediment Gene Catalogue.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1909},
pmid = {41345120},
issn = {2052-4463},
support = {Fi 2089/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STO 414/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Estuaries ; *Geologic Sediments/microbiology ; Archaea/genetics ; Metagenomics ; Bacteria/genetics ; Biodiversity ; Ecosystem ; Eukaryota/genetics ; Viruses/genetics ; },
abstract = {Estuaries are critical transition zones that link marine, riverine, and terrestrial ecosystems, including habitats like intertidal mudflats and tidal marshes. These ecosystems are biodiversity hotspots providing essential ecological functions such as nutrient cycling and pollutant removal. Despite their importance, there is a significant knowledge gap regarding the ecological functioning of these habitats and how they are impacted by anthropogenic pressures. From intertidal estuarine benthos along the Basque Coast 92 microbial metagenomic assemblies were retrieved that allowed us to reconstruct 390 medium plus 81 high quality MAGs, along with 108 million putative genes from bacteria, archaea, eukaryotes, and viruses. This unique dataset will enhance our understanding of ecosystem functioning, biodiversity, and be useful to reveal biogeochemical processes and the role of unculturable biomass.},
}

*Estuaries
*Geologic Sediments/microbiology
Archaea/genetics
Metagenomics
Bacteria/genetics
Biodiversity
Ecosystem
Eukaryota/genetics
Viruses/genetics

@article {pmid41345102,
year = {2025},
author = {Pope, R and Visconti, A and Zhang, X and Louca, P and Baleanu, AF and Lin, Y and Asnicar, F and Bermingham, K and Wong, KE and Michelotti, GA and Wolf, J and Segata, N and Berry, SE and Spector, TD and Leeming, ER and Gibson, R and Menni, C and Falchi, M},
title = {Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10051},
pmid = {41345102},
issn = {2041-1723},
support = {27/2023//Chronic Disease Research Foundation (CDRF)/ ; },
mesh = {Humans ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet ; Male ; Female ; Metabolome ; Middle Aged ; Metabolomics/methods ; Aged ; Metagenomics ; Adult ; Machine Learning ; },
abstract = {The interplay between diet and gut microbiome composition is complex. Faecal metabolites, the end products of human and microbial metabolism, provide insights into these interactions. Here, we integrate faecal metabolomics, metagenomics, and habitual dietary data from 1810 individuals from the TwinsUK and 837 from the ZOE PREDICT1 cohorts. Using machine learning models, we find that faecal metabolites accurately predict reported intakes of 20 food groups (area under the curve (AUC) > 0.80 for meat, nuts and seeds, wholegrains, tea and coffee, and alcohol) and adherence to seven dietary patterns (AUC from 0.71 for the Plant-based Diet Index to 0.83 for the Dietary Approaches to Stop Hypertension score). Notably, the faecal metabolome is a stronger predictor of atherosclerotic cardiovascular disease risk (AUC = 0.86) than the Dietary Approaches to Stop Hypertension score (AUC = 0.66). We identify 414 associations between 19 food groups and 211 metabolites, that significantly correlate with microbial α-diversity and 217 species. Our findings reveal that faecal metabolites capture mediations between diet and the gut microbiome, advancing our understanding of diet-related disease risk and informing metabolite-based interventions.},
}

Humans
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome/physiology
*Diet
Male
Female
Metabolome
Middle Aged
Metabolomics/methods
Aged
Metagenomics
Adult
Machine Learning

@article {pmid41344778,
year = {2026},
author = {Li, Z and Zhao, C and Mao, Z and Zhao, L and Penttinen, P and Zhang, S},
title = {Metagenomics insights into bacterial community, viral diversity and community-scale functions in fermented red pepper.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104986},
doi = {10.1016/j.fm.2025.104986},
pmid = {41344778},
issn = {1095-9998},
mesh = {Fermentation ; *Capsicum/microbiology/virology ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism/virology ; *Fermented Foods/microbiology/virology ; Gene Transfer, Horizontal ; *Viruses/genetics/classification/isolation & purification ; Bacteriophages/genetics/classification/isolation & purification ; *Microbiota ; Food Microbiology ; },
abstract = {Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by Bacillus (21.52 %), Lactobacillus sensu lato (14.27 %), and Pantoea (13.60 %). Bacillus drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.},
}

Fermentation
*Capsicum/microbiology/virology
Metagenomics
*Bacteria/genetics/classification/isolation & purification/metabolism/virology
*Fermented Foods/microbiology/virology
Gene Transfer, Horizontal
*Viruses/genetics/classification/isolation & purification
Bacteriophages/genetics/classification/isolation & purification
*Microbiota
Food Microbiology

