Microbiome最新文献

{"title":"Combatting glufosinate-induced pepper toxicity: jasmonic acid recruiting rhizosphere bacterial strain Rhodococcus gordoniae.","authors":"Jialing Wang, Ziyi Liu, Xiaoyi Wang, Zhijia Zhang, Tianbing Zhou, Mengmeng Li, Shuai Wang, Zhan Hu, Ranfeng Sun, Dong Li","doi":"10.1186/s40168-025-02155-1","DOIUrl":"10.1186/s40168-025-02155-1","url":null,"abstract":"<p><strong>Background: </strong>Plant-microbe interactions are essential for mitigating abiotic and biotic stressors by shaping the rhizosphere environment. However, how rhizosphere beneficial bacteria and plant metabolites respond to glufosinate (GLU)-induced toxicity remains largely unknown.</p><p><strong>Results: </strong>Our study investigates the impact of GLU on chili plant growth and rhizosphere microbiome, emphasizing GLU-induced alterations in amino acid profiles, secondary metabolites, and microbial community composition, with notable enrichment of the Rhodococcus genus. To uncover the underlying mechanisms of Rhodococcus genus-root exudate interactions under GLU stress, we successfully isolated an efficient Rhodococcus gordoniae strain TR-5 from soil samples contaminated with GLU. This strain, isolated from GLU-contaminated soil, demonstrates potential for bioremediation and achieved over 95% GLU degradation efficiency at 35 °C, pH 6.38, and 1% inoculation rate. Through growth analysis, chemotaxis analysis, and molecular docking, caffeic acid disrupts the bacterial strain's metabolic pathways and impedes TR-5 development. In contrast, jasmonic acid (JA) acts as a chemoattractant, promoting bacterial growth and metabolic activity to degrade GLU residues, thereby effectively degrading GLU residues in the soil.</p><p><strong>Conclusions: </strong>This research indicates that GLU significantly influences the metabolic mechanisms of pepper plants. The optimization of microbial remediation strategies may improve soil remediation efficiency and reduce environmental impacts, highlighting opportunities for integrating microbial remediation into sustainable agricultural practices. Our findings provide insights into the role of JA in attracting and promoting the growth and metabolic activities of the Rhodococcus genus, which could be harnessed to improve soil remediation and plant health under GLU stress. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"158"},"PeriodicalIF":13.8,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224680/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evidence of microbial reductive dehalogenation in deep-sea cold seeps and its implications for biogeochemical cycles.","authors":"Yingchun Han, Zhaochao Deng, Yongyi Peng, Jiaxue Peng, Lei Cao, Yangru Xu, Yi Yang, Hao Zhou, Chen Zhang, Dongdong Zhang, Minxiao Wang, Chunfang Zhang, Chris Greening, Xiyang Dong","doi":"10.1186/s40168-025-02147-1","DOIUrl":"10.1186/s40168-025-02147-1","url":null,"abstract":"<p><strong>Background: </strong>Reductive dehalogenation is crucial for halogen cycling and environmental remediation, yet its ecological role is not completely understood, especially in deep-sea environments. To address this gap, we investigated the diversity and expression of genes encoding reductive dehalogenase catalytic subunits (RdhAs), and ecophysiology of potential organohalide reducers in deep-sea cold seeps, which are environments rich in halogenated compounds.</p><p><strong>Results: </strong>Through genome-resolved metagenomic analysis of 165 global cold seep sediment samples, 4 types of RdhA-like sequences were identified based on their features and phylogenetic relationships: prototypical respiratory, transmembrane respiratory, cytosolic, and a novel clade. Cold seeps were found to harbor a higher abundance of these rdhA-like genes compared to other marine sediments, highlighting their potential as microbial reductive dehalogenation hotspots. These rdhA-like genes are encoded by a wide range of microorganisms across 4 archaeal and 36 bacterial phyla, significantly expanding the known diversity of organohalide reducers. Halogen geochemistry, laboratory incubations, metatranscriptomic data, and metabolomic profiling confirmed the presence of organohalides at concentrations of up to 18 mg/g in these sediments and suggested the potential for microbial reductive dehalogenation. Our findings suggest that organohalide reducers in cold seep sediments may participate in diverse biogeochemical processes, as inferred from the presence of genes related to carbon, hydrogen, nitrogen, sulfur, and trace element cycling. Additionally, RdhA-like proteins from cold seeps have diverse N-terminal structures across different gene groups.