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Expanding the human gut microbiome atlas of Africa

Expanding the human gut microbiome atlas of Africa
Expanding the human gut microbiome atlas of Africa
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 research2,3,4. 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.
0028-0836
718–728
Maghini, Dylan G.
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Oduaran, Ovokeraye H.
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Ingasia Olubayo, Lucier A.
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Cook, Jane A.
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Norris, Shane A.
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Smyth, Natalie
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Belger, Carl W.
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Agongo, Godfred
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Boua, Palwendé R.
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Choma, Solomon S.R.
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Gómez-Olivé, F. Xavier
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Kisiangani, Isaac
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Mashaba, Given R.
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Micklesfield, Lisa
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Mohamed, Shukri F.
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Nonterah, Engelbert A.
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Norris, Shane A.
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Sorgho, Hermann
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Tollman, Stephen
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Wafawanaka, Floidy
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Tluway, Furahini
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Ramsay, Michèle
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Wirbel, Jakob
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Bhatt, Ami S.
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Hazelhurst, Scott
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the AWI-Gen 2 Collaborative Centre
Maghini, Dylan G.
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Oduaran, Ovokeraye H.
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Ingasia Olubayo, Lucier A.
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Cook, Jane A.
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Norris, Shane A.
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Smyth, Natalie
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Mathema, Theophilous
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Belger, Carl W.
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Agongo, Godfred
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Boua, Palwendé R.
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Choma, Solomon S.R.
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Gómez-Olivé, F. Xavier
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Kisiangani, Isaac
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Mashaba, Given R.
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Micklesfield, Lisa
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Mohamed, Shukri F.
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Nonterah, Engelbert A.
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Norris, Shane A.
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Sorgho, Hermann
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Tollman, Stephen
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Wafawanaka, Floidy
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Tluway, Furahini
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Ramsay, Michèle
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Wirbel, Jakob
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Bhatt, Ami S.
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Hazelhurst, Scott
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Bhatt, Ami S. and Hazelhurst, Scott , the AWI-Gen 2 Collaborative Centre (2025) Expanding the human gut microbiome atlas of Africa. Nature, 638 (8051), 718–728, [10]. (doi:10.1038/s41586-024-08485-8).

Record type: Article

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 research2,3,4. 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.

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s41586-024-08485-8 - Version of Record
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Accepted/In Press date: 3 December 2024
Published date: 20 February 2025

Identifiers

Local EPrints ID: 503516
URI: http://eprints.soton.ac.uk/id/eprint/503516
ISSN: 0028-0836
PURE UUID: 1fb0a72d-5b8c-4a65-b2e0-ac7349eae984
ORCID for Shane A. Norris: ORCID iD orcid.org/0000-0001-7124-3788
ORCID for Shane A. Norris: ORCID iD orcid.org/0000-0001-7124-3788

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Date deposited: 04 Aug 2025 16:52
Last modified: 01 Oct 2025 02:03

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Contributors

Author: Dylan G. Maghini
Author: Ovokeraye H. Oduaran
Author: Lucier A. Ingasia Olubayo
Author: Jane A. Cook
Author: Shane A. Norris ORCID iD
Author: Natalie Smyth
Author: Theophilous Mathema
Author: Carl W. Belger
Author: Godfred Agongo
Author: Palwendé R. Boua
Author: Solomon S.R. Choma
Author: F. Xavier Gómez-Olivé
Author: Isaac Kisiangani
Author: Given R. Mashaba
Author: Lisa Micklesfield
Author: Shukri F. Mohamed
Author: Engelbert A. Nonterah
Author: Shane A. Norris ORCID iD
Author: Hermann Sorgho
Author: Stephen Tollman
Author: Floidy Wafawanaka
Author: Furahini Tluway
Author: Michèle Ramsay
Author: Jakob Wirbel
Author: Ami S. Bhatt
Author: Scott Hazelhurst
Corporate Author: the AWI-Gen 2 Collaborative Centre

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