Getting ahead of human-associated microbial decline in Africa: the urgency of sampling in light of epidemiological transition

Evidence is growing that human-associated early-life microbial diversity modulates health over the long term, via effects in the infant termed ‘immune and metabolic education’. Documenting high microbial diversity contexts, such as in Africa, thus, has rich potential for understanding this aspect of the landscape of health. Yet, change on the continent is occurring rapidly, and microbial communities are shifting as behaviors and diets are altered, and antibiotic use expands; we may be losing the opportunity to obtain relevant data. After introducing what is known about the effects of early life microbial diversity on late life health, we provide an overview of what is known of the current, and expected future, trajectory of human-associated microbial diversity in Africa, introducing data on the core drivers. We argue that critical insights may be lost if better understanding of infant microbial communities in Africa is not obtained soon.