Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, PSL University, Paris, France.
Muséum national d'Histoire naturelle, UMR 7205 CNRS-MNHN-UPMC-EPHE "Institut de Systématique, Evolution, Biodiversité - ISYEB", Herbier National, 16 rue Buffon, Paris, France.
Mol Ecol Resour. 2019 Nov;19(6):1659-1671. doi: 10.1111/1755-0998.13063. Epub 2019 Aug 10.
Microbiota play a central role in the functioning of multicellular life, yet understanding their inheritance during host evolutionary history remains an important challenge. Symbiotic microorganisms are either acquired from the environment during the life of the host (i.e. environmental acquisition), transmitted across generations with a faithful association with their hosts (i.e. strict vertical transmission), or transmitted with occasional host switches (i.e. vertical transmission with horizontal switches). These different modes of inheritance affect microbes' diversification, which at the two extremes can be independent from that of their associated host or follow host diversification. The few existing quantitative tools for investigating the inheritance of symbiotic organisms rely on cophylogenetic approaches, which require knowledge of both host and symbiont phylogenies, and are therefore often not well adapted to DNA metabarcoding microbial data. Here, we develop a model-based framework for identifying vertically transmitted microbial taxa. We consider a model for the evolution of microbial sequences on a fixed host phylogeny that includes vertical transmission and horizontal host switches. This model allows estimating the number of host switches and testing for strict vertical transmission and independent evolution. We test our approach using simulations. Finally, we illustrate our framework on gut microbiota high-throughput sequencing data of the family Hominidae and identify several microbial taxonomic units, including fibrolytic bacteria involved in carbohydrate digestion, that tend to be vertically transmitted.
微生物在多细胞生物的功能中起着核心作用，但了解它们在宿主进化历史中的遗传仍然是一个重要的挑战。共生微生物要么是在宿主的一生中从环境中获得的（即环境获得），要么与宿主一起通过忠实的关联在世代间传递（即严格的垂直传递），要么偶尔与宿主一起传递（即垂直传递与水平转换）。这些不同的遗传模式影响微生物的多样化，在两个极端情况下，微生物的多样化可以独立于与其相关的宿主，也可以跟随宿主的多样化。少数现有的用于研究共生生物遗传的定量工具依赖于共进化方法，该方法需要宿主和共生生物系统发育的知识，因此通常不适用于 DNA 宏条形码微生物数据。在这里，我们开发了一种基于模型的框架，用于识别垂直传播的微生物分类群。我们考虑了一个在固定宿主系统发育上的微生物序列进化模型，其中包括垂直传播和水平宿主转换。该模型允许估计宿主转换的数量，并测试严格的垂直传播和独立进化。我们使用模拟来测试我们的方法。最后，我们在人科的肠道微生物高通量测序数据上说明了我们的框架，并确定了几个微生物分类单元，包括参与碳水化合物消化的纤维分解细菌，这些细菌往往是垂直传播的。
