When the gut microbe balances are disturbed gut permeability is increased (allowing outside molecules that should never cross into the body directly get in). With this increased permeability a person's immune system will attack the molecules and create antigens that mimic different cell types in the body and attache to these cells. The antigens will attached to these different cell types like thyroid tissue or joint tissue. When our body fights inflammation or our bodies immune response is triggered these antigens can be attacked and produce these autoimmune diseases. You are what you eat comes to mind.
Diseases that we may normally attribute to genetics or autoimmune diseases (like Hypo-Thyroid or RA) may in fact have its origin(a percentage of patients not all) in what we eat and how our body responds to our diet. This is just one mechanism of action in how our gut health and microbe imbalances can affect our health. Can our gut health or lack there of be a cause or a trigger for AD, PD and MS? I'm guessing we will find out much more because science is open to it and research is being done. So as of today this element of health which was/is completely ignored is not anymore!