Microbiome profiles of environmental samples and animals have mostly been based on the analysis of genomic DNA [8] [9] [10] 13, 44, 45] . Further, studies on the microbiomes of humans or animals have been restricted to habitats known to harbor large collections of microorganisms, in particular skin, oral cavity or gut [12] [13] [14] [15] [46] [47] [48] . In this study, we sought evidence for viable microorganisms in lymph nodes, an organ hitherto believed to be largely amicrobic in the absence of overt disease [26] [27] [28] [29] . Our data demonstrate that transcriptional activity of a variety of bacteria and a limited number of archaea and viruses, including novel organisms, can be confirmed in healthy animals using a meta-transcriptomic approach.