</p><p><strong>Conclusions: </strong>These findings collectively suggest that reductive dehalogenation is an important process in deep-sea environments, mediated by a diverse array of microbes and novel enzymes. The discovery of diverse and abundant rdhA-like genes, along with their genomic context and potential metabolic linkages, highlights the role of cold seeps as reservoirs of microbial diversity with possible implications for environmental remediation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"156"},"PeriodicalIF":13.8,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12219181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota.","authors":"Mara D Maeke, Xiuran Yin, Lea C Wunder, Chiara Vanni, Tim Richter-Heitmann, Samuel Miravet-Verde, Hans-Joachim Ruscheweyh, Shinichi Sunagawa, Jenny Fabian, Judith Piontek, Michael W Friedrich, Christiane Hassenrück","doi":"10.1186/s40168-025-02140-8","DOIUrl":"10.1186/s40168-025-02140-8","url":null,"abstract":"<p><strong>Background: </strong>Rare species, especially of the marine sedimentary biosphere, have long been overlooked owing to the complexity of sediment microbial communities, their sporadic temporal and patchy spatial abundance, and challenges in cultivating environmental microorganisms. In this study, we combined enrichments, targeted metagenomic sequencing, and extensive data mining to uncover uncultivated members of the archaeal rare biosphere in marine sediments.</p><p><strong>Results: </strong>In protein-amended enrichments, we detected the ecologically and metabolically uncharacterized class Candidatus Penumbrarchaeia within the phylum Thermoplasmatota. By screening more than 8000 metagenomic runs and 11,479 published genome assemblies, we expanded the phylogeny of Ca. Penumbrarchaeia by 3 novel orders. All six identified families of this class show low abundance in environmental samples characteristic of rare biosphere members. Members of the class Ca. Penumbrarchaeia were predicted to be involved in organic matter degradation in anoxic, carbon-rich habitats. All Ca. Penumbrarchaeia families contain high numbers of taxon-specific orthologous genes, highlighting their environmental adaptations and habitat specificity. Besides, members of this group exhibit the highest proportion of unknown genes within the entire phylum Thermoplasmatota, suggesting a high degree of functional novelty in this class.</p><p><strong>Conclusions: </strong>In this study, we emphasize the necessity of targeted, data-integrative approaches to deepen our understanding of the rare biosphere and uncover the functions and metabolic potential hidden within these understudied taxa. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"155"},"PeriodicalIF":13.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes.","authors":"Paul-Adrian Bulzu, Helena Henriques Vieira, Rohit Ghai","doi":"10.1186/s40168-025-02148-0","DOIUrl":"10.1186/s40168-025-02148-0","url":null,"abstract":"<p><strong>Background: </strong>Polinton-like viruses (PLVs) are diverse eukaryotic DNA viral elements (14-40 kb) that often undergo significant expansion within protist genomes through repeated insertion events. Emerging evidence indicates they function as antiviral defense systems in protists, reducing the progeny yield of their infecting giant viruses (phylum Nucleocytoviricota) and influencing the population dynamics and evolution of both viruses and their hosts. While many PLVs have been identified within the genomes of sequenced protists, most were recovered from metagenomic data. Even with the large number of PLVs identified from metagenomic data, their host-virus linkages remain unknown owing to the scarcity of ecologically relevant protist genomes. Additionally, the extent of PLV diversification within abundant freshwater taxa remains undetermined. In order to tackle these questions, high-quality genomes of abundant and representative taxa that bridge genomic and metagenomic PLVs are necessary. In this regard, cryptophytes, which are among the most widely distributed, abundant organisms in freshwaters and have remained largely out of bounds of genomic and metagenomic approaches, are ideal candidates for investigating the diversification of such viral elements both in cellular and environmental context.