In conclusion, our study demonstrates that endemic microbiota can be detected in lymph nodes of healthy animals using metatranscriptomic approaches. These results suggest that metatranscriptomic analyses of secondary lymphoid organs could be valuable in monitoring endemic infections in wildlife or livestock as well as in detecting novel infectious organisms with the potential for causing emerging zoonotic or epizootic infectious diseases. Further, these studies have the potential to cast new light on the diversity of life within and among individuals.