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The Matses live at an elevation of 150 m above sea level in a pocket of natural hyperdiversity that extends across the Brazilian border, and, until recently, the Matses have been geographically, historically and socially, isolated.The Matses are traditional hunter-gatherers whose subsistence focuses primarily on gathered tubers (Manihot spp.) and invasive plantains (Musa spp.) (Supplementary Table 1).Residents of Tunapuco eat fruits that they buy from lowland rural communities from the same region.Guinea pig, pork, lamb and infrequent cow cheese are the main animal protein sources in their diet.

As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes.

Previous reports have indicated that Western populations have lower microbial richness than non-Western populations.

Our analyses of microbial richness yielded similar results.

Fish is their primary protein source, complemented by sporadic consumption of game meat (monkey, sloth, capybara, alligator and so on.).

Consumption of dairy or processed food is very rare, and only as a result of sporadic visitors.

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.