The American Society for Microbiology has not yet found an archaebacteria that causes disease or is harmful to the human body. While these microorganisms have many characteristics of other disease-causing bacteria, the knowledge of them is limited.
Methanogens are one strain of archae that have been found in the human body. There are questions as to whether they are harmful or beneficial. The difficulty in isolating and cultivating these bacteria is part of the reason so little can be proven about them. It is known that they will only survive and grow in an anaerobic environment. They are among the most abundant life forms on the planet.