First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin

Abstract

Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea. The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts.

The Role of Lung and Gut Microbiota in the Pathology of Asthma

“…Although understudied, archaea are consistently identified in human microbiota studies and their community composition differs according to body site (Koskinen et al, 2017). Methonoarchaea, including Methanobrevibacter smithii and Methanosphaera stadtmanae (M. stadtmanae), have been proposed as keystone members of this microbial community and possess immunogenic properties (Blais Lecours et al, 2011;Bang et al, 2014).…”

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

“…Furthermore, Koskinen et al (2017) have shown for the first time that archaea reveal a body site specific pattern, similar to bacteria: the gastrointestinal tract being dominated by methanogens, the skin by Thaumarchaeota, the lungs by Woesearchaeota, and the nose archaeal communities being composed of mainly methanogens and Thaumarchaeota. Altogether, this indicates a substantial presence of archaea in some, or even all, human tissues.…”

“…Nevertheless, (methanogenic) archaea are part of the commensal microorganisms inhabiting the human body, being regularly detected in the oral cavity and the gastrointestinal tract (Chaudhary et al, 2015;Gaci et al, 2014;Horz and Conrads, 2011;Nkamga et al, 2017); in the latter they sometimes even outnumber the most abundant bacterial species (14%, (Tyakht et al, 2013);). Most human archaea studies use either cultivation or qPCR methods (Grine et al, 2017;Koskinen et al, 2017;van de Pol et al, 2017;Wampach et al, 2017) and only a few, 16S rRNA gene-based archaeacentric studies are available Moissl-Eichinger et al, 2017). These new studies have shown that archaea are also present in the human respiratory tract and on human skin in considerable amounts Probst et al, 2013).…”

No genome is an island: toward a 21st century agenda for evolution

“…When the human intestinal microbiome was first catalogued through the metagenomic analysis of stool samples, previously unknown bacterial taxa were discovered , . In addition to bacteria, the human gut microbiome includes archaea (which constitute ∼10% of the anaerobic intestinal flora), eukaryotic microorganisms, and viruses that infect bacteria or archaea (phages) . The presence of phages indicates that viruses can contribute to microbiome population dynamics by infecting and killing sensitive prokaryotes or transducing DNA segments between cells.…”