Mapping the literature on host genetic variation, ancestry, ethnicity and gut microbiome diversity in South African populations: a scoping review protocol

Background: The gut microbiome is shaped by diet, geography, lifestyle, medication, disease status and host-related factors. In South Africa, where human genetic diversity, population history, urbanization and dietary transitions intersect, the relationships among self-reported ethnicity, genetic ancestry, host genetic variation and gut microbiome diversity remain insufficiently mapped. Objectives: This scoping review aims to map the extent, nature and characteristics of in relation to host genetic variation, measured genetic ancestry, self-reported ethnicity, or a clearly defined population group in South African human populations. Methods: The review will follow Joanna Briggs Institute guidance for scoping reviews and will be reported according to PRISMA-ScR. Searches will be conducted in bibliographic databases and publisher/platform sources including PubMed, Scopus, Web of Science, CINAHL via EBSCOhost and ScienceDirect. For grey literature, targeted searches will be conducted in Google Scholar, institutional repositories, ProQuest Dissertations & Theses and relevant African research platforms. The first 100 results from Google Scholar will be screened for each search string, or until saturation is reached. Literature published from January 2000 to the final search date will be eligible. Two independent reviewers will screen titles, abstracts and full texts. Data will be charted on study characteristics, population descriptors, microbiome methods, host-genetic or ancestry measures, ethnicity definitions, confounders and key findings. Studies that focus solely on geographic, dietary, lifestyle, linguistic, or environmental differences will be excluded. Results: The protocol has been developed, and the review is expected to be completed within six months of protocol publication. The final review will summarize available evidence, methodological approaches and research gaps. Conclusions: This review is expected to clarify how South African gut microbiome studies have incorporated ethnicity, ancestry and host genetic variation, and will identify priorities for future microbiome–genomics research. The review will avoid treating ethnicity as a biological proxy and will distinguish, where possible, among social, geographic and genetic descriptors.