Subsistence strategies in traditional societies distinguish gut microbiomes

Nat Commun. 2015 Mar 25:6:6505. doi: 10.1038/ncomms7505.


Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2-2.5 MB, coverage depth × 26-513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Actinobacteria / genetics
  • Actinobacteria / isolation & purification
  • Adolescent
  • Adult
  • Agriculture*
  • Bacteroidetes / genetics
  • Bacteroidetes / isolation & purification
  • Biodiversity
  • Child
  • Child, Preschool
  • Classification
  • Diet
  • Diet, Paleolithic*
  • Female
  • Firmicutes / genetics
  • Firmicutes / isolation & purification
  • Gastrointestinal Microbiome / genetics*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Industrial Development
  • Infant
  • Male
  • Metagenome / genetics
  • Middle Aged
  • Oklahoma
  • Peru
  • RNA, Ribosomal, 16S / genetics*
  • Treponema / genetics
  • Treponema / isolation & purification
  • Young Adult


  • RNA, Ribosomal, 16S