Subsistence strategies in traditional societies distinguish gut microbiomes

• Published in: Nature communications Vol. 6; no. 1; p. 6505
• Main Authors: Obregon-Tito, Alexandra J., Tito, Raul Y., Metcalf, Jessica, Sankaranarayanan, Krithivasan, Clemente, Jose C., Ursell, Luke K., Zech Xu, Zhenjiang, Van Treuren, Will, Knight, Rob, Gaffney, Patrick M., Spicer, Paul, Lawson, Paul, Marin-Reyes, Luis, Trujillo-Villarroel, Omar, Foster, Morris, Guija-Poma, Emilio, Troncoso-Corzo, Luzmila, Warinner, Christina, Ozga, Andrew T., Lewis, Cecil M.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.03.2015; Nature Publishing Group; Nature Pub. Group
• Subjects: 631/158/670; 631/158/858; 631/326/2565/2134; 631/326/2565/547; 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; Humanities and Social Sciences; Humans; Industrial Development; Infant; Male; Metagenome - genetics; Middle Aged; multidisciplinary; Oklahoma; Peru; RNA, Ribosomal, 16S - genetics; Science; Science (multidisciplinary); Traditional farming; Treponema - genetics; Treponema - isolation & purification; Young Adult; Peru; Oklahoma
• ISSN: 2041-1723; 2041-1723
• 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. The gut microbiomes of urban-industrialized societies differ from those of traditional rural societies and hunter-gatherers. Here the authors perform a comparative analysis of available and new gut microbiome data to provide fresh insight into these differences.