To understand how the gut microbiome is impacted by human adaptation to varying environments,
we explored gut bacterial communities in the BaAka rainforest hunter-gatherers and
their agriculturalist Bantu neighbors in the Central African Republic. Although the
microbiome of both groups is compositionally similar, hunter-gatherers harbor increased
abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome
is dominated by Firmicutes. Comparisons with US Americans reveal microbiome differences
between Africans and westerners but show western-like features in the Bantu, including
an increased abundance of predictive carbohydrate and xenobiotic metabolic pathways.
In contrast, the hunter-gatherer gut shows increased abundance of predicted virulence,
amino acid, and vitamin metabolism functions, as well as dominance of lipid and amino-acid-derived
metabolites, as determined through metabolomics. Our results demonstrate gradients
of traditional subsistence patterns in two neighboring African groups and highlight
the adaptability of the microbiome in response to host ecology.