Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition

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). Conclusions Altogether, this work identifies putative microbial features associated with host health in a historically understudied community undergoing an epidemiological transition. 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.

Gut Microbiome Composition in Obese and Non-Obese Persons: A Systematic Review and Meta-Analysis

“…From a total of 2445 unique hits, 116 studies were selected for full-text review. Of these, 33 primary reports [17][18][19][20][21][32][33][34][35], including 32 studies met the criteria for inclusion and were selected for data extraction and synthesis.…”

Association between clinical and environmental factors and the gut microbiota profiles in young South African children

“…At phylum level, the microbiota profiles in this study were more similar to those of children in studies from the United States of America (USA) than those from Asia, Europe and Africa, with an equal distribution of Firmicutes and Bacteroidota 11 , 39 , 40 . This intermediate state between the microbial profiles of traditionally non-western microbiomes and western microbiomes has also been described in South African adults and has been attributed in part to urbanization and changes in diet 15 . A limitation of our study was that the dietary intake of the children was not recorded, and the impact of different diets on the gut microbiota could therefore not be investigated in this population.…”

“…There is a marked difference between the microbiota in urban westernised populations, and those in rural and developing settings, in adults and children 11 – 14 . In South Africa, the microbiota of adults represents a transitional state between the typical profiles in western populations and other African populations 15 . There is little known about the microbiota of children in South Africa, especially after infancy.…”

Blastocystis in the faeces of children from six distant countries: prevalence, quantity, subtypes and the relation to the gut bacteriome

“…Of note, our populations were very heterogeneous in the abundance of the two genera—this was expected, as both serve as markers for westernized versus non-westernized lifestyle, e.g. [ 41 ]. It is therefore conceivable that in our negative binomial models with the country of origin as one of the terms, an isolated association in one or two populations would not lead to the overall statistical significance.…”