Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most communities in the very diverse African continent. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To characterize the microbiome of African adults living in more mainstream lifestyle settings and investigate associations between the microbiome and obesity, we conducted a pilot study, designed collaboratively with community leaders, in two South African cohorts representative of urban and transitioning rural populations. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, we find that geographical location was more important for sample clustering than lean/obese status and observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in Bushbuckridge. Also, Prevotella, despite its generally high prevalence in the cohorts, showed an association with obesity. In comparisons with benchmarked datasets representative of non-Western populations, relatively higher abundance values were observed in our dataset for Barnesiella (log2fold change (FC) = 4.5), Alistipes (log2FC = 3.9), Bacteroides (log2FC = 4.2), Parabacteroides (log2FC = 3.1) and Treponema (log2FC = 1.6), with the exception of Prevotella (log2FC = − 4.7). Altogether, this work identifies putative microbial features associated with host health in a historically understudied community undergoing an epidemiological transition. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research.

中文翻译：

---

南非农村和城市人群的肠道微生物组分析揭示了生活方式转变人群的生物标志物

将非洲传统狩猎采集者和前农业社区与北美西部和欧洲城市和郊区的人群进行比较，清楚地表明饮食、生活方式和环境与肠道微生物组的组成有关。然而，人们对多样性非洲大陆大多数社区的肠道微生物组成知之甚少。南非拥有丰富多样的民族语言人口，正在经历持续的流行病学转变和肥胖患病率的同时激增，这在很大程度上归因于向更加西化的饮食习惯和越来越不活跃的生活方式的转变。为了描述生活在更主流生活方式环境中的非洲成年人的微生物组特征，并调查微生物组与肥胖之间的关联，我们与社区领袖合作，在代表城市和转型农村人口的两个南非队列中进行了一项试点研究。由于女性超重和肥胖率特别高，我们收集了 170 名 HIV 阴性女性（索韦托 51 名；布什巴克里奇 119 名）的单时间点粪便样本，对这些样本进行了 16S rRNA 基因测序，并将数据与同时收集人体测量数据。我们发现我们队列的整体肠道微生物组反映了他们正在进行的流行病学转变。具体来说，我们发现地理位置对于样本聚类比瘦/肥胖状态更重要，并且在 Bushbuckridge 观察到相对较高丰度的 Melainabacteria、Vampirovibrio（一种捕食性细菌）。此外，尽管普雷沃氏菌在人群中普遍流行，但它与肥胖有关。与代表非西方人群的基准数据集相比，我们的数据集中观察到 Barnesiella（log2fold 变化 (FC) = 4.5）、Alistipes (log2FC = 3.9)、Bacteroides (log2FC = 4.2)、Parabacteroides (log2FC) 的丰度值相对较高= 3.1) 和密螺旋体 (log2FC = 1.6)，但普氏菌 (log2FC = − 4.7) 除外。总而言之，这项工作确定了历史上未被充分研究、正在经历流行病学转变的社区中与宿主健康相关的假定微生物特征。此外，我们注意到社区参与对于非洲研究成功的关键作用，更多针对特定人群的研究对于为有针对性的干预措施提供信息以及为未来研究奠定基础的重要性。