{"title":"动物-肠道细菌-噬菌体 \"三方系统的宿主特异性和同源关系。","authors":"Ye Feng, Ruike Wei, Qiuli Chen, Tongyao Shang, Nihong Zhou, Zeyu Wang, Yanping Chen, Gongwen Chen, Guozhi Zhang, Kun Dong, Yihai Zhong, Hongxia Zhao, Fuliang Hu, Huoqing Zheng","doi":"10.1038/s41522-024-00557-x","DOIUrl":null,"url":null,"abstract":"<p><p>Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the \"animal-gut bacteria-phage\" tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":7.8000,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11350085/pdf/","citationCount":"0","resultStr":"{\"title\":\"Host specificity and cophylogeny in the \\\"animal-gut bacteria-phage\\\" tripartite system.\",\"authors\":\"Ye Feng, Ruike Wei, Qiuli Chen, Tongyao Shang, Nihong Zhou, Zeyu Wang, Yanping Chen, Gongwen Chen, Guozhi Zhang, Kun Dong, Yihai Zhong, Hongxia Zhao, Fuliang Hu, Huoqing Zheng\",\"doi\":\"10.1038/s41522-024-00557-x\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. 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引用次数: 0
摘要
肠道细菌与其动物宿主之间的同源关系已经被确定,并且与宿主的健康高度相关,但延伸到肠道噬菌体的研究却很少。在这里,我们利用蜜蜂模型来研究 "动物-肠道细菌-噬菌体 "三方系统中的宿主特异性和同源关系。通过对不同蜜蜂物种进行元基因组测序,发现肠道噬菌体组的组成比肠道细菌组更多变。然而,细菌组和噬菌体组的差异矩阵显示出显著的关联性,表明这两种群落之间存在相互影响。大多数肠道噬菌体在病毒集群水平上是宿主通才,但在病毒 OTU 水平上是宿主专才。虽然优势肠道细菌 Gilliamella 和 Snodgrassella 与蜜蜂宿主的系统发育相匹配,但它们的大多数噬菌体的同源程度较低。蜜蜂、肠道细菌和肠道噬菌体的进化速度呈显著上升趋势,包括同义和非同义替换以及基因含量变化。然而,对于所有三个编码三方成员来说,它们在进化过程中的正选择基因和涉及增益/损耗的基因同时丰富了营养物质代谢的功能,因此突出了三方的共同进化,从而提高了整个全生物体的生态适应性。
Host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system.
Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.
期刊介绍:
npj Biofilms and Microbiomes is a comprehensive platform that promotes research on biofilms and microbiomes across various scientific disciplines. The journal facilitates cross-disciplinary discussions to enhance our understanding of the biology, ecology, and communal functions of biofilms, populations, and communities. It also focuses on applications in the medical, environmental, and engineering domains. The scope of the journal encompasses all aspects of the field, ranging from cell-cell communication and single cell interactions to the microbiomes of humans, animals, plants, and natural and built environments. The journal also welcomes research on the virome, phageome, mycome, and fungome. It publishes both applied science and theoretical work. As an open access and interdisciplinary journal, its primary goal is to publish significant scientific advancements in microbial biofilms and microbiomes. The journal enables discussions that span multiple disciplines and contributes to our understanding of the social behavior of microbial biofilm populations and communities, and their impact on life, human health, and the environment.