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.
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We acknowledge the collaboration of the Comunidad Nativa Matses Anexo San Mateo and Caserío de Tunapuco who opened their communities to our research enterprise. We acknowledge the contribution of Susan Polo and Maria Elena Medina during fieldwork and Alison Mann during data analysis. Research reported in this publication was primarily supported by the National Institutes of Health under award numbers R01 HG005172 and R01 GM089886. Additional support included grants from the National Institutes of Health (U54GM104938) and the National Science Foundation (#0845314). A.J.O.-T. was partially supported by the National Institutes of Health grant R25 CA085771 during the writing phase of this project.
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