Instituto Gulbenkian de Ciência, Oeiras, Portugal.
PLoS Biol. 2020 Mar 10;18(3):e3000617. doi: 10.1371/journal.pbio.3000617. eCollection 2020 Mar.
Bacteria generally live in species-rich communities, such as the gut microbiota. Yet little is known about bacterial evolution in natural ecosystems. Here, we followed the long-term evolution of commensal Escherichia coli in the mouse gut. We observe the emergence of mutation rate polymorphism, ranging from wild-type levels to 1,000-fold higher. By combining experiments, whole-genome sequencing, and in silico simulations, we identify the molecular causes and explore the evolutionary conditions allowing these hypermutators to emerge and coexist within the microbiota. The hypermutator phenotype is caused by mutations in DNA polymerase III proofreading and catalytic subunits, which increase mutation rate by approximately 1,000-fold and stabilise hypermutator fitness, respectively. Strong mutation rate variation persists for >1,000 generations, with coexistence between lineages carrying 4 to >600 mutations. The in vivo molecular evolution pattern is consistent with fitness effects of deleterious mutations sd ≤ 10-4/generation, assuming a constant effect or exponentially distributed effects with a constant mean. Such effects are lower than typical in vitro estimates, leading to a low mutational load, an inference that is observed in in vivo and in vitro competitions. Despite large numbers of deleterious mutations, we identify multiple beneficial mutations that do not reach fixation over long periods of time. This indicates that the dynamics of beneficial mutations are not shaped by constant positive Darwinian selection but could be explained by other evolutionary mechanisms that maintain genetic diversity. Thus, microbial evolution in the gut is likely characterised by partial sweeps of beneficial mutations combined with hitchhiking of slightly deleterious mutations, which take a long time to be purged because they impose a low mutational load. The combination of these two processes could allow for the long-term maintenance of intraspecies genetic diversity, including mutation rate polymorphism. These results are consistent with the pattern of genetic polymorphism that is emerging from metagenomics studies of the human gut microbiota, suggesting that we have identified key evolutionary processes shaping the genetic composition of this community.
细菌通常生活在物种丰富的群落中，例如肠道微生物群。然而，人们对自然生态系统中细菌的进化知之甚少。在这里，我们跟踪了共生大肠杆菌在小鼠肠道中的长期进化。我们观察到突变率多态性的出现，范围从野生型水平到 1000 倍以上。通过结合实验、全基因组测序和计算机模拟，我们确定了分子原因，并探讨了允许这些超突变体在微生物群中出现和共存的进化条件。超突变表型是由 DNA 聚合酶 III 校对和催化亚基的突变引起的，这些突变分别将突变率提高了约 1000 倍，并稳定了超突变体的适应性。强烈的突变率变化持续了>1000 代，带有 4 到>600 个突变的谱系共存。体内分子进化模式与有害突变的适应性效应 sd ≤ 10-4/代一致，假设恒定效应或具有恒定均值的指数分布效应。这些效应低于典型的体外估计，导致突变负荷低，这一推断在体内和体外竞争中都得到了观察。尽管存在大量有害突变，但我们发现了许多有益突变，这些突变在很长一段时间内都没有达到固定状态。这表明有益突变的动态不是由恒定的正达尔文选择塑造的，而是可以通过其他维持遗传多样性的进化机制来解释。因此，肠道微生物的进化可能是以有益突变的部分扫荡为特征，同时伴随着轻微有害突变的随机漂变，这些突变由于突变负荷低，需要很长时间才能被清除。这两个过程的结合可以使种内遗传多样性长期维持，包括突变率多态性。这些结果与人类肠道微生物组的宏基因组学研究中出现的遗传多态性模式一致，表明我们已经确定了塑造该群落遗传组成的关键进化过程。
