Maghini Dylan G, Oduaran Ovokeraye H, Olubayo Luicer A Ingasia, Cook Jane A, Smyth Natalie, Mathema Theophilous, Belger Carl W, Agongo Godfred, Boua Palwendé R, Choma Solomon S R, Gómez-Olivé F Xavier, Kisiangani Isaac, Mashaba Given R, Micklesfield Lisa, Mohamed Shukri F, Nonterah Engelbert A, Norris Shane, Sorgho Hermann, Tollman Stephen, Wafawanaka Floidy, Tluway Furahini, Ramsay Michèle, Wirbel Jakob, Bhatt Ami S, Hazelhurst Scott
Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
Department of Medicine (Hematology), Stanford University, Stanford, CA, USA.
Nature. 2025 Feb;638(8051):718-728. doi: 10.1038/s41586-024-08485-8. Epub 2025 Jan 29.
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, are not equitably represented in large-scale gut microbiome research. 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.
人群研究为深入了解肠道微生物群与地理、生活方式、基因和环境因素之间的相互作用提供了线索。然而，约84%的世界人口居住的低收入和中等收入国家在大规模肠道微生物群研究中未得到公平体现。在此，我们展示了非洲妇女肠道微生物群基因组学研究项目（AWI-Gen 2 Microbiome Project），这是一项横断面肠道微生物群研究，对来自布基纳法索、加纳、肯尼亚和南非的1801名妇女进行了采样。通过与从农村园艺社区到后工业化和城市非正式定居点等不同社区合作，我们涵盖了世界人口多样性的更广泛范围。使用鸟枪法宏基因组测序，我们确定了与地理和生活方式相关的分类群，包括城市人群中密螺旋体属和隐秘杆菌属物种的减少以及双歧杆菌属物种的增加。我们发现了1005个细菌宏基因组组装基因组，并确定抗生素敏感性是可能导致城市人群中琥珀酸密螺旋体缺失的一个因素。最后，我们发现了一种由几种以前未与HIV相关联的分类群所定义的HIV感染特征，包括韦氏失调菌和肠球菌属。这项研究是迄今为止对非洲个体肠道宏基因组进行的最大规模的具有人群代表性的调查，结合广泛的临床生物标志物和人口统计数据，为微生物群相关的发现提供了广泛机会。