@article {pmid41340567,
year = {2025},
author = {Ouradova, A and Ferrero, G and Bratova, M and Daskova, N and Bohdanecka, A and Dohnalova, K and Heczkova, M and Chalupsky, K and Kralova, M and Kuzma, M and Modos, I and Tichanek, F and Najmanova, L and Pardini, B and Pelantová, H and Tarallo, S and Videnska, P and Gojda, J and Naccarati, A and Cahova, M},
title = {A vegan diet signature from a multi-omics study on different European populations is related to favorable metabolic outcomes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593050},
doi = {10.1080/19490976.2025.2593050},
pmid = {41340567},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Vegan ; Male ; Female ; Adult ; Czech Republic ; Cross-Sectional Studies ; *Metabolome ; Middle Aged ; Italy ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Vegans ; Metagenome ; Multiomics ; },
abstract = {Vegan and omnivorous diets differ markedly in composition, but their effects on the gut microbiome, metabolome, and lipidome across populations remain insufficiently characterized. While both diet and country of origin influence these molecular layers, the relative contribution of diet versus country-specific factors has not yet been systematically evaluated within a multi-omics framework.In this cross-sectional, bicentric, observational study, we profiled healthy vegans (n = 100) and omnivores (n = 73) from the Czech Republic and Italy using integrated microbiome, metabolome, and lipidome analyses. Findings were subsequently validated in an independent cohort (n = 142).Significant differences across all omics layers were observed for both country and diet. The predictive models confirmed diet-associated separation, with validation cohort AUCs of 0.99 (lipidome), 0.89 (metabolome), and 0.87 (microbiome). Functional metagenome analysis revealed enrichment of amino acid biosynthesis, inositol degradation, and the pentose phosphate pathway in vegans, while omnivores presented greater potential for amino acid fermentation, fatty acid biosynthesis, and propanoate metabolism. Linear models identified a robust, country-independent "vegan signature" consisting of 27 lipid metabolites, five non-lipid metabolites, and 11 bacterial species. Several lipid features associated with an omnivorous diet were inversely related to the duration of vegan diet adherence. Some of the vegan-associated metabolites and bacteria have been previously linked to favorable cardiometabolic profiles, although causality remains to be established.These findings demonstrate that vegan diets are associated with reproducible, country-independent molecular and microbial signatures. Our results highlight diet-driven shifts in host-microbiota interactions and provide a framework for understanding how dietary patterns relate to host-microbiota interactions.},
}

Humans
*Gastrointestinal Microbiome
*Diet, Vegan
Male
Female
Adult
Czech Republic
Cross-Sectional Studies
*Metabolome
Middle Aged
Italy
*Bacteria/classification/metabolism/genetics/isolation & purification
Vegans
Metagenome
Multiomics

@article {pmid41340070,
year = {2025},
author = {Jeilu, O and Sumner, JT and Moghadam, AA and Thompson, KN and Huttenhower, C and Catlett, C and Hartmann, EM},
title = {Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {249},
pmid = {41340070},
issn = {2049-2618},
mesh = {*Air Microbiology ; *Metagenomics/methods ; Humans ; *Bacteria/genetics/classification/isolation & purification ; *Aircraft ; *Masks/microbiology ; *Microbiota/genetics ; *Air Filters/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Airborne microbial communities, although often challenging to study due to low biomass, play crucial roles in public health and pathogen transmission. Through shotgun metagenomics, this study utilizes non-invasive air sampling of face masks and aircraft cabin filters to investigate microbial diversity in environments with frequent human interactions, including hospitals and airplanes. A comprehensive sampling and analysis workflow was developed, incorporating environmental and enrichment protocols to enhance microbial DNA recovery and diversity profiling.

RESULTS: Despite limitations in biomass, optimized extraction methods allowed for the successful identification of 407 species, with dominant taxa including Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans. Enrichment processing resulted in greater metagenome-assembled genome (MAG) recovery and higher antimicrobial resistance gene (ARG) identification.

CONCLUSIONS: The findings highlight the presence of ARGs in high-occupancy public spaces, suggesting the importance of monitoring and the potential for mitigating airborne transmission risks in such environments. This study demonstrates the utility of combining environmental and enrichment sampling to capture comprehensive microbial and ARG profiles in confined spaces, providing a framework for enhanced pathogen monitoring in public health contexts. Video Abstract.},
}

*Air Microbiology
*Metagenomics/methods
Humans
*Bacteria/genetics/classification/isolation & purification
*Aircraft
*Masks/microbiology
*Microbiota/genetics
*Air Filters/microbiology
Metagenome

@article {pmid41093108,
year = {2025},
author = {Chandel, N and Patel, P and Somvanshi, PR and Verma, AK and Thakur, V},
title = {Inverse Association between Serum Vitamin B12 Level and Abundance of Potential B12-Producing Gut Microbes in Indian Children.},
journal = {The Journal of nutrition},
volume = {155},
number = {12},
pages = {4284-4295},
doi = {10.1016/j.tjnut.2025.10.021},
pmid = {41093108},
issn = {1541-6100},
mesh = {Humans ; *Vitamin B 12/blood/biosynthesis ; *Gastrointestinal Microbiome ; India ; *Vitamin B 12 Deficiency/blood/microbiology/epidemiology ; Male ; Female ; Feces/microbiology ; Child ; Child, Preschool ; Bacteria/classification/metabolism/genetics ; },
abstract = {BACKGROUND: The human gut microbiome is a natural source of essential micronutrients like B vitamins, which are used by both the host and other community members. The prevalence and abundance of known B-vitamin producers and B-vitamin biosynthesis pathways have already been reported in gut microbiome cohorts of a few countries including India.

