Adaptive Evolution within Gut Microbiomes of Healthy People
Adaptive Evolution within Gut Microbiomes of Healthy People
复制标题
DOI：
10.1016/j.chom.2019.03.007
复制
发表时间：
2019-05-08
影响因子：
30.3
通讯作者：
Alm, Eric J.
中科院分区：
文献类型：
--
作者：
Zhao, Shijie;Lieberman, Tami D.;Alm, Eric J.
自然选择塑造了细菌在所有环境中的进化。然而，共生细菌在人体肠道内多样化和适应的程度尚不清楚。在这里，我们结合基于培养的种群基因组学和元基因组学来研究脆弱类杆菌微生物组内的进化。我们发现，脆弱芽孢杆菌个体内种群包含大量从头开始的核苷酸和移动元件多样性，保存了多年的人内历史。这段历史揭示了人内适应的多个特征，包括16个基因的平行进化。其中许多基因与细胞膜的生物合成和多糖的利用有关。使用几乎每天的元基因组抽样跟踪进化轨迹，我们发现了尽管有适应性动力学，但在一个受试者中多年共存的证据。我们使用公共后基因组研究了我们队列中常见的一种适应性突变，发现它经常出现在西方的微生物群中，而不是中国的微生物群中。总而言之，这些结果表明脆弱芽孢杆菌在单个微生物群中适应，指出了促进长期肠道定植的因素。
Natural selection shapes bacterial evolution in all environments. However, the extent to which commensal bacteria diversify and adapt within the human gut remains unclear. Here, we combine culture-based population genomics and metagenomics to investigate the within-microbiome evolution of Bacteroides fragilis. We find that intra-individual B. fragilis populations contain substantial de novo nucleotide and mobile element diversity, preserving years of within-person history. This history reveals multiple signatures of within-person adaptation, including parallel evolution in sixteen genes. Many of these genes are implicated in cell-envelope biosynthesis and polysaccharide utilization. Tracking evolutionary trajectories using near-daily metagenomic sampling, we find evidence for yearslong coexistence in one subject despite adaptive dynamics. We used public metagenomes to investigate one adaptive mutation common in our cohort and found that it emerges frequently in Western, but not Chinese, microbiomes. Collectively, these results demonstrate that B. fragilis adapts within individual microbiomes, pointing to factors that promote long-term gut colonization.