Human gut microbiome research focuses on populations living in high-income countries or on the other end of the spectrum, namely non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world’s population. We present the first study evaluating gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyzed stool samples from adult females (age 40 - 72) living in rural Bushbuckridge municipality (n=118) or urban Soweto (n=51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterization of microbiomes of individuals living outside high-income countries, resulting in artificially low species-level beta diversity measurements. To improve reference databases, we generated complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas species. Our results suggest that the gut microbiome in South African populations do not exist along a simple “western-nonwestern” axis and that these populations contain microbial diversity that remains to be described.

中文翻译：

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南非城市和农村肠道微生物组的短读长和长读长宏基因组学揭示了一种过渡组成和新型分类群

人类肠道微生物组研究的重点是生活在高收入国家或另一端的人群，即非城市农业和狩猎采集社会。这些极端之间的研究缺乏限制了我们对肠道微生物群如何与世界上大多数人口的健康和疾病相关的理解。我们提出了第一项使用短读长和长读长测序评估南非人口转变中肠道微生物组组成的研究。我们分析了居住在 Bushbuckridge 市农村（n=118）或索韦托城市（n=51）的成年女性（40-72 岁）的粪便样本，发现这些微生物群在分类学上介于生活在高收入国家和传统社区。我们证明，对于生活在高收入国家以外的个人的微生物组的特征描述，参考集合是不完整的，导致人为地降低了物种水平的 beta 多样性测量。为了改进参考数据库，我们生成了未描述分类群的完整基因组，包括密螺旋体、 Lentisphaerae 和Succinatimonas种。我们的研究结果表明，南非人群的肠道微生物组并不存在于简单的“西方-非西方”轴上，这些人群包含的微生物多样性仍有待描述。