The human archaeome: methodological pitfalls and knowledge gaps

Abstract

Forty years ago, archaea were described as a separate domain of life, distinct from bacteria and eukarya. Although it is known for quite a long time that methanogenic archaea are substantial components of the human gastrointestinal tract (GIT) and the oral cavity, the knowledge on the human archaeome is very limited. Various methodological problems contribute to the invisibility of the human archaeome, resulting in severe knowledge gaps and contradictory information. Similar to the bacteriome, the archaeal biogeography was found to be site-specific, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal GIT landscape, (iii) a mixed skin/GIT landscape in nose, and (iv) a woesearchaeal lung landscape, including numerous unknown archaeal clades. Compared with so-called universal microbiome approaches, archaea-specific protocols reveal a wide diversity and high quantity of archaeal signatures in various human tissues, with up to 1 : 1 ratios of bacteria and archaea in appendix and nose samples. The archaeome interacts closely with the bacteriome and the human body cells, whereas the roles of the human-associated archaea with respect to human health are only sparsely described. Methanogenic archaea and methane production were correlated with many health issues, including constipation, periodontitis and multiple sclerosis. However, one of the most burning questions — do archaeal pathogens exist? — still remains obscure to date.

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

“…These observations suggest that the diversity and/or abundance of the human gut archaeome may vary with host factors, including diet and age. Methodological pitfalls (such as the selection of primer pairs and the sequence processing pipeline used) may also contribute to the low resolution of the human gut archaeome [22]. Collectively, there is no sufficient information on the identity of archaea in the gut environment.…”

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

“…These observations suggest that the diversity and/or abundance of the human gut archaeome may vary with host factors, including diet and age. Methodological pitfalls (such as the selection of primer pairs and the sequence processing pipeline used) may also contribute to the low resolution of the human gut archaeome [22]. Collectively, there is no su cient information on the identity of archaea in the gut environment.…”

Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

“…The studies on human archaeome usually employ either cultivation or qPCR methodology [118,119,148], while 16S rRNA gene-based research often uses bacterial-targeted protocols and universal primer pairs to cover the broadest prokaryotic diversity [119,149]. The low abundance of archaeal DNA in human samples, inefficient cell lysis and DNA extraction, failure of the universal primers to fully detect archaeal signatures, as well as incomplete 16S rRNA gene databases, all represent methodological pitfalls of human archaeome analysis [112,150,151]. As archaea feature fundamentally different biology compared to their bacterial and eukaryotic counterparts, a specific methodology is required to investigate the human archaeome.…”