Abstract
Due to their fundamentally different biology, archaea are consistently overlooked in conventional 16S rRNA gene amplicon surveys. Herein, we evaluate different methodological set-ups to detect and quantify archaea signatures in human samples (nose, oral, appendix, stool, and skin) using amplicon sequencing and quantitative PCR. With our optimized protocol, we were able to increase the detection of archaeal RSVs from one (using a so-called universal approach) to 81 RSVs in a representative sample set. Moreover, we confirmed the presence of about 5% archaeal signatures in the human gut, but found, unexpectedly, an almost 1:1 ratio of archaeal to bacterial 16S rRNA genes in appendix and nose samples. This finding indicates a high prevalence of archaeal signatures in body regions thus far not analyzed for the presence of archaea using appropriate methods. In order to assess the archaeome diversity and archaeal abundance, a specific archaea-targeting methodology is required, for which we propose two standard procedures. These methodologies might not only prove useful for analyzing the human archaeome in more detail, but could also be used for other holobionts samples.
