Review Article The human archaeome: methodological pitfalls and knowledge gaps Alexander Mahnert 1,2,* , Marcus Blohs 1* Manuela-Raluca Pausan 1 and Christine Moissl-Eichinger 1,2 1 Department of Internal Medicine, Medical University of Graz, Graz, Austria; 2 BioTechMed, Graz, Austria Correspondence: Christine Moissl-Eichinger (christine.moissl-eichinger@medunigraz.at) Forty years ago, archaea were described as a separate domain of life, distinct from bac- teria 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 pro- blems contribute to the invisibility of the human archaeome, resulting in severe knowl- edge gaps and contradictory information. Similar to the bacteriome, the archaeal biogeography was found to be site-specific, forming (i) the thaumarchaeal skin land- scape, (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 corre- lated 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. Introduction The human microbiome During the last years, the interest of the scientific community grew to understand the composition of the microbial community (‘microbiome’) associated with the human body and its relevance for human health and disease. Trillions of microorganisms are associated with the human body, coloniz- ing the gastrointestinal tract (GIT), oral cavity, vagina, and on our skin, even outnumbering human cells in each body, and with a metabolic capacity similar to that of the liver [1]. Besides the overall microbiome composition [2,3], also the presence and absence of single microbial species can have tre- mendous impact on human health and medical treatments [4]. The overwhelming majority of previous and ongoing work focused on the role of bacteria, even though the human microbiome is additionally composed of small eukaryotes, fungi, viruses/phages, and archaea. The scientific community has communicated the importance of considering these neglected microbiome components in numerous reviews [5–11]. Archaea Forty years ago, archaea were recognized to form a separate domain of life, distinct from bacteria and eukarya [12]. Although they are prokaryotes like bacteria, archaea possess a fundamentally different biology, including a unique cell wall as well as distinctive metabolic pathways and enzymes [13]. For a long time, they have been considered as primitive, ancient, extremophilic microorganisms, but recent, *These authors contributed equally to this work. Version of Record published: 14 December 2018 Received: 29 June 2018 Revised: 20 September 2018 Accepted: 1 October 2018 © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society and the Royal Society of Biology 469 Emerging Topics in Life Sciences (2018) 2 469–482 https://doi.org/10.1042/ETLS20180037