Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle trans
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RESEARCH ARTICLE
Open Access
Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition O. H. Oduaran1,3* , F. B. Tamburini2, V. Sahibdeen3, R. Brewster4, F. X. Gómez-Olivé5,6, K. Kahn5,6, S. A. Norris7,8, S. M. Tollman5,6, R. Twine5, A. N. Wade5, R. G. Wagner5,6, Z. Lombard3, A. S. Bhatt2,4,9 and S. Hazelhurst1,10*
Abstract Background: Comparisons 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 communities in the very diverse African continent. 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 characterize the microbiome of African adults living in more mainstream lifestyle settings and investigate associations between the microbiome and obesity, we conducted a pilot study, designed collaboratively with community leaders, in two South African cohorts representative of urban and transitioning rural populations. 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. Results: We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, we find that geographical location was more important for sample clustering than lean/ obese status and observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in Bushbuckridge. Also, Prevotella, despite its generally high prevalence in the cohorts, showed an association with obesity. In comparisons with benchmarked datasets representative of non-Western populations, relatively higher abundance values were observed in our dataset for Barnesiella (log2fold change (FC) = 4.5), Alistipes (log2FC = 3.9), Bacteroides (log2FC = 4.2), Parabacteroides (log2FC = 3.1) and Treponema (log2FC = 1.6), with the exception of Prevotella (log2FC = − 4.7). (Continued on next page)
* Correspondence: [email protected]; [email protected] 1 Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to
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