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

2022; Nature Portfolio; Volume: 13; Issue: 1 Linguagem: Inglês

10.1038/s41467-021-27917-x

2041-1723

Fiona B. Tamburini, Dylan G. Maghini, Ovokeraye H. Oduaran, Ryan Brewster, Michaella 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, Godfred Agongo, Marianne Alberts, Stuart A. Ali, Gershim Asiki, Vukosi Baloyi, Palwendé Romuald Boua, Jean‐Tristan Brandenburg, Francisco C. Ceballos, Tinashe Chikowore, Solomon Choma, Ananyo Choudhury, Nigel J. Crowther, Cornelius Debpuur, Mwawi Gondwe, Scott Hazelhurst, Kathleen Kahn, Christopher Khayeka–Wandabwa, Isaac Kisiangani, Catherine Kyobutungi, Zané Lombard, Given Mashaba, Felistas Mashinya, Theo Mathema, Lisa K. Micklesfield, Shukri F Mohamed, Busisiwe Mthembu, Freedom Mukomana, Engelbert A. Nonterah, Shane A. Norris, Ovokeraye H. Oduaran, Abraham Oduro, F. Xavier Gómez‐Olivé, Michèle Ramsay, Osman Sankoh, Dhriti Sengupta, Natalie Smyth, Cassandra Claire Soo, Himla Soodyall, Herman Sorgho, Yaniv Swiel, Ernest Tambo, Pauline Tindana, Halidou Tinto, Furahini Tluway, Stephen Tollman, Rhian Twine, Alisha N. Wade, Ryan G. Wagner, Henry Wandera, Chodziwadziwa Kabudula, Daniel Ohene‐Kwofie, Floidy Wafawanaka, Scott Hazelhurst, Ami S. Bhatt,

Indigenous Studies and Ecology

Human 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.