Species-Level Profiling of Ixodes pacificus Bacterial Microbiomes Reveals High Variability across Short Spatial Scales at Different Taxonomic Resolutions

Background and Aims: Outbreaks of severe and chronic tick-borne diseases (TBDs) are on the rise. This is through the transmission of infectious disease agents to humans during tick feeding. The transmission rate and extent of microbial exchange, however, vary based on the tick microbiome composition. While select microbes are determined to be members of the normal tick microbiome and others are clearly recognized mammalian and/or avian pathogens, the status of many other members of the tick microbiota with respect to human and alternate host pathogenesis remains unclear. Moreover, the species-level 16S microbiome of prominent TBD vectors, including Ixodes pacificus, have not been extensively studied. To elucidate the I. pacificus microbiome composition, we performed a pan-domain species-specific characterization of the bacterial microbiome on adult I. pacificus ticks collected from two regional parks within Western California. Our methods provide for characterizing nuances within cohort microbiomes and their relationships to geo-locale of origin, surrounding fauna, and prevalences of known and suspected pathogens in relation to current TBD epidemiological zones. Methods: Ninety-two adult I. pacificus bacterial microbiomes were characterized using a high-fidelity, pan-domain, species-specific, full-length 16S rRNA amplification method using circular consensus sequencing performed on the Pacific Biosciences Sequel platform. Data analyses were performed with the MCSMRT data analysis package and database. Results: The species-specific I. pacificus microbiome composition illustrates a complex assortment of microflora, including over 900 eubacterial species with high taxonomic diversity, which was revealed to vary by sex and geo-locale, though the use of full-length 16S gene sequencing. The TBD-associated pathogens, such as Borrelia burgdorferi, Anaplasma phagocytophilum, and Rickettsia monacensis, were identified along with a host of bacteria previously unassociated with ticks. Conclusion: Species-level taxonomic classification of the I. pacificus microbiome revealed that full-length bacterial 16S gene sequencing is required for the granularity to elucidate the microbial diversity within and among ticks based on geo-locale.