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Abstract

The human microbiome is the sum of all microbiota, their genes, and their mobile
genetic elements associated with an individual. These microbiota, which include
bacteria, archaea, fungi, micro-eukaryotes and viruses, form complex ecological
communities across the human body, including the gastrointestinal tract and skin.
Ancient humans carried their microbiomes as they dispersed across the globe,
and some contemporary microbiota are known to have colonized humans prior to
out of Africa migrations. Yet how microbiomes co-evolved with their hosts, and
how present-day microbiomes relate to patterns of human migration remains
largely to be explored. Aside from a few exceptions, including dental calculus and
coprolite samples, ancient microbiomes cannot be studied directly in the same
manner as skeletal or archaeological artifacts, because they are not well pre-
served in human remains. However, genomic and metagenomic studies of pre-
sent day microbiomes across ethnicities and geography may allow inference of
human evolution and dispersal. Doing so requires microbiome data from across
the globe, but so far human microbiome research has mostly characterized popu-
lations from Europe, North America, and Asia. Much of the African microbiome
remains largely under-sampled, limiting inference for questions of co-evolution
and human dispersal. African populations harbor vast genomic and cultural diver-
sity, with some populations still relatively isolated from the microbially-disruptive
aspects of modern lifestyles (e.g., antibiotics, antimicrobial soap). This chapter
reviews our current understanding of the factors which shape the gut micro-
biome of living African populations, both industrialized and pre-industrialized, and
reviews efforts to use human-associated microbes as tracers of early human
migrations.