The human body (primarily the intestinal tract, the oral cavity, and the skin) harbours approximately 1,000 different bacterial species. However, the number of archaeal species known to colonize man seems to be confined to a handful of organisms within the class Euryarchaeota (including Methanobrevibacter smithii, M. oralis, and Methanosphaera stadtmanae). In contrast to this conspicuously low diversity of Archaea in humans their unique physiology in conjunction with the growing number of reports regarding their occurrence at sites of infection has made this issue an emerging field of study. While previous review articles in recent years have addressed the putative role of particularly methanogenic archaea for human health and disease, this paper compiles novel experimental data that have been reported since then. The aim of this paper is to inspire the scientific community of “Archaea experts” for those unique archaeal organisms that have successfully participated in the human-microbe coevolution. 1. Introduction A striking feature of the human microbiota is the conspicuous imbalance of species diversity between bacteria and archaea. So far, over thousand distinct bacterial species or phylotypes have been recovered from the human intestinal tract, and more than 700 bacterial phylotypes have been identified in the human oral cavity (e.g., [1, 2]). Although most intestinal microbes initially enter through the oral cavity, both compartments share surprisingly few bacterial species [3, 4]. The underlying mechanisms that lead to the spatial separation of bacterial communities seem to apply also to human archaea; however, the striking difference is the extremely reduced diversity compared to bacteria. Only three distinct species within the group of Euryarchaeota have been regularly detected within the human body. Among these is the primary colonizer of the human gut system Methanobrevibacter smithii and the less frequently found species Methanosphaera stadtmanae, while in the oral cavity M. oralis is the predominating methanogenic species. Despite this low diversity and the generally lower abundance compared to human bacteria the unique physiology and energy metabolism of methanogens suggest that they may play a previously underestimated role for human health and disease. Previous reviews have already discussed the theoretical possibility that archaea might act as human pathogens (e.g., [5–7]). The current paper while not recapitulating these reviews compiles knowledge from most recent findings (arising from more than 20 additional studies, primarily from
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