The overall bacterial diversity and the number of unique transcripts assigned to each bacterial taxon varied among the samples. Notably, Helicobacter was only detected in the library constructed from MD 257 but there were 12 unique transcript-tags assigned to this genus. More commonly, bacterial taxon identification was based on a single tag. Many of the single transcript-tags came from MD 80228, which had the highest bacterial diversity profile of all libraries analyzed, and from MD 84730. Bacterial genera detected solely in either one or both of these two samples include Acinetobacter, Legionella, Enterobacter, Salmonella, Yersinia, Vibrio, Listeria, Mannheimia, and members of the Corynebacterineae, all of which contain known pathogens. In addition, both specimens depicted by far the highest numbers of reads taxonomically assigned to the family Enterobacteriaceae. The lowest diversity of bacterial genera was found in the MD OCT-pool, which was derived from eight different mule deer. Pooling RNA from several animals potentially increases the representation of transcripts common to all animals but might decrease the ability to detect transcripts that are unique to one animal. Consistent with this, the MD Bonner-pool, which was derived from four animals, provided a broader spectrum of bacterial genera than the MD OCT-pool. Thus, pooling samples did not improve our ability to detect microbial diversity in lymph node samples.