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

Abstract

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

The human gut archaeome: identification of diverse haloarchaea in Korean subjects

“…2). Archaeal abundance in the human gut has been estimated previously, ranging from 0.1-21.3% [28,32]. Our abundance estimation did not vary significantly from those of previous studies, although the values were based on a relatively larger sample (n = 150), thereby enhancing the reliability of the estimation.…”

“…S5 show weak (or no) relationship between archaeal abundances and host dietary factors. Next, we assessed whether these enterotypes are the results of more ancient features (such as host immune system and gut physiology) that might be derived before or during the diversification of the great ape species by comparing the Korean gut archaeome with other human gut archaeomes [26,28] and those of the great apes, including orangutan, gorilla, chimpanzee, and bonobo [29]. PCoA of the Bray-Curtis dissimilarity matrix showed the typical horseshoe shape of all merged samples (see Additional file 1: Supplementary Fig.…”

“…DNA was extracted from the faecal samples as described above. In total, 150 samples were randomly selected and subjected to real-time quantitative PCR [28] in three replicates. The archaeal primer sequences are listed in Additional file 2: Supplementary Table S4.…”

A Novel Description of the Human Sinus Archaeome During Health and Chronic Rhinosinusitis

“…Most of the human microbiome research investigating the archaeome (the archaeal portion of the human microbiome) focuses on the gut, where methanogens are the dominant archaea (Miller and Wolin, 1985;Dridi et al, 2009;Miragoli et al, 2017;Wampach et al, 2017). More recently, archaeal signatures have been detected in subgingival dental plaque, skin, lung, sinus and nares samples (Lepp et al, 2004;Dridi et al, 2011;Hulcr et al, 2012;Probst et al, 2013;Oh et al, 2014;Koskinen et al, 2017;Moissl-Eichinger et al, 2017;Pausan et al, 2018;Wagner Mackenzie et al, 2018).…”

“…Recent studies have evaluated primer-pairs and data processing pipelines for targeting the archaeal component of the human microbiome for amplicon sequencing (Koskinen et al, 2017;Pausan et al, 2018). Studies by Pausan et al optimized the detection and quantification of archaea in a variety of samples from different sites, including swab samples from the upper nasal cavity.…”