School of Life Sciences, Xiamen University, Xiamen 361102, China.
Department of Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, D-38124 Braunschweig, Germany.
Genomics Proteomics Bioinformatics. 2022 Apr;20(2):334-349. doi: 10.1016/j.gpb.2021.10.006. Epub 2022 Feb 3.
Prevotella copri and its related taxa are widely detected in mammalian gut microbiomes and have been linked with an enterotype in humans. However, their microevolution and macroevolution among hosts are poorly characterized. In this study, extensively collected marker genes and genomes were analyzed to trace their evolutionary history, host specificity, and biogeographic distribution. Investigations based on marker genes and genomes suggest that a P. copri-containing lineage (PCL) harbors diverse species in higher primates. Firstly, P. copri in the human gut consisted of multiple groups exhibiting high genomic divergence and conspicuous but non-strict biogeographic patterns. Most African strains with high genomic divergence from other strains were phylogenetically located at the root of the species, indicating the co-evolutionary history of P. copri and Homo sapiens. Secondly, although long-term co-evolution between PCL and higher primates was revealed, sporadic signals of co-speciation and extensive host jumping of PCL members were suggested among higher primates. Metagenomic and phylogenetic analyses indicated that P. copri and other PCL species found in domesticated mammals had been recently transmitted from humans. Thirdly, strong evidence was found on the extensively horizontal transfer of genes (e.g., genes encoding carbohydrate-active enzymes) among sympatric P. copri groups and PCL species in the same primate host. Our study provides panoramic insights into the combined effects of vertical and horizontal transmission, as well as potential niche adaptation, on the microevolutionary and macroevolutionary history for an enterotype-representative lineage.
普雷沃氏菌属及其相关分类群广泛存在于哺乳动物的肠道微生物群中，并与人类的一种肠型有关。然而，它们在宿主间的微观进化和宏观进化特征还知之甚少。在这项研究中，广泛收集的标记基因和基因组被用于追踪它们的进化历史、宿主特异性和生物地理分布。基于标记基因和基因组的研究表明，含有普雷沃氏菌属的谱系（PCL）在高等灵长类动物中拥有多样化的物种。首先，人类肠道中的普雷沃氏菌属包含多个表现出高基因组分化且具有明显但非严格的生物地理模式的群体。与其他菌株高度基因组分化的大多数非洲菌株在系统发育上位于物种的根部，表明了普雷沃氏菌属和智人之间的共同进化历史。其次，尽管揭示了 PCL 与高等灵长类动物之间的长期共同进化，但也提示了 PCL 成员之间存在偶发性的协同进化和广泛的宿主跳跃。宏基因组和系统发育分析表明，在驯化哺乳动物中发现的普雷沃氏菌属和其他 PCL 物种最近是从人类传播而来的。第三，在同一灵长类动物宿主中，同域的普雷沃氏菌属群体和 PCL 物种之间存在基因（如编码碳水化合物活性酶的基因）广泛水平转移的有力证据。我们的研究为垂直和水平传播以及潜在的生态位适应对代表性肠型谱系的微观进化和宏观进化历史的综合影响提供了全面的见解。
