Use of the ion torrent PGM for studying the microbiome and metagenome of ticks

We used the Ion Torrent Personal Genome Machine to examine the microbiome and metagenome of several hard tick species. Our initial analyses of the platform with the Ion 318 chip (version 2) and 200 bp sequencing chemistry included the high depth 16S rRNA V4 gene region sequencing of one female Gulf Coast tick (Amblyomma maculatum) sample for which we had Roche 454 pyrosequencing data (V3-V5 region), and two shotgun metagenome sequencing runs with individual female American dog ticks (Dermacentor variabilis) from Georgia and Ohio. The 16S microbiome data was comparable to our existing 454 data, but with a much greater number of usable reads for a single sample, a larger number of identified OTUs, and very deep coverage of our two most common primary targets, the Francisella endosymbiont and Midichloria mitochondrii. Our shotgun sequencing analyses provided 2.8 - 4.5 million usable reads per tick.  Most of the sequence reads were from the ticks (chromosomes) which have genome sizes >3 Gbp. However, we were able to detect the Francisella-like endosymbiont (FLE) with low but broad genome coverage in both D. variabilis samples. In contrast, a quality (16X coverage) nearly-complete genome sequence was obtained for Rickettsia bellii from the Ohio tick. Sufficient Ion Torrent PGM read depth can be obtained for indexing (barcoding) tick microbiome samples and for direct sequencing of tick mitochondrial DNA and the genomes of high abundance agents in ticks.