Gut Microbiome Functional and Taxonomic Diversity within an Amazonian semi-nomadic hunter-gatherer group

BackgroundHuman gut microbiome profiles have been associated with human health and disease. These profiles have been defined based on microbes taxonomy and more recently, on their functionality. Human groups that still maintain traditional modes of subsistence (hunter-gatherers and rural agriculturalists) represent the groups non-impacted by urban-industrialized lifestyles, and therefore study them provide the basis for understanding the human microbiome evolution. The Yanomami is the largest semi-nomadic hunter-gatherer group of the Americas, exploring different niches of the Amazon rainforest in Brazil and Venezuela. In order to extend the analysis of this unique and diverse group, we focused on the gut microbiome of the Yanomami from Brazil and compared with those from Venezuela, and also with other traditional groups from the Amazon, considering taxonomic and functional profiles. ResultsA diversity of taxonomic biomarkers were identified to each South American traditional group studied, including the two Yanomami groups, despite their overall similarity in the taxonomic gut microbiome profiles. Broader levels of functional categories poorly discriminated traditional and urban-industrialized groups. Interestingly, a diversity was observed with the stratification of these categories, clearly segregating those groups. The Yanomami/Brazil gut microbiome presented unique functional features, such as a higher abundance of gene families involved in regulation/cell signaling, motility/chemotaxis, and virulence, contrasting with the microbiomes from the Yanomami/Venezuela and other groups. ConclusionsOur study revealed biomarkers, taxonomic and functional differences between the gut microbiome of Yanomami/Brazil and Yanomami/Venezuela individuals. This intra-Yanomami group diversity was accessed due to the increase number of individuals and group studied. These differences may reflect their semi-nomadic behavior, as well as, the local and seasonal diversity of the vast rainforest niche they explore, despite their shared cultural and genetic background. Overall, their microbiome profiles are shared with South American and African traditional groups, probably due to their lifestyle. The unique features identified within the Yanomami highlight the bias imposed by underrepresented sampling, and factors such as variations over space and time (seasonality) that impact, mainly, the hunter-gatherers. Therefore, to reach knowledge about human microbiome variations and their implications in human health, it is essential to enlarge data concerning the number of individuals, as well as the groups representing different lifestyles.