Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence

Abstract

The human gut microbiota is impacted by host nutrition and health status and therefore represents a potentially adaptive phenotype influenced by metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that industrialization is strongly correlated with patterns in human gut microbiota; however, we know little about the relative contribution of factors such as climate, diet, medicine, hygiene practices, host genetics, and parasitism. Here, we focus on fine-scale comparisons of African rural populations in order to (i) contrast the gut microbiota of populations inhabiting similar environments but having different traditional subsistence modes and either shared or distinct genetic ancestry, and (ii) examine the relationship between gut parasites and bacterial communities. Characterizing the fecal microbiota of Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon, we found that the gut parasite Entamoeba is significantly correlated with microbiome composition and diversity. We show that across populations, colonization by this protozoa can be predicted with 79% accuracy based on the composition of an individual's gut microbiota, and that several of the taxa most important for distinguishing Entamoeba absence or presence are signature taxa for autoimmune disorders. We also found gut communities to vary significantly with subsistence mode, notably with some taxa previously shown to be enriched in other hunter-gatherers groups (in Tanzania and Peru) also discriminating hunter-gatherers from neighboring farming or fishing populations in Cameroon.

Culture as an ingredient of personalized medicine

“…Dietary alterations can promote rapid changes in gut microbiota, but the roles of habituation to these diets and adaptations that occur across generations are unclear. 25 As noted, traditional foods of Aboriginal peoples differed from those of European cultures (although there were likely commonalities with circumpolar countries), resulting in variations of microbiota. However, diminished access to tra ditional hunting grounds and food sources, together with more recent climate change impacts on wildlife migration patterns, fish stocks and plant habitats as well as the in creased migration to urban settings have all resulted in sub stantial and relatively rapid dietary changes.…”

Entamoeba histolytica: Host parasite interactions at the colonic epithelium

“…24 Interestingly, susceptibility to Eh infection can be predicted to a 79% accuracy based on analysis of microbiota distribution in the host. 25 Several taxa that are strongly associated to a facilitative microbiota to allow for Eh infection have been linked to autoimmune disorders and exacerbating a pro-inflammatory state in the intestine including Prevotella copri. There is a direct correlation between Eh burden in infected individuals and abundance of P. copri in endemic areas of amebaisis.…”

Inferences of African evolutionary history from genomic data

“…In CAHG populations from Cameroon, Morton et al . [77] found associations between infection with gut parasites and particular gut microbial composition. Gomez et al .…”

“…Agropastoralist, Afroasiatic populations migrated from Ethiopia into Kenya and Tanzania within the past 5 ky [42]. After admixing with Bantu groups, pastoralist populations from eastern Africa migrated through Tanzania to southern Africa around 2.4 kya [77]. Migrations through the Sahel occurred bidirectionally between east and west Africa in the past 8 ky [27,30].…”