Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes

Matthew M. Carter, Matthew R. Olm, Bryan D. Merrill, Dylan Dahan, Surya Tripathi, Sean P. Spencer, Feiqiao B. Yu, Sunit Jain, Norma Neff, Aashish R. Jha, Erica D. Sonnenburg, Justin L. Sonnenburg

Research output: Contribution to journalArticlepeer-review

Abstract

The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.

Original languageEnglish (US)
Pages (from-to)3111-3124.e13
JournalCell
Volume186
Issue number14
DOIs
StatePublished - Jul 6 2023

Keywords

  • human gut microbiome
  • hunter-gatherer
  • industrialization
  • metagenomic assembly
  • metagenomic metaanalysis
  • metagenomics
  • strain sharing
  • Treponema succinifaciens

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology

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