Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa

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dc.contributor.authorFiona B Tamburini
dc.contributor.authorDylan Maghini
dc.contributor.authorOvokeraye H Oduaran
dc.contributor.authorRyan Brewster
dc.contributor.authorMichaella R Hulley
dc.contributor.authorVenesa Sahibdeen
dc.contributor.authorShane A Norris
dc.contributor.authorStephen Tollman
dc.contributor.authorKathleen Kahn
dc.contributor.authorRyan G Wagner
dc.contributor.authorAlisha N Wade
dc.contributor.authorFloidy Wafawanaka
dc.contributor.authorF Xavier Gómez-Olivé
dc.contributor.authorRhian Twine
dc.contributor.authorZané Lombard
dc.contributor.authorH3Africa AWI-Gen Collaborative Centre
dc.contributor.authorScott Hazelhurst
dc.contributor.authorAmi S Bhatt
dc.date.accessioned2024-04-30T06:43:18Z
dc.date.available2024-04-30T06:43:18Z
dc.date.issued2022-02-22
dc.description.abstractHuman gut microbiome research focuses on populations living in high-income countries and to a lesser extent, 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. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (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 characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis and contains undescribed microbial diversity.
dc.description.librarianPM2023
dc.facultyFaculty of Health Sciences
dc.identifier.urihttps://hdl.handle.net/10539/38400
dc.language.isoen
dc.schoolPublic Health
dc.titleShort- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa
dc.typeArticle
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