Abstract
ABSTRACTHuman-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.
Highlights
Human-associated archaea remain understudied in the field of microbiome research, in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes
Numerous studies have indicated the potential of humanassociated archaea to represent keystone species, as they can be major drivers of metabolic processes in the gut
Recent studies have shown that the human archaeome still holds many surprises, including the discovery of the seventh order of methanogens in the human gut [13], the cultivation of a halophilic archaeon from human samples [24], and the detection of Thaumarchaeota on human skin [27]
Summary
Human-associated archaea remain understudied in the field of microbiome research, in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract, on the skin, and for the first time in the respiratory tract, i.e., the nose and lungs. Four species of methanogenic archaea have been cultivated and isolated from human body samples: the first isolated and described human-associated archaeon Methanobrevibacter smithii [11], Methanosphaera stadtmanae [12], and most recently Methanomassiliicoccus luminyensis [13] were all isolated from human feces. Together with the recently discovered species M. luminyensis, with a prevalence of 4% in the population studied [17], M. smithii and M. stadtmanae are currently known to predominantly inhabit the human gut
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