Adaptive Evolution within Gut Microbiomes of Healthy People.
Publication Title
Cell Host Microbe
Document Type
Article
Publication Date
5-8-2019
Keywords
Bacteroides; adaptive evolution; de novo mutation; horizontal gene transfer; human microbiome; metagenomics; microbial evolution; microbial genomics; whole-genome sequencing
Abstract
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 years-long 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.
Area of Special Interest
Digestive Health
Specialty/Research Institute
Institute for Systems Biology
Specialty/Research Institute
Gastroenterology
