Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Department of Botany and Biodiversity Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
Cell Host Microbe. 2020 Jul 8;28(1):12-22. doi: 10.1016/j.chom.2020.06.013.
Mammalian gut microbiomes profoundly influence host fitness, but the processes that drive the evolution of host-microbiome systems are poorly understood. Recent studies suggest that mammals and their individual gut symbionts can have parallel evolutionary histories, as represented by their congruent phylogenies. These "co-phylogenetic" patterns are signatures of ancient co-speciation events and illustrate the cohesiveness of the mammalian host-gut microbiome entity over evolutionary times. Theory predicts that co-speciation between mammals and their gut symbionts could result from their co-evolution. However, there is only limited evidence of such co-evolution. Here, we propose a model that explains cophylogenetic patterns without relying on co-evolution. Specifically, we suggest that individual gut bacteria are likely to diverge in patterns recapitulating host phylogeny when hosts undergo allopatric speciation, limiting inter-host bacterial dispersal and genomic recombination. We provide evidence that the model is empirically grounded and propose a series of observational and experimental approaches to test its validity.
哺乳动物的肠道微生物组深刻地影响着宿主的适应性，但驱动宿主-微生物组系统进化的过程还知之甚少。最近的研究表明，哺乳动物及其个体肠道共生体可以有平行的进化历史，这反映在它们一致的系统发育上。这些“共进化”模式是古老协同进化事件的特征，说明了哺乳动物宿主-肠道微生物组实体在进化过程中的凝聚力。理论预测，哺乳动物与其肠道共生体之间的协同进化可能是它们共同进化的结果。然而，只有有限的证据表明存在这种共同进化。在这里，我们提出了一个模型，该模型无需依赖共同进化来解释共进化模式。具体来说，我们认为当宿主经历异域物种形成时，个体肠道细菌可能会以再现宿主系统发育的模式发生分歧，从而限制宿主间细菌的传播和基因组重组。我们提供了证据表明该模型具有实证基础，并提出了一系列观察和实验方法来检验其有效性。