OBJECTIVES: This study tested whether the presence of B-vitamin producers/biosynthetic pathways associates with serum B-vitamin levels, taking vitamin B12 as a case example.

METHODS: Fecal samples were collected from non-deficient (serum vitamin B12 level > 210 pg/mL; n = 29) and vitamin B12 deficient (serum vitamin B12 level < 210 pg/mL; n = 30) children from a tribal region of central India. Whole metagenomic DNA was extracted, sequenced, and analyzed for taxonomic profiling and diversity comparisons. Differentially abundant taxa between two groups were identified. The prevalence and abundance of potential vitamin B12 producers were compared, and their association with serum vitamin B12 level was established.

RESULTS: A comparison of within-sample diversity between the two groups did not show any difference; however, between-sample diversity was significantly less in the vitamin B12-deficient group. Differential abundance testing also showed different microbiome structure in the vitamin B12-deficient group, where a higher abundance of vitamin B12 transporter-carrying Bacteroides thetaiotaomicron, a few pathogenic species, and ten known vitamin B12 producers was observed. Potential vitamin B12 producers were also significantly prevalent and abundant in the deficient group. Their cumulative abundance was also significantly higher in the deficient group and showed a negative association with serum vitamin B12 levels.

CONCLUSIONS: A higher abundance of potential vitamin B12 producers in the deficient group suggest an adaptive mechanism by the gut microbiome to meet the community's vitamin B12 requirements, by selectively promoting the growth of vitamin B12 producers, but causality remains to be proved.},
}

Humans
*Vitamin B 12/blood/biosynthesis
*Gastrointestinal Microbiome
India
*Vitamin B 12 Deficiency/blood/microbiology/epidemiology
Male
Female
Feces/microbiology
Child
Child, Preschool
Bacteria/classification/metabolism/genetics

@article {pmid41025564,
year = {2025},
author = {Zeng, S and Wang, H and Zhang, L and Li, S and Yuan, Y and Tian, M and Qu, Y and Ying, J and Zhou, M and Hu, Y and Huang, J and Zou, R and Zhao, F and Su, X and Liu, Q and He, Y and Feng, J and Huang, W and Luo, Y and Zhou, Z and Shen, W and Mu, D and Wang, S},
title = {The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {45},
pages = {e05154},
doi = {10.1002/advs.202505154},
pmid = {41025564},
issn = {2198-3844},
support = {2021YFC2701704//National Key Research and Development Program/ ; 2021YFC2701700//National Key Research and Development Program/ ; 82402025//National Natural Science Foundation of China/ ; 82241036//National Natural Science Foundation of China/ ; 82271749//National Natural Science Foundation of China/ ; 82371717//National Natural Science Foundation of China/ ; 82201905//National Natural Science Foundation of China/ ; 82571980//National Natural Science Foundation of China/ ; 82530056//National Natural Science Foundation of China/ ; 2025ZNSFSC1677//Department of Science and Technology of Sichuan Province/ ; SCU2023D006//Fundamental Research Funds for the Central University/ ; SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; },
mesh = {Humans ; *Enterocolitis, Necrotizing/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature ; Infant, Newborn ; Female ; Male ; Metagenome/genetics ; Machine Learning ; },
abstract = {The accelerating threat from antimicrobial resistance (AMR) has become a global health issue. The properties of AMR in the gut microbiome of preterm infants and its clinical relevance with necrotizing enterocolitis (NEC) remain unknown. In-depth integrative analyses of 5,684 gut metagenomes are performed to build an AMR genes (ARGs) landscape. A subset of 107 preterm infants who developed NEC is sampled to examine the trajectory and predictive potential of ARGs preceding NEC onset. The variation and core set of ARGs, their higher burden and diversity, and potential ARGs-enriched gut bacteria in preterm infants compared to full-term infants are comprehensively discovered, reflecting a strain shift in genomic functions. Moreover, the gut resistome converged over 9 days before NEC onset is observed, which is driven by 24 ARGs. Machine learning analysis reveals potential usage of the gut resistome as an indicator for predicting NEC onset in an external validation preterm birth cohort (the area under the receiver operating characteristic curve, AU-ROC = 0.823), which is significantly higher than that based on the bacterial species (AU-ROC = 0.727). Overall, the findings can be referenced to mitigate the burden and spread of ARGs, and specific ARGs have potential for disease risk stratification to improve clinical management.},
}

Humans
*Enterocolitis, Necrotizing/microbiology/diagnosis
*Gastrointestinal Microbiome/genetics
*Infant, Premature
Infant, Newborn
Female
Male
Metagenome/genetics
Machine Learning

