I saw an interesting 2001 study that showed a benefit of nystatin vs placebo, for people with presumed "Candida" symptoms.
The study subjects were selected from volunteers, because of their answers to 7 questions supposed to indicate a "Candida problem":
Have you, at any time in your life, taken ‘broad spectrum’ antibiotics?
Have you taken tetracycline or other broad spectrum antibiotics for 1 month or longer ?
Are your symptoms worse on damp, muggy days or in mouldy places?
Do you crave sugar?
Do you have a feeling of being ‘drained’?
Are you bothered with vaginal burning, itching or discharge (do you have similar symptoms from the penis)?
Are you bothered by burning, itching or watery eyes ?
The 120 people who had a high-enough score on these 7 questions were enrolled in the study.
Those people were given a choice of adhering to an anti-candida diet or not; and also they were randomly given nystatin vs. placebo.
And the nystatin showed a benefit vs. placebo. They measured benefit with a symptom questionnaire given at the start and end of the study.
This is remarkable because only one of those 7 questions is specific to mold. The vaginal-burning question is related to possible vaginal yeast infections. But oral Nystatin, which is what was used, is not effective for vaginal yeast infections. Nystatin isn't absorbed into the bloodstream, so when it's taken orally, it can treat yeast infections only in the GI tract.
Their 7 questions are similar to the questionnaires in books like The Yeast Connection.
The "anti-candida diet" also made a difference in symptoms, but that wasn't blinded (hard to blind).
Since Nystatin kills many different kinds of fungi, it wasn't possible to say whether the benefit was due to killing Candida or some other fungus. Other fungi besides Candida live in the GI tract, and might also overgrow if one has taken antibiotics, eats a lot of sugar, etc.
So this study does suggest that fungi in the GI tract can cause health problems.