The sequence data was analyzed using the QIIME (Quantitative Insights Into Microbial Ecology) version 1.8.0 software program (Caporaso et al., 2010b). Raw sequence data was demultiplexed into samples by barcode and filtered by mean quality score below 25, homopolymers greater than 6, uncorrected barcodes, barcodes not found in the mapping file, chimeric sequences and mismatched primers. Sequences were grouped into operational taxonomic units (OTUs) at the 97% sequence similarity level using UCLUST (Edgar, 2010) and a consensus taxonomic classification was assigned to each representative OTU using the UCLUST classifier with a Greengenes 13_8 reference database (DeSantis et al., 2006) in which at least 90% of the sequences within the OTU matched the consensus taxonomic classification 16S rRNA gene. Sequences were aligned using PyNAST (Caporaso et al., 2010a) against the Greengenes 13_8 reference core set and a phylogenetic tree of the OTUs inferred using FastTree (Price, Dehal & Arkin, 2010). In order to remove spurious OTU’s and samples with low numbers of sequences, OTU’s that occurred only once in the data and samples with less than 150 OTUs were removed. Rickettsia, Francisella and other selected taxonomic sequence identifications were crosschecked against the NCBI nucleotide database using BLASTn. Sequence, OTU table and map files can be downloaded from Figshare: 10.6084/m9.figshare.2056275, 10.6084/m9.figshare.2068644, and 10.6084/m9.figshare.2056272, respectively.