@article {pmid41015376,
year = {2025},
author = {Zhao, JX and Wang, XY and Zhang, X and Tang, LY and Xie, SC and Lv, YH and Zheng, Z and Gao, YQ and Jiang, J and Zhang, XX and Ma, H},
title = {Toxoplasma gondii alters gut microbiota and systemic metabolism in cats: A multi-omics approach.},
journal = {Veterinary journal (London, England : 1997)},
volume = {314},
number = {},
pages = {106455},
doi = {10.1016/j.tvjl.2025.106455},
pmid = {41015376},
issn = {1532-2971},
mesh = {Animals ; Cats ; *Toxoplasmosis, Animal/metabolism/parasitology/microbiology ; *Gastrointestinal Microbiome ; *Toxoplasma/physiology ; *Cat Diseases/parasitology/metabolism/microbiology ; Female ; Metabolomics ; Male ; Feces/microbiology ; Host-Parasite Interactions ; Multiomics ; },
abstract = {Toxoplasma gondii (T. gondii) is an obligate intracellular parasite with a complex life cycle that culminates in cats-its only definitive host. While its immunological impact is well studied, how T. gondii shapes the feline gut microbiota and systemic metabolism remains largely unexplored. To investigate host-parasite-microbiome interactions, we performed a multi-omics study combining metagenomic sequencing and untargeted serum metabolomics in cats before and after T. gondii infection. Fecal samples were used to construct a comprehensive microbial gene catalog and assess functional shifts, while serum samples were analyzed via liquid chromatography-tandem mass spectrometry (LC-MS/MS) to capture systemic metabolic changes. Infection with T. gondii, particularly during its sexual replication phase, significantly disrupted gut microbial diversity, composition, and function. Functional annotation revealed downregulation of microbial genes involved in vitamin, cofactor, and energy metabolism, alongside upregulation of carbohydrate metabolism pathways. Concurrently, metabolomic profiling showed marked alterations in lipid profiles, amino acid pathways, and folate-mediated one-carbon metabolism. Integrated analysis uncovered strong correlations between specific microbial taxa-such as Bifidobacterium adolescentis and Ligilactobacillus animalis-and host metabolites, underscoring a tight link between microbial function and host metabolic responses to infection. To our knowledge, this is the first study to comprehensively map the microbiome and metabolic landscape of T. gondii infection in the feline host. Our findings reveal profound parasite-induced shifts in microbial function and systemic metabolism, offering new insights into the molecular interplay between host, parasite, and microbiota. These insights may inform future strategies for therapeutic modulation of host responses in toxoplasmosis.},
}

Animals
Cats
*Toxoplasmosis, Animal/metabolism/parasitology/microbiology
*Gastrointestinal Microbiome
*Toxoplasma/physiology
*Cat Diseases/parasitology/metabolism/microbiology
Female
Metabolomics
Male
Feces/microbiology
Host-Parasite Interactions
Multiomics

@article {pmid41000006,
year = {2026},
author = {Hodgson, RJ and Cando-Dumancela, C and Davies, T and Dinsdale, EA and Doane, MP and Edwards, RA and Liddicoat, C and Peddle, SD and Ramesh, SA and Robinson, JM and Breed, MF},
title = {Contrasting Microbial Taxonomic and Functional Colonisation Patterns in Wild Populations of the Pan-Palaeotropical C4 Grass, Themeda triandra.},
journal = {Plant, cell & environment},
volume = {49},
number = {1},
pages = {209-225},
doi = {10.1111/pce.70205},
pmid = {41000006},
issn = {1365-3040},
support = {//This metagenomics sequencing for this project was supported by the Flinders University Accelerator for Microbiome Exploration. We also received funding from the Holsworth Wildlife Research Endowment with the Ecological Society of Australia, the Conservation Biology Grant 2022 with the Biological Society of South Australia and Nature Conservation Society of South Australia and the Lirabenda Wildlife Research Fund from the Field Naturalists Society of South Australia. We also received support from the Australian Research Council (grant numbers LP190100051 and LP190100484) and the New Zealand Ministry of Business Innovation and Employment (grant UOWX2101)./ ; },
mesh = {*Soil Microbiology ; *Poaceae/microbiology ; Rhizosphere ; *Microbiota ; Plant Roots/microbiology ; Metagenomics ; Biodiversity ; },
abstract = {The interactions between native plants and soil microbiota are not well characterised, despite growing recognition of their importance for host plant fitness and ecological functioning. We used shotgun metagenomics to examine microbial taxonomic and functional colonisation patterns in wild populations of the pan-palaeotropical C4 grass, Themeda triandra, across a globally representative aridity gradient (aridity index 0.318-0.903). We investigated these patterns through the two-step selection process whereby microbes are recruited from bulk soils into rhizospheres (soil on the root surface), and root interiors (endospheres). We provide clear evidence of this process through decreasing microbial taxonomic diversity from bulk soil to T. triandra roots. Surprisingly, microbial functional potential showed the opposite trend: the diversity of potential functions (exponent of Shannon's diversity) increased from bulk soil to the rhizosphere and endosphere, but functional richness did not. Finally, we found that increasing aridity was associated with rhizospheres that were more compositionally similar, yet remained highly diverse in functional potential. Overall, aridity is strongly associated with the root-associated microbiome of T. triandra, selecting for microbiota that likely support plant resilience under dry conditions. Furthermore, microbial functional potential closely tracks taxonomic composition and aridity trends, highlighting how native plants can shape their microbial communities.},
}

