Although they typically reside only in extreme conditions such as hot springs recent studies have shown that archaea are essential components of the human microbiome.

A variety of archaeal species have been identified in the human skin respiratory tract urogenital tract and gastrointestinal tract microbiome. Predominant examples include ammonia-oxidizing Nitrososphaeria on the skin methane-producing (methanogenic) archaea in the urogenital and gastrointestinal tracts and unknown Nanoarchaeota in the respiratory tract. These discoveries indicate a broader ecological role for archaea than previously understood.

Biological processes necessary for bacterial pathogenicity include invasion colonization damage and transmission. Archaea also exhibit some of these traits including host adherence and colonization.

Archaeal immunogenicity is highly species-specific with Methanobrevibacter spp. showing low immunogenic potential and Methanosphaera spp. showing strong immunogenic potential. 

The robust ability of methanogens to produce methane can lead to the optimization of the entire microbiome for fiber degradation and coping with B12 deficiency. Furthermore a symbiotic relationship has been found between archaea and bacteria where archaea utilize hydrogen and other byproducts of bacterial fermentation for methanogenesis.

Archaeal involvement in oral cavity infections  

Endodontic infection is a microbial infection in a tooth's central part (pulp) that contains nerves blood vessels and connective tissues. Methanogenic archaea especially M. smithii and M. oralis have been identified in 85% of infected pulp tissues. 

Archaeal species particularly M. smithii have been found to foster the growth of pathogenic bacteria within Tonsillar phlegmon which is a retropharyngeal abscess caused by infections in the peritonsillar space and the pharyngeal sphincter.

Source: https://www.news-medical.net/news/20240716/Archaea-Unseen-players-in-human-microbiome-and-infectious-diseases.aspx