Our study confirms that there are viable microorganisms in intact lymph nodes of apparently healthy mule deer. In the analyzed samples, we identified members of all bacterial phyla, as well as archaea, a DNA virus and a Retrovirus. The bacteria were representative of organisms that are commensal to mule deer and to their external environment. For example, we detected the common rumen and intestine dwellers, Ruminococcus and Abiotrophia, based on transcript-and rRNA-tags, respectively, in most libraries, indicating that commensal gut and mucosal microorganisms may routinely be sampled in secondary lymphoid tissue, presumably from transient bacteremia. Streptomyces was the most common soil dwelling bacteria identified. Of interest, Legionella, which is found near hot springs, was identified only in an individual mule deer from the Yellowstone region. The finding of a considerable number of archaeal transcripts in MD OCT-pool and MD Bonner-pool libraries implies that members of this domain of life are likely present in mule deer habitats or resident in mule deer gastrointestinal tracts, as has been recently documented in humans [52] . Correspondingly, environmental bacteria identified in healthy deer lymph nodes may reflect the animal's habitat.