| Dylan G Maghini, Ovokeraye H Oduaran, Jakob Wirbel, Luicer A Ingasia Olubayo, Natalie Smyth, Theophilous Mathema, Carl W Belger, Godfred Agongo, Palwendé R Boua, Solomon SR 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, Ami S Bhatt, Scott Hazelhurst Expanding the human gut microbiome atlas of Africa Journal Article In: bioRxiv : the preprint server for biology, 2024, ISSN: 2692-8205. @article{Maghini2024,
title = {Expanding the human gut microbiome atlas of Africa},
author = {Dylan G Maghini and Ovokeraye H Oduaran and Jakob Wirbel and Luicer A Ingasia Olubayo and Natalie Smyth and Theophilous Mathema and Carl W Belger and Godfred Agongo and Palwend\'{e} R Boua and Solomon SR Choma and F Xavier G\'{o}mez-Oliv\'{e} and Isaac Kisiangani and Given R Mashaba and Lisa Micklesfield and Shukri F Mohamed and Engelbert A Nonterah and Shane Norris and Hermann Sorgho and Stephen Tollman and Floidy Wafawanaka and Furahini Tluway and Mich\`{e}le Ramsay and Ami S Bhatt and Scott Hazelhurst},
url = {https://pubmed.ncbi.nlm.nih.gov/38559015/},
doi = {10.1101/2024.03.13.584859},
issn = {2692-8205},
year = {2024},
date = {2024-01-01},
journal = {bioRxiv : the preprint server for biology},
publisher = {bioRxiv},
abstract = {Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is 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 to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.},
keywords = {doi:10.1101/2024.03.13.584859, Dylan G Maghini, MEDLINE, National Center for Biotechnology Information, National Institutes of Health, National Library of Medicine, NCBI, NIH, NLM, Ovokeraye H Oduaran, PMC10980044, pmid:38559015, Preprint, PubMed Abstract, Scott Hazelhurst},
pubstate = {published},
tppubtype = {article}
}
Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is 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 to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research. |
