Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and novel taxa
Year: 2020
Type: preprint
Study design: Observational Study
Abstract: Human gut microbiome research focuses on populations living in high-income countries or on the other end of the spectrum, namely non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world’s population. We present the first study evaluating gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyzed stool samples from adult females (age 40 - 72) living in rural Bushbuckridge municipality (n=118) or urban Soweto (n=51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterization of microbiomes of individuals living outside high-income countries, resulting in artificially low species-level beta diversity measurements. To improve reference databases, we generated complete genomes of undescribed taxa, including Treponema , Lentisphaerae, and Succinatimonas species. Our results suggest that the gut microbiome in South African populations do not exist along a simple “western-nonwestern” axis and that these populations contain microbial diversity that remains to be described.
Authors: Fiona B. Tamburini, Dylan Maghini, Ovokeraye H. Oduaran, Ryan Brewster, Michaella R. Hulley, Venesa Sahibdeen, Shane A. Norris, Stephen Tollman, Kathleen Kahn, Ryan G. Wagner, Alisha N. Wade, Floidy Wafawanaka, F. Xavier Gómez-Olivé, Rhian Twine, Zané Lombard, Scott Hazelhurst, Ami S. Bhatt
Language: English
Topic: Gut microbiota and health
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funders: National Science Foundation, Wellcome Trust, National Research Foundation, National Institutes of Health, Stanford Research Computing Center, Stanford University, Medical Research Council, National Human Genome Research Institute, National Cancer Institute, National Institute of Allergy and Infectious Diseases, Fogarty International Center, Stanford University Center for Innovation in Global Health, Stanford Cancer Institute
Awards: Strengthening and stabilising a demographic and health surveillance in Agincourt: foundation for a health and population research programme in South Africa's rural northeast, Emerging novel mechanisms of antibiotic resistance in the prevalent foodborne pathogen, Salmonella, G1119205115, G1289894384, G2649945114, G3198294062, Health, population and social transitions in rural Southern Africa: Elucidating pathways and testing interventions., Preventing cardiometabolic diseases in Africa: life-course and multi-sector approaches., G4029150292, G4469057728, Investigating and responding to health, population and social transitions in rural Southern Africa., G5111443808, Endocrine and metabolic diseases in rural South Africa-establishing burden and improving detection, G7414671634, G7746010289, G8186070293, G8276714428, G8488095431, G869355282, G8741868736, AWI-Gen Phase 2: Genomic and environmental risk factors for cardiometabolic disease in Africans, Stanford Cancer Institute
OpenAlex ID: W3028477838