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

BMC Microbiology

F. B. Tamburini¹  A. S. Bhatt²  Z. Lombard³  V. Sahibdeen³  R. Twine⁴  A. N. Wade⁴  K. Kahn⁵  F. X. Gómez-Olivé⁵  R. G. Wagner⁵  S. M. Tollman⁵  S. A. Norris⁶  R. Brewster⁷  O. H. Oduaran⁸  S. Hazelhurst⁹ 

[1] Department of Genetics, Stanford University, Stanford, CA, USA;Department of Genetics, Stanford University, Stanford, CA, USA;School of Medicine, Stanford University, Stanford, CA, USA;Department of Medicine (Hematology), Stanford University, Stanford, CA, USA;Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa;MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa;MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa;INDEPTH Network, East Legon, Accra, Ghana;SAMRC Developmental Pathways for Health Research Unit, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa;School of Human Development and Health, University of Southampton, Southampton, UK;School of Medicine, Stanford University, Stanford, CA, USA;Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa;Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa;Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa;School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa;

关键词: 16S;    African microbiome;    South African microbiome;    Obesity;    Transitional microbiome;    Epidemiological transition;   

DOI  :  10.1186/s12866-020-02017-w

来源: Springer

【 摘 要 】

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 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.ResultsWe 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).ConclusionsAltogether, 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.

【 授权许可】

CC BY