A great thread. If I may add that bacteria could be a problem but so can parasites, yeast/fungal strains and even viral strains.
The gut holds 70% of the immune system and Dr. Galland states there is a reason for this in that the gut has a high probability of infection. Also the gut is a microcosm to itself in that the variety of different organisms are all creating a microuniverse.
When a pathogen enters this arena then the immune system goes nutso and creates a toxic milieu of immune factors which cause damage to the gut lining which provokes further inflammatory immune responses elsewhere in the body. Which in turns sets off the adrenal response, neurological and everything else.
Galland states that when he sees a Chronic-Fatigue-Syndrome patient, the first he looks for is the gut and in his case, parasites.
I have found that avoiding high lactose containing dairy and processed foods makes a big difference. It is tricky to try to balance the gut as one poster said meaning that if you kill off the bad, then you may throw off the balance.
Colostrum, Vitamin A & D all support sIgA which is a key immune factor that is present in the gut. Probiotics are tricky in that you may be adding some that can further provoke immune responses. Personally I think that pre biotics such as apple cider vinegar may provide a better choice. But this requires experimentation since there is not a one size fits all.