The human Microbiome (a.k.a. Microbiota) has been the focus of intense research for many decades. We are hosts to a vast array of microorganisms, including Bacteria, eukaryotes, Archaea, and viruses - many of which are now known to be beneficial to human health, while many others are classed as pathogens. Of these groups, one in particular, the Archaea has until recently been almost entirely ignored.
There are two reasons for this -
1) Archaea are difficult to study in vivo. and
2) No known archaeal pathogens have yet been discovered.
“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.”
“However, one of the most burning questions — do archaeal pathogens exist? — still remains obscure to date.”
Source: The human archaeome: methodological pitfalls and knowledge gaps in Emerging Topics in Life Sciences Dec 14, 2018
To sum up, it's possible that there are no commonly occurring pathogenic [disease causing] archaea in the human microbiome - or, that there are, but they haven't been identified yet.