Although 58 of the ticks were negative for SFGR by real-time PCR of the rompA gene and IGR, all of the ticks contained OTUs whose partial 16S rRNA gene segments aligned with SFGR in GenBank. The cause of this discrepancy may be due to the increased sensitivity of the Illumina sequencing platform compared to real-time PCR of rompA and IGR sequences and/or the presence of other Rickettsia spp. with highly conserved 16S rRNA genes but that lack rompA and IGR sequences complementary to the PCR primers used. Analysis of other genes would be required to resolve them at the species level (Eremeeva, Yu & Raoult, 1994; Regnery, Spruil & Plikaytis, 1991). Additional data support that more than two different Rickettsia species were present within the tick population tested. R. rhipicephali was detected by real-time PCR of the rompA gene and/or IGR in ticks that had OTU 837189 counts greater than 5900/tick, except for two ticks, T14-0667 and T14-0769 that had high OTU 837189 counts of 73,527 and 53,714, respectively, but were negative for R. rhipicephali. Similarly, R. philipii was detected in ticks with OTU 553807 counts ranging from 11 to 2,158, except for one sample, T14-0667, that had 884 counts of OTU 553807 yet was negative for R. philipii by real-time PCR of rompA gene and IGR. These findings are consistent with the presence of species of Rickettsia different from R. rhipicephali and R. philipii that could not be discriminated by the partial 16S rRNA gene or rompA and IGR sequences. The two most abundant Francisella OTUs, 840032 and 399541, accounted for over 90% of all Francisella OTUs and were 100% identical to Francisella-like endosymbionts (FLE) of D. occidentalis (GenBank accession numbers AY805304 and AY375402 for OTU 840032, and KU355875 for OTU 399541). Taken as a whole, these results are consistent with tick co-infection with a mixture of Rickettsias and FLEs.