*Soil Microbiology
*Poaceae/microbiology
Rhizosphere
*Microbiota
Plant Roots/microbiology
Metagenomics
Biodiversity

@article {pmid40974529,
year = {2025},
author = {Tian, C and Tang, Z and Zhang, X and Yao, X and Li, Y and Zhuang, D and Luo, Y and Li, T and Bai, L and Zhao, F and Zhu, L and Shi, G and Jiang, P and Gong, Q and Zhou, H and Gao, H and Wu, Q and Sang, J and Liu, X and Li, X and Yu, L and Zhang, Z},
title = {Uncovering the gut microbiome and antibiotic resistome of mammals on the Tibetan Plateau.},
journal = {Science China. Life sciences},
volume = {68},
number = {12},
pages = {3646-3663},
pmid = {40974529},
issn = {1869-1889},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; Tibet ; *Mammals/microbiology ; Humans ; Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics/classification/drug effects ; },
abstract = {The mammalian species on the Tibetan Plateau are diverse and abundant, yet our understanding of their gut microbiome and antibiotic resistome remains limited. Here, we used metagenomics to analyse the gut microbiota of 2,561 mammals from the Tibetan Plateau, covering 14 species across six orders. Using de novo metagenome assembly, we reconstructed a total of 112,313 high- to medium-quality metagenomic assembly genomes (MAGs), representing 21,902 microbial species, 86% of which were unclassified. More than 8,000 nonredundant antibiotic resistance genes (ARGs) encompassing 28 types were identified in the gut microbiome of Tibetan Plateau mammals. We further conducted a risk assessment of these ARGs, identifying 334 nonredundant ARGs with high-risk characteristics related to human health. Importantly, seven cross-species horizontal gene transfer events involving high-risk ARGs were identified, three of which occurred between human and nonhuman mammalian gut microbiota. Additionally, we found that the abundance of ARGs in human gut microbiomes on the Tibetan Plateau was greater than that in those from eastern China, Europe, and the United States, whereas the abundance of ARGs in livestock gut microbiomes from the Tibetan Plateau was lower than that in livestock gut microbiomes from those regions. This study reveals that the gut microbiota of Tibetan Plateau mammals is a largely unexplored resource and a significant reservoir of ARGs, offering crucial insights into microbiome research and demonstrating potential public health implications.},
}

*Gastrointestinal Microbiome/genetics
Animals
Tibet
*Mammals/microbiology
Humans
Metagenomics/methods
Anti-Bacterial Agents/pharmacology
Metagenome/genetics
*Drug Resistance, Microbial/genetics
Gene Transfer, Horizontal
Bacteria/genetics/classification/drug effects

@article {pmid40966389,
year = {2025},
author = {Yan, Y and Zhou, X and Liu, L and Cai, Z and Penuelas, J and Huang, X},
title = {Soil Nutrient Enrichment Induces Trade-Offs in Bacterial Life-History Strategies Promoting Plant Productivity.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {45},
pages = {e10066},
doi = {10.1002/advs.202510066},
pmid = {40966389},
issn = {2198-3844},
support = {U21A20226//National Natural Science Foundation of China/ ; 42430701//National Natural Science Foundation of China/ ; KYCX24_1825//Graduate Research and Innovation Projects of Jiangsu Province/ ; CX(23)1038//Jiangsu Provincial Agricultural Science and Technology Independent Innovation Fund/ ; 2023YFD1902000//Key Technologies Research and Development Program/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; *Nutrients ; *Plant Development/physiology ; Microbiota ; },
abstract = {Despite the global prevalence of anthropogenic soil nutrient enrichment, its impacts on the trade-offs in microbial life-history strategies remain poorly understood, which is critical for agroecosystem productivity. Here, large-scale observational studies are integrated with controlled experiments to systematically evaluate how soil nutrient enrichment affects bacterial functional potential and growth-rate potential, ultimately determining microbial functions and plant productivity. These findings reveal stark contrasts between nutrient-poor open field (OF) and nutrient-rich greenhouse (GH) soils across multiple paired sites using 16S rRNA gene amplicon and metagenomic sequencing. OF microbial communities dominated by oligotrophs have higher taxonomic diversity, larger average genome sizes with abundant nutrient-cycling genes, but lower 16S ribosomal RNA gene operon copy numbers and predicted maximum growth rates. Conversely, GH communities dominated by copiotrophs have higher growth-rate potential, more plant-beneficial bacteria, and higher diversity of functional genes (e.g., biofilm formation, secondary metabolism, and bacterial chemotaxis), but lower bacterial functional potential. Controlled pot experiments demonstrate that GH-enriched microbial functions strongly promote plant growth, particularly under sufficient nutrients and abiotic stress. These findings reveal a nutrient-driven trade-off between bacterial functional potential and growth rate, with implications for optimizing nutrient management strategies in precision agriculture to enhance specific microbial functions and plant productivity.},
}

*Soil Microbiology
*Soil/chemistry
*Bacteria/genetics
RNA, Ribosomal, 16S/genetics
*Nutrients
*Plant Development/physiology
Microbiota

