The gut microbiome of Baka forager-horticulturalists from southeastern Cameroon is optimized for metabolizing wild plant foods.

There is growing interest in gaining insight on how gut microbiome can contribute to human health and its resilience, resulting in an extraordinary capacity to be successful in different lifeways and environment. This came together with the hurry of characterizing the diversity of the human gut microbiome, including the one from individuals relying on a rural subsistence strategy, that are currently disappearing and constitute a biodiversity sink to be characterized in depth. Here, we applied shotgun metagenomics for characterizing the gut microbiome of the Baka, a group of forager-horticulturalists from southern Cameroon, who combine hunting and gathering with growing a small number of crops and working for the neighboring Bantu-speaking farmer. In particular, we analyzed the gut microbiome of a cohort of individuals with different accessibility to wild plant foods and processed foods, for exploring the variation of their gut microbiome along the transition from hunter-gatherer to agricultural communities. Shotgun data have been analyzed by applying network approaches and genome scale metabolic models to species-level genome bins. We found that 26 species-level genome bins were pivotal for the degradation of the wild plant food substrates. These microbes include both Old Friend species and microorganisms that are commonly present in the gut microbiome of Western individuals. However, they encoded also for genes that are no longer present in industrialized gut microbiome, such as specific CAZymes for complex carbohydrate degradation and bioisinthetic gene clusters for the production of secondary metabolites. We found an uncovering microbiome gradient associated with the consumption of wild plant foods, at both taxonomic and functional scale. Further, our results describe in depth the functional peculiarities of microorganisms related to wild plant foods consumption and their potential relevance for the human biology and for the protection of our health.