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 (nasal cavity), digestive tract (mouth, appendix, and stool) and skin. With 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. The results from this extensive primer-evaluation led to the identification of the primer pair combination 344f-1041R/519F-806R which performed superior for the analysis of the archaeome of gastrointestinal tract, oral cavity and skin. The proposed protocol might not only prove useful for analyzing the human archaeome in more detail but could also be used for other holobiont samples.

15Due to their fundamentally different biology, archaea are consistently overlooked in conventional 16 microbiome surveys. Using amplicon sequencing, we evaluated methodological set-ups to detect 17 archaea in samples from five different body sites: respiratory tract (nose), digestive tract (mouth, 18 appendix, and stool) and skin. With the optimized protocols, the detection of archaeal ribosomal 19 sequence variants (RSVs) was increased from one (found in currently used, so-called "universal" 20 approach) to 81 RSVs in a representative sample set. In order to assess the archaeome diversity, a 21 specific archaea-targeting methodology is required, for which we propose a standard procedure. This 22 methodology might not only prove useful for analyzing the human archaeome in more detail but 23 could also be used for other holobionts' samples. 24 25 26 27

Previous studies have shown that individual, isolated microorganisms may influence secondary metabolism of plants and induce or stimulate the production of medicinally relevant secondary metabolism. Here, we analyzed the microbiome-metabolome linkage of the medicinal plant Alkanna tinctoria , which is known to produce valuable compounds, particularly the naphthoquinones alkannin and shikonin and their derivatives.