Investigating differences in modern human populations based on genetic markers is difficult since the human migration out of Africa resulted in a bottleneck that reduced the genetic diversity of modern humans outside Africa. Studying their differentiation would require genetic markers with fast evolutionary rates.
While the mutation rate of eukaryotic and prokaryotic organisms doesn’t vary a lot, the advantage of applying a proxy marker in terms of prokaryotic pathogens is the smaller generation time. The most commonly applied proxy marker is the gut pathogen Helicobacter pylori, which is characterized by its high genetic variability and by the vertical transmission from mother-to-child. The downsides of using H. pylori is that as a pathogen it cannot be found in every human individual and its recovery from the human stomach requires endoscopy.
An alternative source for prokaryotes as proxy markers is the saliva microbiome. It is the most diverse of all human microbiomes, available in all humans, transmitted vertically from mother-to-child and can be easily recovered by spiting in a tube. It has been shown that the inter-individual difference in the oral microbiome diversity is linked to the genetic difference of their hosts.
Therefore, I hope that investigating both the inter-individual diversity of the oral microbiome and intra-species diversity of candidate strains could lead to an increased resolution for the differentiation of their host populations.