|MadSci Network: Microbiology|
It's not often that I get a question from MadSci and I can say "I wrote an article about that"!
You are quite right - although many Archaea live in extreme environments (high temperature, very saline, high/low pH and so on), many of them also live in "ordinary" environments - soil, water and of course, in association with other organisms.
Most of the archaea that colonise humans are methanogens. This means that they have to inhabit areas where there is little oxygen, as they generate energy anaerobically producing methane in the process. So they are found mostly in the gastrointestinal tract and also in microscopic fissures in the teeth.
We don't know of any archaea that are harmful or can cause disease. But we don't know if that's because we haven't looked for them or because they are incapable of becoming pathogenic. Many scientists, particularly in the biomedical field are not even aware that archaea exist, that they are different from bacteria or that they can colonise humans. So it's quite possible that there are diseases which have not been diagnosed simply because nobody thought to look for archaea.
Myself and some colleagues wrote an article about 3 years ago called "Pathogenic archaea: do they exist?" We concluded that there was nothing to stop archaea from becoming pathogenic - for instance they possess complex secretion systems (as do many pathogenic bacteria), they can synthesise toxins and they can acquire genes from other organisms, including bacteria. There are also some cases of intestinal disease (such as periodontitis or bowel cancer) where high numbers of methanogens are found in the affected region, but it's unclear if they cause the disease or just colonised the tissue afterwards. We concluded that there should be more effort to screen human tissues (e.g. using molecular probes specific to archaea) in cases where disease cannot be diagnosed.
I've included some links to references - hope you can access the articles, otherwise you can at least read the abstracts and Google around for more information.
of the human intestinal microbial flora.
Methanogenic Archaea and human periodontal disease.
Archaea and their potential role in human disease.
Pathogenic archaea: do they exist?
Try the links in the MadSci Library for more information on Microbiology.