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

BioRxiv : the Preprint Server for Biology
F. B. TamburiniAmi S Bhatt


While human gut microbiome research often focuses on western populations or nonwestern agriculturalist and hunter-gatherer societies, most of the world's population resides between these extremes. 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=117) or urban Soweto (n=51) and find that these microbiomes are intermediate between those of western industrialized and previously studied non-industrialized African populations. We demonstrate that reference collections are incomplete for nonwestern microbiomes, resulting in within-cohort beta diversity patterns that are in some cases reversed compared to reference-agnostic sequence comparison patterns. To improve reference databases, we generated complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas species. 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.

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