Short- and long-read metagenomics of South African gut microbiomes reveal a transitional composition and novel taxa

While human gut microbiome research has largely focused on western populations, with a small minority of studies investigating nonwestern agriculturalist and hunter-gatherer societies, most of the world’s population resides between these two lifestyle extremes. We present the first study evaluating gut microbiome composition of two transitioning South African populations using short- and long-read sequencing. We analyzed shotgun sequencing samples from adult females living in rural Bushbuckridge (n=117) or urban Soweto (n=51) and find that these microbiomes are intermediate between those of western populations and previously studied agriculturalist and hunter-gatherer African populations. We found that widely used reference collections are incomplete for nonwestern microbiomes, resulting in a larger portion of unclassified sequencing in transitional and nonwestern populations and within-cohort beta diversity patterns that are reversed compared to reference-agnostic sequence comparison patterns. To improve reference databases, we performed de novo metagenomic assembly of long-read sequencing data to generate complete genomes of undescribed taxa, including Treponema and Lentisphaerae species. Collectively, our results suggest that South Africa’s transitional lifestyle and epidemiological conditions are reflected in gut microbiota compositions, and that these populations contain microbial diversity that remains to be described. This work underscores the critical need to broaden the scope of human gut microbiome research and include understudied, nonwestern populations to improve the relevance and accuracy of microbiome discoveries to broader populations.