I wonder how many other diseases will wind up having bacterial or viral causes.
I was speaking to virologist socially a year or two back, and they stressed that most viruses are only discovered because we go looking for them after acute, serious symptoms. The new tools for trivial DNA sequencing are going to be interesting, it means getting a much more complete picture of the presence of viruses and bacteria, which could then be combined with epidemiology. That virologist thought that a lot of inflammatory diseases like atherosclerosis or arthritis could actually be triggered or exacerbated by infection. The next 10 years will be interesting.
In the case of CFS, there are probably multiple underlying etiologies, only some of which are induced by microbes.
Stress/anxiety and other strong negative mental states can impact the functions of the GI tract's such as peristalsis and digestive efficiency of food.
This in turn sets up a negative feedback loop as things like nutrient absorption declines and toxin levels rise worsening the functionality of the tract. By toxins I also imply bacteria and viruses besides just 'regular' chemicals.
Erosion of various parts of the GI tract happens slowly and you get an ulcer. Ulcers in the stomach aren't the only place to see bleeding in the GI tract.
At least the last time I checked, mouth flora bacteria had been found growing in atherosclerosis lesions, and poor dental hygiene was linked to and increased risk of cardiovascular disease.
Eating disorders (both bulimia and anorexia) may be caused by an auto-immune response to a hormone look-alike produced by (some strains? of) e. coli. Both the hormone and the bacterial substitute cause satiety. Depending on the kind of antibodies produced, their effect can be amplified or inhibited.