Unbiased Characterization of the Microbiome and Virome of Questing Ticks

Abstract

Due to their vector capacity, ticks are ectoparasites of medical and veterinary significance. Modern sequencing tools have facilitated tick-associated microbiota studies, but these have largely focused on bacterial pathogens and symbionts. By combining 16S rRNA gene sequencing with total RNA-sequencing methods, we aimed to determine the complete microbiome and virome of questing, female Ixodes holocyclus recovered from coastal, north-eastern New South Wales (NSW), Australia. We present, for the first time, a robust and unbiased method for the identification of novel microbes in ticks that enabled us to identify bacteria, viruses, fungi and eukaryotic pathogens. The dominant bacterial endosymbionts were Candidatus Midichloria sp. Ixholo1 and Candidatus Midichloria sp. Ixholo2. Candidatus Neoehrlichia australis and Candidatus Neoehrlichia arcana were also recovered, confirming that these bacteria encompass I. holocyclus’ core microbiota. In addition, seven virus species were detected—four previously identified in I. holocyclus and three novel species. Notably, one of the four previously identified virus species has pathogenic potential based on its phylogenetic relationship to other tick-associated pathogens. No known pathogenic eukaryotes or fungi were identified. This study has revealed the microbiome and virome of female I. holocyclus from the environment in north-eastern NSW. We propose that future tick microbiome and virome studies utilize equivalent methods to provide an improved representation of the microbial diversity in ticks globally.

Metatranscriptomic profiling reveals diverse tick‐borne bacteria, protozoans and viruses in ticks and wildlife from Australia

“…The complete or partial genomes of 12 viruses were identified in tick samples (Table 2). The virome of I. holocyclus has been interrogated previously (Chandra et al, 2021;Harvey et al, 2019;O'Brien et al, 2018), and seven of the eight viruses identified are 6).…”

Extended characterisation of five archival tick-borne viruses provides insights for virus discovery in Australian ticks

“…However, the presence of PVL1 in the viscera and salivary glands of ticks from Queensland is particularly interesting in the context of IhIV, which was also identified in both the salivary glands and viscera of I. holocyclus ticks but did not replicate in ISE6 cells [ 34 ]. Neither the four virus-like sequences described in this study nor their relatives described in [ 20 ] were identified in a recent meta-transcriptomic study performed on unfed adult I. holocyclus ticks collected in Northern NSW [ 21 ].…”

“…Recent meta-transcriptomic surveys of ticks from New South Wales (NSW), Australia, have identified a number of novel virus sequences including Shelly Headland virus, which groups with the human pathogens Colorado tick fever virus and Eyach virus [ 20 , 21 ]. While next generation sequencing technologies are an invaluable asset in the field of virus discovery, isolation of viruses of interest is necessary to further our understanding of host range and pathogenesis for potential emerging viruses [ 22 ].…”

A global dataset of microbial community in ticks from metagenome study

“…An increasing number of tick-borne pathogens have been reported, heartland virus 11 , tick-borne encephalitis virus 12 , Borrelia burgdorferi sensu lato 13 , Rickettsia rickettsi 14 , severe fever with thrombocytopenia syndrome virus 8 , are just a few examples of important pathogens that pose threats to human health. However, the diversity of tick-borne infectious diseases remained underestimated, since the investigations tended to be heavily biased toward research on microorganisms that infect humans or animals of economic and social importance 15 , 16 . The advent of advanced technologies such as high-throughput sequencing, meta-genomics, meta-transcriptomics, etc., had enabled a systematic understanding on a high variety of pathogenic or non-pathogenic, known or unknown, endogenous or exogenous microorganisms that are carried by ticks 9 , 15 , 16 .…”