Abstract
BackgroundThe 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.ResultsAnalysis 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.ConclusionThis 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.
Highlights
The genetic diversity of the human microbiome holds great potential for shedding light on the history of our ancestors
Instead of a combined analysis of a set of 6 to 8 house keeping genes, as is usually performed with multi-locus sequence typing (MLST) for characterizing bacterial isolates [26], we examined genetic variation within single genes, thereby accounting for the multiple clonal types that exist within individuals
9 to 10 individuals tested positive in each country, except for Georgia which showed the lowest number of positive cases
Summary
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. It is generally recognized that the structure and diversity of the human microbiome is of medical importance at the species level and at the intra-species level given that. The fact that human history is characterized by numerous migration events with the microbiome being a permanent companion suggests that the global distribution of bacterial clones is likely to be biogeographically structured. The concept of a shared history and co-migration between humans and microbes has been exemplified in the case of Helicobacter pylori, whose genetic.
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