</p><p><strong>Results: </strong>We leveraged long-read sequencing to recover large (200-600 Mb), high-quality, and highly repetitive (> 60%) genomes of representative freshwater and marine photosynthetic cryptophytes. We uncovered over a thousand complete PLVs within these genomes, revealing vast lineage-specific expansions, particularly in the common freshwater cryptophyte Rhodomonas lacustris. By combining deep sequence homology annotation with biological network analyses, we discern well-defined PLV groups defined by characteristic gene-sharing patterns and the use of distinct strategies for replication and integration within host genomes. Finally, the PLVs recovered from these cryptophyte genomes also allow us to assign host-virus linkages in environmental sequencing data.</p><p><strong>Conclusions: </strong>Our findings provide a primer for understanding the evolutionary history, gene content, modes of replication and infection strategies of cryptophyte PLVs, with special emphasis on their expansion as endogenous viral elements (EVEs) in freshwater bloom-forming R. lacustris. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"154"},"PeriodicalIF":13.8,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"β-Elemonic acid mediated enrichment of Paenibacillus to help Salvia miltiorrhiza Bunge alleviate drought stress.","authors":"Hong-Mei Jia, Jie Zhou, Wen-Cheng Zhao, Dong-Mei He, Zhu-Yun Yan","doi":"10.1186/s40168-025-02154-2","DOIUrl":"10.1186/s40168-025-02154-2","url":null,"abstract":"<p><strong>Background: </strong>Microorganisms can improve the adaptability of crops to drought and high-temperature stress. However, the changes of rhizosphere microbial communities under climate stress and the potential mechanisms driving microbial changes remain poorly understood.</p><p><strong>Results: </strong>In this study, the medicinal plant Salvia miltiorrhiza was used as the research object. ITS, 16S rRNA amplicon sequencing, and liquid chromatography-mass spectrometry-based metabolomics were integrated to investigate its physiological and biochemical responses to drought, high-temperature, and combined drought-high temperature under greenhouse. Additionally, we determined the seedling weight, leaf water content, active ingredient content of underground part, and the content of chlorophyll, leaf nitrogen, phosphorus, and potassium. The results demonstrated that microorganisms can alleviate stress by enhancing the water retention capacity of S. miltiorrhiza leaves; TD group increased by about 13%, promoting nutrient absorption; and the chlorophyll content of group D increased by about 78%, boosting photosynthetic efficiency and increasing the levels of stress-resistant compounds. We found that bacteria exhibited greater sensitivity to climatic stress factors, with Paenibacillus being significantly enriched only in the stress-treated group. Moreover, the synthetic community comprising Paenibacillus was confirmed to help S. miltiorrhiza alleviate drought stress. We further found that β-elemonic acid, a triterpene acid secreted by plant roots, specifically enriched Paenibacillus under drought stress. In addition, β-elemonic acid significantly promoted the growth of S. miltiorrhiza in the presence of Paenibacillus under drought stress.</p><p><strong>Conclusions: </strong>Our findings suggest that S. miltiorrhiza enrich beneficial Paenibacillus to combat drought stress through the secretion of the key metabolite β-elemonic acid. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"153"},"PeriodicalIF":13.8,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12183831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144475782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of hydrogen oxidation coupled with antimonate reduction, a novel antimony biogeochemical cycling, in two contrasting antimony-contaminated environments.","authors":"Yize Wang, Xiaoxu Sun, Yubo Cao, Zhimin Xu, Huicai Sun, Xiaojie Guan, Muhammad Usman Ghani, Lin Zheng, Baoqin Li, Duanyi Huang, Weimin Sun","doi":"10.1186/s40168-025-02149-z","DOIUrl":"10.1186/s40168-025-02149-z","url":null,"abstract":"<p><strong>Background: </strong>Antimony (Sb) contamination is a serious environmental problem owing to its extensive production worldwide. High concentration of Sb is often detected in mining-contaminated environments, leading to the risk of contamination to the downstream environments through waterflow. Microorganisms play an important role in the fate and transport of Sb. Microbially mediated Sb(V) reduction performs an important environmental service because it can reduce the mobility of Sb and prevent the transport of Sb to downstream. As a commonly found intermediate in mining and aquatic environments, molecular hydrogen (H₂) may serve as an electron donor to drive Sb(V) reduction, although this biogeochemical process has not yet been reported.</p><p><strong>Results: </strong>In this study, Sb(V) reduction coupled with H₂ oxidation (HOSbR) was identified in two contrasting Sb-contaminated habitats, i.e., oligotrophic tailings and organic-rich river sediments. DNA-stable isotope probing identified Azospirillum and Hydrogenophaga spp. as the bacteria potentially responsible for HOSbR in oligotrophic tailings and organic-rich river sediments, respectively. Further, Azospirillum spp. were identified as keystone taxa in tailings. The causal inference framework suggested that Azospirillum spp. may contribute to the increased nitrogenase activity in oligotrophic tailings during HOSbR.</p><p><strong>Conclusions: </strong>These results suggest that bacteria responsible for HOSbR may play various important ecological roles including reducing the mobility of Sb and improving nutrient conditions in oligotrophic habitats. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"152"},"PeriodicalIF":13.8,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12183865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144475762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wild wisdom meets cultivation: comparative rhizomicrobiome analysis unveils the key role of Paraburkholderia in growth promotion and disease suppression in Coptis chinensis.","authors":"Xianhe Cao, Qingjun Yuan, Chengcheng Hu, Hanxing Zhang, Xianyun Sun, Binbin Yan, Xiaojing Ma, Long Zhang, Luqi Huang, Shaojie Li, Zhenying Zhang","doi":"10.1186/s40168-025-02136-4","DOIUrl":"10.1186/s40168-025-02136-4","url":null,"abstract":"<p><strong>Background: </strong>The sustained monoculture and irregular planting practices rendered the cultivated Coptis chinensis more prone to various diseases compared to its wild counterparts. Rewilding the rhizomicrobiome of cultivated plants has emerged as a promising strategy to promote plant growth, but ancestral microbiota suitable for C. chinensis remain largely uncharted.</p><p><strong>Results: </strong>The amplicon data analyses revealed that habitat transition strongly influenced the rhizosphere microbial communities. The rhizomicrobiomes of wild C. chinensis encompassed a more diverse array of ecological groups and exhibited a greater functional diversity compared to their cultivated counterparts. A higher proportion of beneficial fungi was observed in the rhizosphere of wild C. chinensis, while the cultivated plants had a higher population of pathogenic fungi. Furthermore, a well-documented plant-growth-promoting rhizobacterium genus, Paraburkholderia, was found to play an essential role in the resistance of the wild C. chinensis to potential disease caused by Ilyonectria. Two strains of Paraburkholderia (Paraburkholderia nemoris and Paraburkholderia phytofirmans) were isolated, and in vitro experiments confirmed that these isolates possess various growth-promoting properties and antagonistic activities against known pathogens for C. chinensis root rot. Both of the Paraburkholderia isolates could markedly promote the plant immune response and enhance the overall health of the cultivated C. chinensis.</p><p><strong>Conclusions: </strong>By a comprehensive comparison of the rhizosphere microbiome between wild and cultivated C. chinensis, the promising bacterial genus Paraburkholderia was identified as a beneficial microbe significantly promoting the growth of C. chinensis, providing pivotal insights for future endeavors aimed at engineering the rhizosphere microbiome of C. chinensis, as well as other medicinal herbs. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"150"},"PeriodicalIF":13.8,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uncovering encrypted antimicrobial peptides in health-associated Lactobacillaceae by large-scale genomics and machine learning.","authors":"Rubing Du, Fei Han, Zhen Li, Jing Yu, Yan Xu, Yongguang Huang, Qun Wu","doi":"10.1186/s40168-025-02145-3","DOIUrl":"10.1186/s40168-025-02145-3","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial peptides (AMPs) are well known for their broad-spectrum activity and have shown great promise in addressing the antibiotic-resistant crisis. The Lactobacillaceae family, recognized for its health-promoting effects in humans, represents a valuable source of novel AMPs. However, the global prevalence and distribution of AMPs within Lactobacillaceae remains largely unknown, which limits the efficient discovery and development of novel AMPs.</p><p><strong>Results: </strong>We analyzed all available genomes (10,327 genomes), encompassing 38 genera and 515 species, to investigate the biosynthetic potential (indicated by the number of AMP sequences in the genome) of AMP in the Lactobacillaceae family. We demonstrated Lactobacillaceae species had ubiquitous (69.90%) biosynthetic potential of AMPs. Overall, 9601 AMPs were identified, clustering into 2092 gene cluster families (GCFs), which showed strong interspecies specificity (95.27%), intraspecies heterogeneity (93.31%), and habitat uniqueness (95.83%), that greatly expanded on the AMP sequence landscape. Novelty assessment indicated that 1516 GCFs (72.47%) had no similarity to any known AMPs in existing databases. Machine learning predictions suggested that novel AMPs from Lactobacillaceae possessed strong antimicrobial potential, with 664 GCFs having an additive minimum inhibitory concentration (MIC) below 100 μM. We randomly synthesized 16 AMPs (with predicted MIC < 100 μM) and identified 10 AMPs exhibiting varied-spectrum activity against 11 common pathogens. Finally, we identified one Lactobacillus delbrueckii-originated AMP (delbruin_1) having broad-spectrum (all 11 pathogens) and high antimicrobial activity (average MIC = 38.56 µM), which proved its potential as a clinically viable antimicrobial agent.</p><p><strong>Conclusions: </strong>We uncovered the global prevalence of AMPs in Lactobacillaceae and proved that Lactobacillaceae is an untapped and invaluable source of novel AMPs to combat the antibiotic-resistance crisis. Meanwhile, we provided a machine learning-guided framework for AMP discovery, offering a scalable roadmap for identifying novel AMPs not only in Lactobacillaceae but also in other organisms. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"151"},"PeriodicalIF":13.8,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Interactions with native microbial keystone taxa enhance the biocontrol efficiency of Streptomyces.","authors":"Tianyu Sun, Hongwei Liu, Ningqi Wang, Mingcong Huang, Samiran Banerjee, Alexandre Jousset, Yangchun Xu, Qirong Shen, Shimei Wang, Xiaofang Wang, Zhong Wei","doi":"10.1186/s40168-025-02171-1","DOIUrl":"10.1186/s40168-025-02171-1","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"148"},"PeriodicalIF":13.8,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12180144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144336738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic analysis reveals gut phage diversity across three mammalian models.","authors":"Menghao Yu, Yunmeng Chu, Yongming Wang, Luofei Mo, Xin Tan, Shun Guo, Shengjian Yuan, Yingfei Ma","doi":"10.1186/s40168-025-02144-4","DOIUrl":"10.1186/s40168-025-02144-4","url":null,"abstract":"<p><strong>Background: </strong>The gut virome plays a pivotal role in shaping the host's microbiota. However, gut viruses across different mammalian models, and their connections with the human gut microbiota remain largely unknown.</p><p><strong>Results: </strong>We identified 977 high-confidence species-level viral operational taxonomic units (vOTUs) in mice (hcMGV), 12,896 in pigs (hcPGV), and 1480 in cynomolgus macaques (hcCMGV) from metagenomes, respectively. Clustering these vOTUs at approximately genus level uncovered novel clades with high prevalence across animal guts (> = 60%). In particular, crAss-like phages and cas-harboring jumbophages were characterized. Comparative analysis revealed that hcCMGV had a closer relationship with hcPGV than hcMGV, despite the animal-specific characteristics, and that 55.88% hcCMGV had connections with the human microbiota.</p><p><strong>Conclusions: </strong>Our findings shed light on the diversity of gut viruses across these three animals, contributing to future gut microbial studies using model animals. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"146"},"PeriodicalIF":13.8,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12180220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144336741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}