Gut Microbiome Profiling of a Rural and Urban South African Cohort Reveals Biomarkers of a Population in Lifestyle Transition

Abstract

BackgroundComparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most African adults. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To better characterize the microbiome of African adults living in more mainstream lifestyle settings and to investigate associations between the microbiome and obesity, we conducted a pilot study in two South African cohorts that are representative of urban and rural populations. The study was designed collaboratively with community leaders. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. ResultsWe found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, our results show a relatively higher than expected abundance of Western gut-associated taxa such as Barnesiella and the presence of Bifidobacteria and Bacteroides together with the more traditionally non-Western gut-associated Prevotella, Treponema and Succinivibrio. Interestingly, we observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in the rural cohort. We also found Prevotella, despite its generally high prevalence relative to all taxa present in the cohort, to be associated with obesity. ConclusionsAltogether, this work identifies putative microbial features associated with host health in a historically understudied community. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research in this regard.