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, fungi 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 - despite the fact that in some parts of the body (e.g. the appendix) there are roughly the same number of resident archea as there are bacteria.

There are two reasons for the lack of research :

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 (i.e. disease causing) archaea in the human microbiome - or, that there are, but they haven't been identified yet.

Further reading :

First insights into the diverse human archaeome: Specific detection of archaea in the gastrointestinal tract, lung, and nose and on skin MBio, 2017

Archaea: forgotten players in the microbiome Emerging Topics in Life Sciences Nov 22, 2018, 2 (4) 459-468

The human Archaeome Emerging Topics in Life Sciences Nov 22, 2018, 2 (4) 469-482

Also see Microbiome interactionsplugin-autotooltip__plain plugin-autotooltip_bigMicrobiome interactions

"The human gut harbors trillions of invisible microbial inhabitants, referred to as the microbiota, that collectively produce thousands of unique small molecules. The sources and biological functions of the vast majority of these molecules are unknown.