Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence, and adaptation

Despite the importance of horizontal gene transfer for rapid bacterial evolution, reliable assignment of mobile genetic elements to their microbial hosts in natural communities such as the human gut microbiota is lacking. We used high-throughput chromosomal conformation capture coupled with probabilistic modelling of experimental noise to resolve 88 strain-level metagenome-assembled genomes of distal gut bacteria from two participants, including 12,251 accessory elements. Comparisons of two samples collected 10 years apart for each of the participants revealed extensive in situ exchange of accessory elements as well as evidence of adaptive evolution in core genomes. Accessory elements were predominantly promiscuous and prevalent in the distal gut metagenomes of 218 adult individuals. This research provides a foundation and approach for studying microbial evolution in natural environments. High-throughput chromosomal conformation capture identified changes in the gut microbiome over 10 years, including substantial exchange of accessory elements and adaptive evolution in core genomes.

• Publication year

  2019

• Venue

  Nature Microbiology

• Publication date

  2019-11-02

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/s41564-019-0625-0PMID 31873203PMCID 6992475
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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