There is emerging interest concerning the influence of human adaptation to varying environments on the gut microbiome. A recent study, published by the microbial ecologist Dr. Andres Gomez, a staff scientist at the J. Craig Venter Institute, studied diet and environmental factors in traditional populations and how they were associated with gut microbiome composition.


Gomez and his team analysed faecal microbiota composition and functional profiles in the BaAka and Bantu, two coexisting populations in the Central African Republic. The BaAka have hunter-gatherer lifestyles, which rely on wild game meat, vegetables, fruits, and fish for sustenance. On the other hand, the Bantu population relies on a market economy based on growing tubers and other vegetables, using flour-like products, and raising goats for meat; they also use antibiotics and other therapeutic drugs. Thus, the Bantu community incorporates some westernized lifestyle practices compared to the BaAka. The BaAka could represent ancient humans, with their Bantu neighbours representing a transition to the western lifestyle. The researchers also included data on US Americans from the Human Microbiome Project.


Although the gut microbiota of both traditional communities was compositionally similar, the abundance of specific microbes was different between them. Indeed, the abundance of traditional bacterial groups was diminished in the Bantu. The BaAka harboured increased abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome was dominated by Firmicutes. The Bacteroidetes phylum was more represented in the BaAka than the Bantu. Bacteroidetes is thought to help digest plant-derived fibre, and the ratio of Firmicutes to Bacteroidetes differs in obese and lean humans. Prevotella and Treponema genera are also involved in breaking down plant fibre and were lower in the Bantu.


The Bantu microbiome composition fell on a spectrum between the BaAka and western populations. The researchers hypothesized that the Bantu may have lost some traditional microbiome features as they have adopted more westernized subsistence patterns. Besides this, of the three populations studied, US Americans had the smallest number of Prevotella and Treponema. Taken together, these data suggest that giving up hunting and gathering may have somehow changed our gut microbiota to make them less diverse. “This is one of the first studies to show that the microbiota of a traditional agriculturalist group exhibit an intermediate state, between the microbiota of hunter-gatherers and that of a western industrialized society”, says first author Andres Gomez.


With regard to the functions of bacterial communities, the researchers found that both Bantu and US Americans exhibited higher abundances of metabolic pathways involved in the degradation of carbohydrates and chemical products, such as food additives and drugs. On the whole, westernization could lead to an increase in sugar and xenobiotic processing and a loss of traditional microbes. According to the authors, the gradient observed in the gut microbiome of coexisting BaAka and Bantu groups could be the way modern humans evolved their gut microbiomes.


To sum up, this study offers insight into how subsistence patterns, such as diet and environment, influence the gut microbiota of isolated populations. Other previous studies in Yanomami subjects in the Amazon, who had no documented previous contact with western people, and in rural Africans, suggested that diet is an important driver of microbiome composition in humans. As our microbiome differences are thought to be linked to metabolic and immune disorders in western populations, it is important to consider the impact of subsistence patterns in modulating gut microbiota composition.



Gomez A, Petrzelkova KJ, Burns MB, et al. Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep. 2016.


Clemente JC, Pehrsson EC, Blaser MJ, et al. The microbiome of uncontacted Amerindians. Sci Adv. 2015;1(3):e1500183. doi:10.1126/sciadv.1500183.


O’Keefe SJ, Li JV, Lahti L, et al. Fat, fibre and cancer risk in African Americans and rural Africans. Nat Commun. 2015;6:6342. doi:10.1038/ncomms7342.