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Background  Ticks of the group  Rhipicephalus sanguineus  ( sensu lato ) are distributed worldwide and are major pathogen vectors of both dogs and humans. Previous phylogenetic reconstructions have suggested the existence of two main lineages within this group, “Tropical” and “Temperate”. Symbiotic interactions contribute to vector development, survival, reproduction and competence. The diversity of microbial communities associated with different populations of  R. sanguineus  ( s.l. ) remains poorly characterized, however, this knowledge will aid in future studies of hosts-microbiota-pathogen interactions. To gain insight into the bacterial communities associated with  R. sanguineus  ( s.l. ) ticks, 40 specimens from France, Senegal and Arizona were analyzed by high-throughput  16S  amplicon sequencing. All tick specimens were taxonomically classified using the mitochondrial  12S  rDNA gene, which provides sufficient phylogenetic resolution to discriminate different lineages of  R. sanguineus .    Results    Rhipicephalus sanguineus  ( s.l. ) samples from Senegal belonged to the “Tropical” lineage, samples from France belonged to the “Temperate” lineage, whereas both lineages were identified in samples from Arizona. Regardless of origin, each bacterial microbiota was dominated by three genera:  Coxiella ,  Rickettsia  and  Bacillus .  Rickettsia  and  Coxiella  were the two main genera found in females whereas males had a higher proportion of  Bacillus . Significant differences of relative abundances were evidenced between specimens from different geographical origins.    Conclusions  This study highlights differences in the microbiota composition within  R. sanguineus  ( s.l. ) specimens from different genotypes, genders and geographical origins. This knowledge will help in future studies of the symbiotic interactions, biology and vector competence of the  R. sanguineus  ( s.l. ) complex.    Electronic supplementary material  The online version of this article (10.1186/s13071-017-2352-9) contains supplementary material, which is available to authorized users.

Bacterial microbiota associated with Rhipicephalus sanguineus (s.l.) ticks from France, Senegal and Arizona