Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
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DOI：
10.1038/s41564-019-0494-6
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发表时间：
2019-10-01
影响因子：
28.3
通讯作者：
Dutilh, Bas E.
中科院分区：
文献类型：
--
作者：
Edwards, Robert A.;Vega, Alejandro A.;Dutilh, Bas E.
微生物组是遍布所有自然生态系统的微生物和病毒的巨大群落。病毒已被认为是微生物组中最可变的组分，如病毒组调查和高基因组嵌合现象的例子所支持的。然而，最近的证据表明，与其他环境相比，人类肠道病毒组非常稳定。在这里，我们调查的起源，进化和流行病学的crAsphalage，一个广泛的人类肠道病毒。通过全球合作，我们从世界上超过三分之一的国家获得了craseparage的DNA序列，并表明craseparage的地理分布在国家，城市和个人中局部聚集。我们还在旧世界和新世界的灵长类动物中发现了完全共线的crAsphalage样基因组，这表明crAsphalage与灵长类动物的关联可能有数百万年的历史。最后，通过利用一个超过1,000人的大型队列，我们测试了CrAsA年龄是否与肠道微生物组的细菌分类组，不同的人类健康参数和广泛的饮食因素相关。我们发现与拟杆菌门相关的不同细菌分支存在强相关性，与几种饮食类别存在弱相关性，但与健康或疾病没有显着相关性。我们的结论是，crAspharage是一种良性的世界性病毒，可能与人类谱系共同进化，是正常的人类肠道病毒组的一个组成部分。
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.