A massive number of microorganisms, belonging to different species, continuously divide inside the guts of animals and humans. The large size of these communities and their rapid division times imply that we should be able to watch microbial evolution in the gut in real time, in a similar manner to what has been done in vitro. Here, we review recent findings on how natural selection shapes intrahost evolution (also known as within-host evolution), with a focus on the intestines of mice and humans. The microbiota of a healthy host is not as static as initially thought from the information measured at only one genomic marker. Rather, the genomes of each gut-colonizing species can be highly dynamic, and such dynamism seems to be related to the microbiota species diversity. Genetic and bioinformatic tools, and analysis of time series data, allow quantification of the selection strength on emerging mutations and horizontal transfer events in gut ecosystems. The drivers and functional consequences of gut evolution can now begin to be grasped. The rules of this intrahost microbiota evolution, and how they depend on the biology of each species, need to be understood for more effective development of microbiota therapies to help maintain or restore host health.

大量属于不同物种的微生物在动物和人类的肠道内不断分裂。这些群落的庞大规模及其快速的分裂时间意味着我们应该能够以与体外类似的方式实时观察肠道中微生物的进化。在这里，我们回顾了关于自然选择如何塑造宿主内进化（也称为宿主内进化）的最新发现，重点关注小鼠和人类的肠道。健康宿主的微生物群并不像最初从仅在一个基因组标记处测量的信息中想象的那样静态。相反，每个肠道定殖物种的基因组都可以是高度动态的，这种动态似乎与微生物群物种多样性有关。遗传和生物信息学工具以及时间序列数据分析可以量化肠道生态系统中新兴突变和水平转移事件的选择强度。现在我们可以开始掌握肠道进化的驱动因素和功能后果。需要了解这种宿主内微生物群进化的规则，以及它们如何依赖于每个物种的生物学，以便更有效地开发微生物群疗法，以帮助维持或恢复宿主健康。