@article {pmid40848091,
year = {2025},
author = {Dong, Y and Fan, S and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Li, Y and Wang, W},
title = {RNA-viromics unveils diverse RNA viral communities in Large-billed crows and Northern Ravens.},
journal = {Virus genes},
volume = {61},
number = {6},
pages = {657-667},
pmid = {40848091},
issn = {1572-994X},
support = {grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; grant No. 2022-HZ-812//program of science and technology international cooperation project of Qinghai province/ ; },
mesh = {Animals ; *Crows/virology ; *RNA Viruses/genetics/classification/isolation & purification ; *Virome/genetics ; Metagenomics ; Feces/virology ; RNA, Viral/genetics ; Phylogeny ; },
abstract = {Birds have historically served as key vectors for viruses causing significant diseases. Corvid birds, often living in close proximity to livestock, poultry, and humans, provide substantial opportunities for cross-species viral transmission. Such transmission can occur through their feces or via ectoparasites (such as ticks, mites, and fleas) on their bodies, thereby releasing viruses into the environment. Despite the development of viral metagenomics, an increasing number of RNA viruses are being characterized across different species. RNA viruses in birds' gut microbial communities remain poorly studied. Here we report an extensive analysis of an RNA virome in fecal samples from Large-billed crows (Corvus macrorhynchos) and Northern Ravens (Corvus corax), both of which are common Corvus species found in the high-altitude forest and grassland regions of the Qinghai-Tibetan Plateau. This study aims to assess the RNA viruses present in the intestines of these corvids and provides the first comprehensive characterization of the diversity of gut-colonizing viruses in these two crow species.},
}

Animals
*Crows/virology
*RNA Viruses/genetics/classification/isolation & purification
*Virome/genetics
Metagenomics
Feces/virology
RNA, Viral/genetics
Phylogeny

@article {pmid40707808,
year = {2025},
author = {Liu, Y and Shen, J and Zhang, X and Ping, F and Qyu, K and Shen, X},
title = {Xiaoyao Pill Regulates Gut Microbiota and Tryptophan Metabolism to Alleviate Depression Induced by Chronic Stress in Rats.},
journal = {Chinese journal of integrative medicine},
volume = {31},
number = {12},
pages = {1087-1096},
pmid = {40707808},
issn = {1993-0402},
mesh = {Animals ; *Tryptophan/metabolism ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Depression/drug therapy/microbiology/etiology/metabolism/blood ; Male ; *Stress, Psychological/complications/drug therapy ; Behavior, Animal/drug effects ; Rats ; Chronic Disease ; Hippocampus/pathology/drug effects ; },
abstract = {OBJECTIVE: To investigate the antidepressant effects of Xiaoyao Pill (XYP) by exploring its interactions with gut microbiota and tryptophan metabolism.

METHODS: Utilizing network pharmacology, the functional substance groups, key targets, and pathways of XYP in the treatment of depression were identified. The chronic unpredictable mild stress (CUMS) protocol was implemented in male Sprague-Dawley rats to establish depression model. Thirty rats were randomly divided into 3 groups according to their body weight (10 for each): control, CUMS and XYP groups (1.8 g/kg). After 28-day interventions, behavioral phenotyping including sucrose preference test (SPT) and open field test (OFT) were performed. Biochemical validation encompassed enzyme-linked immunosorbent assay for serum cortisol, hematoxylin-eosin histopathology, and immunohistochemistry. Liquid chromatography-mass spectrometry was utilized to profile serum metabolites, while fecal samples underwent metagenomic sequencing for gut microbiota characterization.

RESULTS: Network pharmacology studies predicted that key components can protect the nervous system by regulating inflammatory pathways through the blood-brain barrier. SPT and OFT showed that XYP treatment significantly ameliorated depressive-like behaviors (all P<0.05). XYP treatment also restored hippocampal neuronal density, increased serum neurotransmitter levels of neurotransmitters such as 5-hydroxytryptamine and vasoactive intestinal peptide, and while suppressing inflammatory markers such as tumor necrosis factor-alpha, interleukin-1 beta (IL-1 β), and IL-6 (all P<0.05). Metagenomics revealed significant restructuring of gut microbiota, notably the regulation of Parabacteroides distasonis (P<0.05). Non-targeted metabolomics analysis showed that the level of metabolites in the tryptophan and kynurenine pathway significantly changed (variable importance in the projection >1, P<0.05), and the change of metabolic flux was significantly correlated with behavioral improvement (P<0.05).

