Adaptive Evolution within Gut Microbiomes of Healthy People.

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PubMed ID: 31028005

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Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM, Groussin M, Xavier RJ, Alm EJ

Cell Host Microbe. Apr 2019

COMMENT: The authors study how commensal bacteria diversify and adapt within the human gut of each individual. For that, they analyze the intra-individual evolution of Bacteroides fragilis using culture-based population genomics and metagenomics. They find specific individual signatures of SNPs and mobile elements and parallel evolution in a set of genes, especially those involved in cell-envelope biosynthesis and polysaccharide utilization.


We set out to survey intra-species diversity and evolution of B. fragilis within 12 healthy subjects, all donors to the OpenBiome stool bank (ages 22–37; Table S1). A total of 30 fecal samples from these subjects were studied. These fecal samples included longitudinal samples from 7 subjects spanning up to 2 years and single samples from 5 subjects (Table S2). Subjects did not take antibiotics for at least 3 months prior to initial sampling or during longitudinal sampling. We sequenced the genomes of 602 B. fragilis isolates cultured from these 30 fecal samples. Each isolate was derived from an independent single cell in the original microbiome community.

We identified SNPs between these 602 isolates and built a phylogeny for these isolates. Isolate genomes from different subjects differed by more than 10,000 SNPs, while genomes from the same subject differed by fewer than 100 SNPs

We report 16 genes in which adaptive mutations are concentrated, which warrant further study and whose identities provide hints about the nature of within-person selection. Six of thegenes identified as under selection are members of the SusC/SusD family of nutrient import proteins



  • Bacteroides fragilis adapts via de novo mutations within healthy people
  • Polysaccharide utilization and capsule synthesis pathways change during colonization
  • B. fragilis diversifies into coexisting sublineages within individuals
  • An adaptive mutation emerges with different likelihood between human populations

Within-person evolution, in addition to ecological forces, may need to be considered as a possible driver of community dynamics, such as increases or decreases in species abundances over time. In particular, the eco-evolutionary force of monopolization—in which adaptation to a unique local environment enables early colonizers to prevent subsequent invasion by new potential colonizers (De Meester et al.,2016)—may need more attention in the microbiome field. Monopolization may be responsible for the observed stability of individual lineages in the microbiome and the microbiome’s ability to provide colonization resistance


Raquel Tobes