Dylan Maghini and Luicer Olubayo

Researchers, Sydney Brenner Institute for Molecular Bioscience, University of Witwatersrand, Johannesburg, SOUTH AFRICA

Expanding the human gut microbiome atlas of Africa

Host:S. Cacciatore


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. 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 and 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.

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