CONCLUSIONS: XYP exerts antidepressant effects by increasing neurotransmitter levels, reducing inflammatory makers and modulating Parabacteroides distasonis. Through further exploration of metabolomics, we found that XYP may play a protective role in depression by regulating tryptophan metabolism.},
}

Animals
*Tryptophan/metabolism
*Drugs, Chinese Herbal/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Depression/drug therapy/microbiology/etiology/metabolism/blood
Male
*Stress, Psychological/complications/drug therapy
Behavior, Animal/drug effects
Rats
Chronic Disease
Hippocampus/pathology/drug effects

@article {pmid41339392,
year = {2025},
author = {Muratore, E and Conti, G and Fabbrini, M and Zama, D and Decembrino, N and Muggeo, P and Mura, R and Perruccio, K and Leardini, D and Barone, M and Zecca, M and Cesaro, S and Brigidi, P and Turroni, S and Masetti, R},
title = {Distinct functional and compositional properties in the gut microbiome of children with acute lymphoblastic leukaemia identified by shotgun metagenomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43082},
pmid = {41339392},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Child ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology ; Male ; Female ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Adolescent ; Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {Acute lymphoblastic leukaemia (ALL) represents the most common childhood malignancy, and emerging evidence underscores the impact of the gut microbiome (GM) on its pathogenesis. In this study, we used shotgun metagenomics to investigate the GM of 30 ALL patients at diagnosis-19 with B-ALL and 11 with T-ALL-and compared them to 176 healthy controls (HCs). When considered as a single ALL group versus HCs, clear compositional differences emerged: ALL patients exhibited higher relative abundances of Enterococcus faecium, oral commensals such as Rothia dentocariosa, and multiple opportunistic species, whereas HCs were enriched in short-chain fatty acid producers like Anaerostipes hadrus and Intestinibacter bartlettii. Functionally, the ALL GM relied more on protein and amino acid catabolism, while HCs possessed enhanced pathways for carbohydrate and folate metabolism. These findings broadly align with 16S rRNA-based analyses from previous publications, though some discrepancies highlight differences in technique-driven resolution. In contrast, comparing the two major molecular phenotypes-B-ALL and T-ALL-revealed only minimal taxonomic and functional differences, primarily confined to BAs metabolism pathways. Overall, our results indicate that children with ALL at the time of diagnosis already display a dysbiotic signature, bolstering the notion that a disturbance in GM development during childhood may be linked to the multistep pathogenesis model of ALL.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Child
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology
Male
Female
Child, Preschool
RNA, Ribosomal, 16S/genetics
Adolescent
Bacteria/genetics/classification
Case-Control Studies

@article {pmid41339319,
year = {2025},
author = {Harrison, LC and Allnutt, TR and Hanieh, S and Roth-Schulze, AJ and Ngui, KM and Stone, NL and Bandala-Sanchez, E and Backshell, L and Gurruwiwi, G and Gondarra, V and Couper, JJ and Craig, ME and Davis, EA and Huynh, T and Soldatos, G and Wentworth, JM and Vuillermin, P and Penno, MAS and Biggs, BA and , },
title = {Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9904},
pmid = {41339319},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Australia ; Female ; Male ; Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Infant, Newborn ; Indigenous Peoples ; Metagenome ; },
abstract = {Studies of traditional Indigenous compared to 'Western' gut microbiomes are underrepresented, and lacking in young children, limiting knowledge of early-life microbiomes in different cultural contexts. Here we analyze the gut metagenomes of 50 Indigenous Australian infants (median age }

Humans
*Gastrointestinal Microbiome/genetics
Infant
Australia
Female
Male
Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Infant, Newborn
Indigenous Peoples
Metagenome

@article {pmid41339710,
year = {2025},
author = {Pacheco-Valenciana, A and Tausch, A and Veseli, I and Dharamshi, JE and Bergland, F and Delgado, LF and Rodríguez-Gijón, A and Andersson, AF and Garcia, SL},
title = {Microbial model communities exhibit widespread metabolic interdependencies.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09306-y},
pmid = {41339710},
issn = {2399-3642},
support = {grant 2022-03077//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-03077//Vetenskapsrådet (Swedish Research Council)/ ; grant 2018-05973//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-06725//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-03077//Science for Life Laboratory (SciLifeLab)/ ; },
abstract = {Microorganisms thrive in complex communities shaped by intricate interactions, yet the extent and ecological implications of biosynthetic dependencies in natural communities remain underexplored. Here, we used a dilution approach to cultivate 204 microbial model communities from the Baltic Sea and recovered 527 metagenome-assembled genomes (MAGs) that dereplicated into 72 species-clusters (>95% average nucleotide identity, ANI). Of these species, at least 70% represent previously uncultivated lineages. Combined with 1073 MAGs from Baltic Sea metagenomes, we generated a genomic catalog of 701 species-clusters. Our results show that cultures with more than three species included microorganisms with smaller genome sizes, lower biosynthetic potential for amino acids and B vitamins, and higher prevalence and abundance in the environment. Moreover, the taxa found together in the same model communities had complementary biosynthetic gene repertoires. Our results demonstrate that cultivating bacteria in dilution model communities facilitates access to previously uncultivated but abundant species that likely depend on metabolic partners for survival. Together, our findings highlight the value of community-based cultivation for unraveling ecological strategies. Finally, we confirm that metabolic interdependencies and genome streamlining are widespread features of successful environmental microorganisms.},
}

