On average, 51% of total transcript-tags could be assigned to known taxa with a bit score cutoff of 50 (see Table S2 ). Of the assigned tags, 99.3% were of eukaryotic origin, predominantly matching to Bos taurus and other close relatives of mule deer that are represented in the protein database. Approximately 0.3% of the assigned tags were to bacteria. Proteobacteria represented 60% of all bacterial hits; Enterobacteriaceae in the Gammaproteobacteria were the most commonly identified within this group. Firmicutes and Actinobacteria represented 22% and 5% of the identified bacterial taxa. Table S3 lists all bacterial genera detected in the seven data sets. Transcripts assigned to Archaea, family Halobacteriaceae, were identified in both pooled samples but none of the individual libraries. Only 37 transcripts were assigned to viruses. Twenty-nine of these matched to the Retroviridae and Poxviridae while the remaining were to phages, insect viruses, and a single assignment to herpesvirus. These results suggest that representatives of many bacterial phyla, archaea, and two major virus families are transcriptionally active in mule deer retropharyngeal lymph nodes.