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Background  The genetic diversity of the human microbiome holds great potential for shedding light on the history of our ancestors.  Helicobacter pylori  is the most prominent example as its analysis allowed a fine-scale resolution of past migration patterns including some that could not be distinguished using human genetic markers. However studies of  H. pylori  require stomach biopsies, which severely limits the number of samples that can be analysed. By focussing on the house-keeping gene  gdh  (coding for the glucose-6-phosphate dehydrogenase), on the virulence gene  gtf  (coding for the glucosyltransferase) of mitis-streptococci and on the 16S-23S rRNA internal transcribed spacer (ITS) region of the  Fusobacterium nucleatum/periodonticum -group we here tested the hypothesis that bacterial genes from human saliva have the potential for distinguishing human populations.    Results  Analysis of 10 individuals from each of seven geographic regions, encompassing Africa, Asia and Europe, revealed that the genes  gdh  and ITS exhibited the highest number of polymorphic sites (59% and 79%, respectively) and most OTUs (defined at 99% identity) were unique to a given country. In contrast, the gene  gtf  had the lowest number of polymorphic sites (21%), and most OTUs were shared among countries. Most of the variation in the  gdh  and ITS genes was explained by the high clonal diversity within individuals (around 80%) followed by inter-individual variation of around 20%, leaving the geographic region as providing virtually no source of sequence variation. Conversely, for  gtf  the variation within individuals accounted for 32%, between individuals for 57% and among geographic regions for 11%. This geographic signature persisted upon extension of the analysis to four additional locations from the American continent. Pearson correlation analysis, pairwise Fst-cluster analysis as well as UniFrac analyses consistently supported a tree structure in which the European countries clustered tightly together and branched with American countries and South Africa, to the exclusion of Asian countries and the Congo.    Conclusion  This study shows that saliva harbours protein-coding bacterial genes that are geographically structured, and which could potentially be used for addressing previously unresolved human migration events.

Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies