Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
ISME J. 2023 May;17(5):682-692. doi: 10.1038/s41396-023-01379-z. Epub 2023 Feb 17.
Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria.
理解宿主与其肠道常驻细菌之间的进化关系，可以改变我们对适应性表型特征的理解。宿主与其常驻细菌之间的相互作用不可避免地会影响肠道环境，从而影响宿主和微生物群落的生存条件。这种共存很可能影响细菌和宿主的适应性。这种共存是否会导致动物的进化共同多样化在很大程度上尚未得到探索，主要是由于环境和微生物群落的复杂性以及宿主选择通常较低。我们展示了野生大西洋鲑（Salmo salar）的肠道宏基因组，这是一种新的野生生物模型，其肠道微生物群落具有低复杂性和描述良好的种群结构，非常适合研究共同进化。我们的数据显示，宿主对以单一支原体物种为主导的核心肠道微生物群有很强的选择性。我们发现，大西洋鲑的种群结构与肠道支原体种群的核苷酸变异性之间存在明显的共同多样化，这符合宿主和常驻细菌之间共同进化的预期。我们的研究结果表明，大西洋鲑稳定的肠道微生物群已经与其鲑鱼宿主种群一起进化，同时可能为鲑鱼宿主种群提供适应性特征，包括防御机制、必需氨基酸的生物合成以及 B 族维生素的代谢。我们强调大西洋鲑是研究脊椎动物宿主与其常驻细菌之间共同进化的新型模型。
