article · Nature
Large-scale gut microbiome studies historically underrepresent populations from low- and middle-income regions. A cross-sectional survey of 1,801 women across Burkina Faso, Ghana, Kenya and South Africa provides a broad assessment of gut metagenomic variation across diverse rural, horticultural, post-industrial and urban settings. Metagenomic sequencing revealed distinct microbial shifts linked to urbanisation, including the loss of Treponema and Cryptobacteroides species and an increase in Bifidobacterium species. The research reconstructed 1,005 bacterial metagenome-assembled genomes and identified antibiotic susceptibility as a possible cause for the absence of Treponema succinifaciens in urban cohorts. Additionally, the analysis identified a distinct gut microbiome signature associated with HIV infection, featuring bacteria such as Dysosmobacter welbionis and Enterocloster species not previously tied to the condition. Paired with clinical and demographic data, these resources present substantial opportunities for further microbiome discovery.
Most global microbiome research has overlooked populations in low- and middle-income nations, limiting the understanding of human microbial diversity. By capturing gut metagenomes across varied African communities and lifestyles, this work provides a critical benchmark for global health. It reveals how urban transitions and health conditions such as HIV reshape human gut ecosystems, aiding future clinical and epidemiological investigations.
This research represents an early-stage discovery resource for biotechnology, diagnostic and pharmaceutical developers investigating microbiome-based therapies. By detailing previously uncharacterised genomes and identifying bacterial markers linked to urbanisation and HIV infection, the dataset could inform future diagnostic biomarkers or targeted live biotherapeutic interventions. However, the findings are observational and foundational, remaining several steps removed from clinical development or market-ready commercial applications.
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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 lives<sup>1</sup>, are not equitably represented in large-scale gut microbiome research<sup>2-4</sup>. 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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DOI: 10.1038/s41586-024-08485-8
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