Meta-genomics studies evaluating microbial rich communities were pioneered based on genomic DNA sequences [8] [9] [10] 13] . Thus, we compared genomic libraries prepared from retropharyngeal lymph node tissue of MD 72360, MD 80228, MD 84709, and MD 84730 with our data from transcript libraries derived from those animals (Fig. 1 ). Many sequences from the genomic DNA libraries were to non-coding regions and could not be used for taxonomic profiling (Fig 1B, Table S2 ). Based on proteincoding sequences, only four bacterial genera were identified in the comprehensive MEGAN analysis of the four genomic data sets. Xylella and Burkholderia were identified in MD 72360, Acidovorax was found in MD 84709, and Bartonella was found in both MD 84709 and MD 84730. Bartonella and Xylella, as well as a member of the beta retroviruses (found in MD 80228 and MD 84709), were identified only in the genomic DNA data, suggesting that they might not represent actively replicating organisms. These findings indicate that meta-transcriptomics may be the preferred method for detecting the viable endemic microbial community in the tissues of healthy animals.