Ecological and evolutionary adaptations shape the gut microbiome of BaAka African rainforest hunter-gatherers
Andres Gomez , Klara Petrzelkova , Carl J Yeoman , Micahel B Burns , Katherine R Amato , Klara Vlckova , David Modry , Angelique Todd , Carolyn A Jost Robbinson , Melissa Remis , Manolito Torralba , Karen E Nelson , Franck Carbonero , H Rex Gaskins , Brenda A Wilson , Rebecca M Stumpf , Bryan A White , Steven R Leigh , Ran Blekhman
doi: http://dx.doi.org/10.1101/019232

The gut microbiome provides access to otherwise unavailable metabolic and immune functions, likely affecting mammalian fitness and evolution. To investigate how this microbial ecosystem impacts evolutionary adaptation of humans to particular habitats, we explore the gut microbiome and metabolome of the BaAka rainforest hunter-gatherers from Central Africa. The data demonstrate that the BaAka harbor a colonic ecosystem dominated by Prevotellaceae and other taxa likely related to an increased capacity to metabolize plant structural polysaccharides, phenolics, and lipids. A comparative analysis shows that the BaAka gut microbiome shares similar patterns with that of the Hadza, another hunter-gatherer population from Tanzania. Nevertheless, the BaAka harbor significantly higher bacterial diversity and pathogen load compared to the Hadza, as well as other Western populations. We show that the traits unique to the BaAka microbiome and metabolome likely reflect adaptations to hunter-gatherer lifestyles and particular subsistence patterns. We hypothesize that the observed increase in microbial diversity and potential pathogenicity in the BaAka microbiome has been facilitated by evolutionary adaptations in immunity genes, resulting in a more tolerant immune system.