Expanding the human gut microbiome atlas of Africa

Dylan G. Maghini, Ovokeraye H. Oduaran, Luicer A. Ingasia Olubayo, Jane A. Cook, Natalie Smyth, Theophilous Mathema, Carl W. Belger, Godfred Agongo, Palwendé R. Boua, Solomon S. R. Choma, F. Xavier Gómez-Olivé, Isaac Kisiangani, Given R. Mashaba, Lisa Micklesfield, Shukri F. Mohamed, Engelbert A. Nonterah, Shane Norris, Hermann Sorgho, Stephen Tollman, Floidy Wafawanaka, Furahini Tluway, Michèle Ramsay, Jakob Wirbel, Ami S. Bhatt () and Scott Hazelhurst ()
Additional contact information
Dylan G. Maghini: University of the Witwatersrand
Ovokeraye H. Oduaran: University of the Witwatersrand
Luicer A. Ingasia Olubayo: University of the Witwatersrand
Jane A. Cook: Stanford University
Natalie Smyth: University of the Witwatersrand
Theophilous Mathema: University of the Witwatersrand
Carl W. Belger: University of the Witwatersrand
Godfred Agongo: C. K. Tedam University of Technology and Applied Sciences
Palwendé R. Boua: University of the Witwatersrand
Solomon S. R. Choma: University of Limpopo
F. Xavier Gómez-Olivé: University of the Witwatersrand
Isaac Kisiangani: African Population Health and Research Center
Given R. Mashaba: University of Limpopo
Lisa Micklesfield: University of the Witwatersrand
Shukri F. Mohamed: African Population Health and Research Center
Engelbert A. Nonterah: Ghana Health Science
Shane Norris: University of the Witwatersrand
Hermann Sorgho: Institut de Recherche en Sciences de la Santé
Stephen Tollman: University of the Witwatersrand
Floidy Wafawanaka: University of the Witwatersrand
Furahini Tluway: University of the Witwatersrand
Michèle Ramsay: University of the Witwatersrand
Jakob Wirbel: Stanford University
Ami S. Bhatt: Stanford University
Scott Hazelhurst: University of the Witwatersrand

Nature, 2025, vol. 638, issue 8051, 718-728

Abstract: Abstract Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors. However, low- and middle-income countries, in which approximately 84% of the world’s population lives1, are not equitably represented in large-scale gut microbiome research2–4. Here we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,801 women from Burkina Faso, Ghana, Kenya and South Africa. By engaging with communities that range from rural and horticultural to post-industrial and urban informal settlements, we capture a far greater breadth of the world’s population diversity. Using shotgun metagenomic sequencing, we identify taxa with geographic and lifestyle associations, including Treponema and Cryptobacteroides species loss and Bifidobacterium species gain in urban populations. We uncover 1,005 bacterial metagenome-assembled genomes, and we identify antibiotic susceptibility as a factor that might drive Treponema succinifaciens absence in urban populations. Finally, we find an HIV infection signature defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals so far, and paired with extensive clinical biomarkers and demographic data, provides extensive opportunity for microbiome-related discovery.

Date: 2025
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DOI: 10.1038/s41586-024-08485-8

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