The microbiome of Ixodes scapularis, the vector of Lyme disease in the eastern United States, may influence rates of disease transmission by altering vector fitness and/or colonization by human pathogens. However, current research often focuses on bacterial communities, with much less is known about other microbial groups inhabiting I. scapularis. The objectives of this study were to characterize the bacterial, archaeal, fungal and protistan communities inhabiting I. scapularis, and to identify microbial taxa associated with colonization by Borrelia burgdorferi, the agent of Lyme disease in the United States. We performed multiplexed PCR with universal primers on 103 I. scapularis nymphs from southern Vermont, targeting 16S, ITS and 18S gene regions (for bacteria, fungi and protists, respectively). This was followed by high throughput sequencing on a HiSeq 2500 machine. For each primer pair we performed a sub-OTU analysis, with DADA2 denoising, using Qiime (v2-2018-11). The presence of B. burgdorferi infection was determined independently using quantitative real-time PCR. The correlation between bacterial and fungal beta diversity and B. burgdorferi presence/absence was analyzed with three-way Analysis of Similarity.
Results/Conclusions
The most abundant bacterial taxa were Rickettsia spp., Borrelia spp., Paraburkholderia spp., Sphingomonas spp. and Anaplasma spp., comprising 55% of sequences. ANOSIM revealed a significant difference in bacterial community composition by B. burgdorferi infection status with the Bray Curtis similarity matrix (R = 0.188, p = 1.4%). We identified a relatively abundant and influential Pseudomonas spp. with a sequence count that was 2.17x higher in nymphs lacking B. burgdorferi vs. B. burgdorferi-positive nymphs. For fungi, PERMDISP indicated a significant difference in average deviations from the centroid for B. burgdorferi-infected vs. uninfected ticks (p = 0.027). The most abundant fungal taxa were Malassezia spp. (13% of sequences). As a skin-associated taxa, this finding suggests that fungi are acquired during physical contact between vector and host. We detected the entomopathogenic fungi Beauvaria bassiana and Lecanicillium lecanii in six samples. With one 18S primer set we detected the wildlife pathogen Babesia odocoilei (7% of samples), and a Spirurida nematode (18% of samples). A one-way ANOSIM revealed a highly significant difference in bacterial communities based on Spirurida presence (R= 0.153; p = 2.20%). Thus, our analyses uncovered a variety of new insights into the I. scapularis microbiome.