Few viruses were identified with our analysis methods. This could represent the paucity of viruses in healthy animals. However, viral detection may be more difficult than bacterial identification using this technology in part due to extensive sequence diversity among viruses in the same family. For example, we were only able to detect the gamma retrovirus because a transcript was present which was homologous to a conserved region of the viral env gene, and the cervid poxvirus was detected because sequence data for this virus was present in the database. Other persistent viruses, such as herpes viruses (for which we detected a single transcript), would be expected to be present in some animals. However, detection of latent herpes virus infection may be difficult because protein-coding transcript levels are low and latent viruses express non-coding RNA [53] . In addition, viral detection can be compromised if viral sequence tags were misassigned to the host organism because of homology of viral and host genes. Thus, many virus tags might be found among the host transcripts or in the not-assigned or no-hits groups of the MEGAN analysis, which together comprise nearly half of the total sequenced transcript-tags of our data.