Adaptive evolution within the gut microbiome of individual people
Tami D. Lieberman,
Sean M. Gibbons,
Ramnik J. Xavier,
Eric J. Alm
Posted 24 Oct 2017
bioRxiv DOI: 10.1101/208009 (published DOI: 10.1016/j.chom.2019.03.007)
Posted 24 Oct 2017
Individual bacterial lineages stably persist for years in the human gut microbiome. However, it is unknown if these lineages adapt during colonization of healthy people. Here, we assess evolution within individual microbiomes by sequencing the genomes of 602 Bacteroides fragilis isolates cultured from 12 healthy subjects. We find that B. fragilis within-subject populations contain significant de novo nucleotide and mobile element diversity, which preserve years of within-person evolutionary history. This evolutionary history contains signatures of within-person adaptation to both subject-specific and common selective forces, including parallel mutations in seventeen genes. These seventeen genes are involved in cell-envelope biosynthesis and polysaccharide utilization, as well as yet under-characterized pathways. Notably, one of these genes has been shown to be critical for B. fragilis colonization in mice, indicating that key genes have not already been optimized for survival in vivo. This lack of optimization, given historical signatures of purifying selection in these genes, suggests that varying selective forces with discordant solutions act upon B. fragilis in vivo. Remarkably, in one subject, two B. fragilis sublineages coexisted at a stable relative frequency over a 1.5-year period despite rapid adaptive dynamics within one of the sublineages. This stable coexistence suggests that competing selective forces can lead to B. fragilis niche-differentiation even within a single person. We conclude that B. fragilis adapts rapidly within the microbiomes of individual healthy people, providing a new route for the discovery of key genes in the microbiome and implications for microbiome stability and manipulation.
- Downloaded 4,335 times
- Download rankings, all-time:
- Site-wide: 883 out of 83,933
- In evolutionary biology: 22 out of 5,214
- Year to date:
- Site-wide: 18,998 out of 83,933
- Since beginning of last month:
- Site-wide: 17,605 out of 83,933
Downloads over time
Distribution of downloads per paper, site-wide
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!