Assessing genetic variation and gut microbiome diversity in South African ethnic groups: a scoping review protocol

Background: The gut microbiome is regarded as a forgotten organ, although it plays a crucial role in human health and disease. However, microbial composition can fluctuate significantly even in well-established cohorts in response to host behavioral patterns. Factors that can affect the function and structure of gut microbiota include diet, geographical location, and lifestyle. Although a healthy lifestyle plays a vital role in maintaining a healthy microbiome, the interactions among the host genome, ethnicity, and the microbial community remain unclear. Objective: This scoping review aims to identify, explore, and map how genetic variation and ethnicity affect the gut microbiome in South Africa. Methods and analysis: This protocol was developed using the Joanna Briggs Institute methodology for scoping reviews. The proposed study will use peer-reviewed articles and grey literature from PubMed, Scopus, ScienceDirect, and CINAHL via EBSCOhost and Google. The data accessed will be limited to January 2006 and November 2026. Two independent reviewers will screen the titles and abstracts of all publications that meet the inclusion and exclusion criteria. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses flow diagram will be used to document the selection process. The review will summarize and disseminate findings on the gut microbiome and genetic variation in the South African ethnic groups. Results: The scoping review is expected to be completed at least six months after the protocol is published.