The key question behind this study was whether viable microorganisms could be detected within healthy mammalian lymphoid organs by employing massively parallel sequencing coupled with computational techniques able to detect transcripts of microorganisms among the abundant transcripts of the mule deer host. Lymph nodes are the specific replication sites for certain pathogenic viruses and bacteria [24] [25] [26] [27] [28] [29] . Moreover, although the blood and the lymph systems are considered to be essentially free of viable microorganisms in healthy individuals, the transient and often asymptomatic presence of both bacteria and viruses have been detected in the circulation [30, 31] . Phagocytic cells engulf these microbes and migrate to lymph nodes. Thus, lymph nodes should concentrate the commensal, endemic, and potential pathogenic microbial communities of a host species.