Maghini Dylan G, Oduaran Ovokeraye H, Wirbel Jakob, Olubayo Luicer A Ingasia, Smyth Natalie, Mathema Theophilous, Belger Carl W, Agongo Godfred, Boua Palwendé R, Choma Solomon Sr, 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, 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.
bioRxiv. 2024 Mar 14:2024.03.13.584859. doi: 10.1101/2024.03.13.584859.
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 and species and gain of 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 . Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including and . 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.
人群研究对于理解肠道微生物群与地理、生活方式、遗传和环境因素之间的复杂相互作用至关重要。然而，占世界人口约84%的低收入和中等收入国家的人群被排除在大规模肠道微生物群研究之外。在此，我们介绍了AWI-Gen 2微生物群项目，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1803名女性进行了采样。通过深入接触从农村园艺社区到城市非正式定居点和后工业化社区等不同社区，我们捕捉到了代表世界人口更广泛范围的人群多样性。使用鸟枪法宏基因组测序，我们发现研究地点比疾病状态能解释更多的微生物变异。我们确定了与地理和生活方式有强烈关联的分类群，包括城市人群中某些物种的减少和另一些物种的增加。我们发现了大量原核生物和病毒的新物种，包括1005个新的细菌宏基因组组装基因组，并在某些物种中识别出系统地理学特征。最后，我们发现了一种HIV感染的微生物群特征，该特征由几个以前与HIV无关的分类群定义，包括某些物种。这项研究是迄今为止非洲个体肠道宏基因组最大规模的具有人群代表性的调查，并与广泛的临床生物标志物、人口数据和生活方式信息相结合，为微生物群相关的发现和研究提供了广泛的机会。
