Exploring the archaeome: detection of archaeal signatures in the human body

Due to their fundamentally different biology, archaea are consistently overlooked in conventional microbiome surveys. Using amplicon sequencing, we evaluated methodological set-ups to detect archaea in samples from five different body sites: respiratory tract (nose), digestive tract (mouth, appendix, and stool) and skin. With the optimized protocols, the detection of archaeal ribosomal sequence variants (RSVs) was increased from one (found in currently used, so-called “universal” approach) to 81 RSVs in a representative sample set. In order to assess the archaeome diversity, a specific archaea-targeting methodology is required, for which we propose a standard procedure. This methodology might not only prove useful for analyzing the human archaeome in more detail but could also be used for other holobionts’ samples.