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Study Detects Gut Microbiome Differences in African Agriculturist, Hunter-Gatherer Populations

NEW YORK (GenomeWeb) – An international team led by investigators at the University of Minnesota has uncovered new details about the relationship between diet and gut microbial community composition, using samples from hunter-gatherer and agricultural populations in the Central African Republic.

The researchers used 16S ribosomal RNA gene sequencing to identify microbial community members in fecal samples from dozens of individuals from Central African Republic's Dzanga region, including members of a rainforest hunter-gatherer group — the BaAka — and individuals from a Bantu-speaking population practicing subsistence agriculture with some westernized diet and lifestyle practices.

The team's results, published online today in Cell Reports, revealed a diet-related gut microbiome continuum: the Bantu gut microbiomes edged closer to those described in individuals from the US. At the other end of the spectrum, the BaAka individuals had gut microbiomes that seemed to coincide with more traditional diets, resembling those described in studies of other hunter-gatherer groups.

"The study supports the idea that diet is the most important driver of microbiome composition in humans … [O]ur microbiome is a very important reflection of lifestyle," first author Andres Gomez — a University of Minnesota researcher at the time of the study, who is now affiliated with the J. Craig Venter Institute — said in a statement.

The BaAka hunter-gatherers, a Western African pygmy population, have been included in past genomic studies, including a PLOS Genetics paper published in 2012 by the University of Pennsylvania's Sarah Tishkoff and colleagues that described the search for genetic factors involved in short stature in the BaAka and other pygmy populations in Cameroon. Tishkoff and her colleagues also included BaAka individuals in a 2012 Cell study that compared and contrasted whole genome sequences from Western Pygmy individuals in Cameroon with sequences found in hunter-gatherers from click-speaking populations in Tanzania.

For this new study, Gomez and his colleagues became interested in the interplay between lifestyle and the gut microbiome in the more traditional BaAka and the nearby, more industrialized Bantu. They used the Roche 454 FLX Titanium instrument to sequence 16S gene segments in DNA from fecal samples of 28 BaAka and 29 Bantu individuals, and used gas chromatography and mass spectrometry to measure fecal metabolite levels in a subset of the BaAka samples.

The team noted that the traditional gut microbial features found in the BaAka are likely a consequence of diet and lifestyle differences, coupled with population-specific phenotypes and adaptations. For example, specific microbes present in the BaAka gut seemed to coincide with the high fiber, high starch foods they consume, including wild yams and koko leaves. The BaAka gut microbiomes had particularly high representations of bacteria from Prevotellaceae and Clostridiaceae families, along with Treponema and Prevotella species.

In the BaAka individuals' fecal metabolome, meanwhile, the researchers saw lipid- and amino acid-related metabolites, suspected of coming from dietary items such as game meat, fish, and fatty nuts, along with metabolites associated with bacterial pathogens.

On the other hand, Bantu individuals had lower levels of Prevotellaceae, Clostridiaceae, Treponema, and Prevotella genera in their gut communities — patterns that resembled those in the gut microbiomes of American individuals tested for the Human Microbiome Project, albeit to a lesser extent. Those changes were coupled with an apparent boost in representation by genes from metabolic pathways involved in carbohydrate use and the degradation of xenobiotics such as food additives.

Even so, the Bantu gut microbiomes maintained an overall phylogenetic diversity that eclipsed that described in gut microbial communities in the US, and was on par with the diversity in BaAka gut microbiomes. And the BaAka and Bantu microbiomes shared more general features with one another than with gut microbiomes in the American individuals, despite the Bantu microbiome shift toward more industrialized features.