Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with <i>Ixodes persulcatus</i>, <i>Ixodes pavlovskyi</i> and <i>Dermacentor reticulatus</i> Ticks

<div><p><i>Ixodes persulcatus</i>, <i>Ixodes pavlovskyi</i>, and <i>Dermacentor reticulatus</i> ticks inhabiting Western Siberia are responsible for the transmission of a number of etiological agents that cause human and animal tick-borne diseases. Because these ticks are abundant in the suburbs of large cities, agricultural areas, and popular tourist sites and frequently attack people and livestock, data regarding the microbiomes of these organisms are required. Using metagenomic 16S profiling, we evaluate bacterial communities associated with <i>I</i>. <i>persulcatus</i>, <i>I</i>. <i>pavlovskyi</i>, and <i>D</i>. <i>reticulatus</i> ticks collected from the Novosibirsk region of Russia. A total of 1214 ticks were used for this study. DNA extracted from the ticks was pooled according to tick species and sex. Sequencing of the V3-V5 domains of 16S rRNA genes was performed using the Illumina Miseq platform. The following bacterial genera were prevalent in the examined communities: <i>Acinetobacter (all three tick species)</i>, <i>Rickettsia (I</i>. <i>persulcatus</i> and <i>D</i>. <i>reticulatus)</i> and <i>Francisella (D</i>. <i>reticulatus)</i>. <i>B</i>. <i>burgdorferi</i> sensu lato and <i>B</i>. <i>miyamotoi</i> sequences were detected in <i>I</i>. <i>persulcatus</i> and <i>I</i>. <i>pavlovskyi</i> but not in <i>D</i>. <i>reticulatus</i> ticks. The pooled samples of all tick species studied contained bacteria from the Anaplasmataceae family, although their occurrence was low. DNA from <i>A</i>. <i>phagocytophilum</i> and <i>Candidatus</i> Neoehrlichia mikurensis was first observed in <i>I</i>. <i>pavlovskyi</i> ticks. Significant inter-species differences in the number of bacterial taxa as well as intra-species diversity related to tick sex were observed. The bacterial communities associated with the <i>I</i>. <i>pavlovskyi</i> ticks displayed a higher biodiversity compared with those of the <i>I</i>. <i>persulcatus</i> and <i>D</i>. <i>reticulatus</i> ticks. Bacterial community structure was also diverse across the studied tick species, as shown by permutational analysis of variance using the Bray-Curtis dissimilarity metric (<i>p</i> = 0.002). Between-sex variation was confirmed by PERMANOVA testing in <i>I</i>. <i>persulcatus</i> (<i>p</i> = 0.042) and <i>I</i>. <i>pavlovskyi</i> (<i>p</i> = 0.042) ticks. Our study indicated that 16S metagenomic profiling could be used for rapid assessment of the occurrence of medically important bacteria in tick populations inhabiting different natural biotopes and therefore the epidemic danger of studied foci.</p></div

Between-class analysis plots for taxon-based distances.

<p>A) MDS plot based on PCA for 150 taxa with the largest share. Principal component analysis was performed using package “ade4” with data scaling and centering. B) MDS plot based on the UniFRAC distance. Calculation of UniFRAC distance was performed using QIIME package. First and second principal components describe 40.69% and 32.82% of total variance respectively.</p

Heatmap based on 30 mostly reprepreted OTUs.

<p>Heatmap was constructed using euclidean distance method for log-scaled in-sample taxon share values. Sample names on the X axis consist of tick species, sex and library number. OTU names on the Y axis contain OTU's lowest common ancestor name and unique integer OTU key.</p

Diversity analysis.

<p>Diversity analysis.</p

Bar graph with the share of the 8 most represented taxa.

<p>Share of Rickettsiales order and Enterobacteriaceae family cover only hits that hadn't be included in the lower levels of these taxa.</p

Library description.

<p>Library description.</p