Data for: Multi-omics analysis identifies symbionts and pathogens of blacklegged ticks (Ixodes scapularis) from a Lyme disease hotspot in southeastern Ontario, Canada
Creators: name: Paulson, Amber
name: Colautti, Robert
Publisher: name: Zenodo
Year: 2022
Subjects: Lyme disease
16S metabarcoding
Ixodes scapularis
tick-borne diseases
transcriptomics
Anaplasma
Rickettsia
Borrelia
South Bay virus

description: Ticks in the family Ixodidae are recognized as important vectors of zoonoses including Lyme disease (LD), which is caused by spirochete bacteria from the <em>Borreliella</em> (<em>Borrelia</em>) <em>burgdorferi</em> sensu lato (<em>Bbsl</em>) complex. The blacklegged tick (<em>Ixodes scapulars</em>) continues to expand across Canada, creating hotspots of elevated LD risk at the leading edge of its expansion range. Current efforts to understand the risk of pathogen transmission associated with <em>I. scapularis</em> in Canada focus primarily on targeted screens, while variation in the tick microbiome remains poorly understood. Using multi-omics consisting of 16S metabarcoding and ribosome-depleted, whole-shotgun RNA transcriptome sequencing, we examined the microbial communities associated with adult <em>I. scapularis</em> (N = 32), sampled from four tissue types (whole tick, salivary glands, midgut, and viscera) and three geographical locations within an LD hotspot near Kingston, Ontario. The communities consisted of both endosymbiotic and known or potentially pathogenic microbes, including RNA viruses, bacteria, and a <em>Babesia</em> sp. intracellular parasite. We show that β-diversity is significantly higher between individual tick salivary gland and midgut bacterial communities, compared to whole ticks; while linear discriminant analysis (LDA) effect size (LEfSe) determined that the three potentially pathogenic bacteria detected by V4 16S rDNA sequencing were also discriminatory for dissected tissues only, including a <em>Borrelia</em> from the <em>Bbsl</em> complex, <em>Borrelia miyamotoi</em>, and <em>Anaplasma phagocytophilum. </em>Importantly, we find co-infection of <em>I. scapularis</em> by multiple microbes, in contrast to diagnostic protocols for LD, which typically focus on infection from a single pathogen of interest (<em>B. burgdorferi</em> sensu stricto).
description: All code is based on the dada2 pipeline in R, which uses text-based files. Funding provided by: Government of Canada<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000023<br>Award Number: Funding provided by: Queen's University<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100003321<br>Award Number: Funding provided by: Ontario Government<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100013873<br>Award Number:
description: See methods in paper, supplementary material, and README.md file. Latest version of the analysis pipeline available on GitHub: https://github.com/damselflywingz/tick_microbiome A Small Read Archive of this sequencing data is available on GenBank under Accession: SRR17194087 - 16S of Ixodes: 2016-2017 A Sequence Read Archive of this sequencing data is available on GenBank under Accession: SRR17194086