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Background  The Australian paralysis tick ( Ixodes holocyclus ) is of significant medical and veterinary importance as a cause of dermatological and neurological disease, yet there is currently limited information about the bacterial communities harboured by these ticks and the risk of infectious disease transmission to humans and domestic animals. Ongoing controversy about the presence of  Borrelia burgdorferi  sensu lato (the aetiological agent of Lyme disease) in Australia increases the need to accurately identify and characterise bacteria harboured by  I. holocyclus  ticks.    Methods  Universal PCR primers were used to amplify the V1-2 hyper-variable region of bacterial 16S rRNA genes present in DNA samples from  I. holocyclus  and  I. ricinus  ticks, collected in Australia and Germany respectively. The 16S amplicons were purified, sequenced on the Ion Torrent platform, and analysed in USEARCH, QIIME, and BLAST to assign genus and species-level taxonomy. Initial analysis of  I. holocyclus  and  I. ricinus  identified that > 95 % of the 16S sequences recovered belonged to the tick intracellular endosymbiont “ Candidatus  Midichloria mitochondrii” (CMM). A CMM-specific blocking primer was designed that decreased CMM sequences by approximately 96 % in both tick species and significantly increased the total detectable bacterial diversity, allowing identification of medically important bacterial pathogens that were previously masked by CMM.    Results   Borrelia burgdorferi  sensu lato was identified in German  I. ricinus , but not in Australian  I. holocyclus  ticks. However, bacteria of medical significance were detected in  I. holocyclus  ticks, including a  Borrelia  relapsing fever group sp.,  Bartonella henselae,  novel “ Candidatus  Neoehrlichia” spp.,  Clostridium histolyticum ,  Rickettsia  spp., and  Leptospira inadai .    Conclusions  Abundant bacterial endosymbionts, such as CMM, limit the effectiveness of next-generation 16S bacterial community profiling in arthropods by masking less abundant bacteria, including pathogens. Specific blocking primers that inhibit endosymbiont 16S amplification during PCR are an effective way of reducing this limitation. Here, this strategy provided the first evidence of a relapsing fever  Borrelia  sp. and of novel “ Candidatus  Neoehrlichia” spp. in Australia. Our results raise new questions about tick-borne pathogens in  I. holocyclus  ticks.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-015-0958-3) contains supplementary material, which is available to authorized users.

parasites and vectors

Inhibition of the endosymbiont “Candidatus Midichloria mitochondrii” during 16S rRNA gene profiling reveals potential pathogens in Ixodes ticks from Australia