@article {pmid41335477,
year = {2025},
author = {Riskumäki, M and Ruuskanen, MO and Mäenpää, K and Ruokolainen, L and Mäkelä, MJ and Jousilahti, P and Vartiainen, E and Ottman, N and Laatikainen, T and Haahtela, T and Alenius, H and Fyhrquist, N and Sinkko, H},
title = {Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001527},
pmid = {41335477},
issn = {2057-5858},
mesh = {Humans ; *Metagenomics/methods ; *Allergens/immunology ; *Skin/microbiology/virology ; Finland ; Adolescent ; *Microbiota/genetics ; Male ; Russia ; Female ; *Hypersensitivity/microbiology/immunology ; Malassezia/genetics/isolation & purification ; Immunoglobulin E/immunology ; Bacteria/genetics/classification ; Child ; },
abstract = {The Karelian region, which spans the border between Finland and Russia, presents distinct environmental exposures and lifestyles on either side of the governmental border. In the more urbanized Finnish Karelia, allergic diseases are markedly more prevalent than in the more rural Russian Karelia. Prior studies, based on amplicon sequencing, have demonstrated major differences in skin microbiotas between the two populations. However, compositional differences in microbiota between sensitized and non-sensitized (NS) individuals have not been characterized. Here, in a selected population of 112 allergen-sensitized and NS adolescents, we used shotgun metagenomics to characterize the prokaryotic, eukaryotic and viral species in the skin potentially involved in allergic sensitization via distinct environmental exposures. In the more urban Finnish Karelia, the microbiome species composition was associated with IgE-mediated allergen sensitization status, while in the more rural Russian Karelia, the composition was associated with exposure to furry pets. Finnish participants showing high IgE-mediated sensitization to common allergens (allergen-specific IgE >7.5 kU/L) had less Cutibacterium acnes and Malassezia in their skin and displayed weaker interconnectedness of the microbial co-occurrence network compared with NS participants. Moreover, Malassezia restricta strain-level differences were related to allergen sensitization in both Finnish and Russian participants. In summary, we found distinct skin microbiomes between allergen-sensitized and NS participants and tracked the bacterial and fungal species associated with the degree of allergic sensitization in the more urbanized part of the Karelian region. These findings provide new insights into the factors that shape the human skin microbiome and influence allergic diseases.},
}

Humans
*Metagenomics/methods
*Allergens/immunology
*Skin/microbiology/virology
Finland
Adolescent
*Microbiota/genetics
Male
Russia
Female
*Hypersensitivity/microbiology/immunology
Malassezia/genetics/isolation & purification
Immunoglobulin E/immunology
Bacteria/genetics/classification
Child

@article {pmid41334589,
year = {2025},
author = {Li, J and Xu, Y and Wang, M and Lin, J and Sun, J and Ma, J and Zhang, H},
title = {Dual-source DPP4 drives intestinal fibrosis in Crohn's disease: synergistic therapeutic targeting of host and microbiota pathways.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593119},
doi = {10.1080/19490976.2025.2593119},
pmid = {41334589},
issn = {1949-0984},
mesh = {Animals ; Humans ; *Dipeptidyl Peptidase 4/metabolism/genetics ; *Crohn Disease/pathology/drug therapy/microbiology/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Male ; Myofibroblasts/metabolism ; Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Intestines/pathology ; Sitagliptin Phosphate/pharmacology ; Mice, Inbred C57BL ; Female ; Dextran Sulfate ; },
abstract = {Crohn's disease (CD), a chronic inflammatory bowel disorder, often progresses to intestinal fibrosis and stricture, yet no effective anti-fibrotic treatments exist. This study reveals dipeptidyl peptidase 4 (DPP4) as a pivotal driver of fibrosis through bioinformatics analysis, clinical samples, and experimental models. Elevated DPP4 expression was observed in stenotic intestinal tissues of CD patients and dextran sodium sulfate (DSS)-induced fibrotic mice. Mechanistically, both membrane-bound DPP4 and soluble DPP4 (sDPP4) activated human intestinal myofibroblasts (HIMFs) via the PI3K-AKT pathway, stimulating migration, proliferation, and extracellular matrix deposition. Importantly, metagenomic sequencing revealed enrichment of microbial Dpp4 genes in fecal samples from CD patients with stenosis, and in vivo colonization with engineered E. coli overexpressing microbial DPP4 exacerbated fibrotic remodeling, confirming microbiota-derived DPP4 (mDPP4) as a pathogenic driver. Furthermore, pharmacological inhibition of host DPP4 (sitagliptin) or selective blockade of mDPP4 (Dau-d4) attenuated fibrosis in murine models, with combined therapy showing enhanced efficacy. These findings underscore the roles of DPP4, originating from both host and microbiota, and existing in membrane-bound and soluble forms, in promoting CD-associated intestinal fibrosis. This study identifies DPP4 as a novel therapeutic target, proposing dual-source inhibition as a promising strategy to prevent stricture formation in CD patients, thereby addressing a critical unmet clinical need.},
}

Animals
Humans
*Dipeptidyl Peptidase 4/metabolism/genetics
*Crohn Disease/pathology/drug therapy/microbiology/metabolism
Mice
Fibrosis
*Gastrointestinal Microbiome/drug effects
Disease Models, Animal
Male
Myofibroblasts/metabolism
Dipeptidyl-Peptidase IV Inhibitors/pharmacology
*Intestines/pathology
Sitagliptin Phosphate/pharmacology
Mice, Inbred C57BL
Female
Dextran Sulfate