There is a complex relationship between your diet, your gut microbiota (which pre-process your diet for you), and your immune system (which is sensitive to both

There is a complex relationship between your diet, your gut microbiota (which pre-process your diet for you), and your immune system (which is sensitive to both gross and fine (signaling molecule) changes in the gut). The scope of this relationship was only recently realized, much of it due to new molecular biology techniques. For example there's the recent article about a boost in neuroinflammation observed from the presence of gut microbiota implicated in Parkison's progression in a mouse model, http://www.cell.com/cell/pdf/S0092-8674(16)31590-2.pdf http://www.cell.com/cell/pdf/S0092-8674(16)31590-2.pdf ). Celiac disease and inflammatory bowel disease are two well-known categories of disorders, but more generally your gut is the most permeable interface of your body, so the immune system is very buffed up and sensitive to all kinds of signals there, affecting the background state of the entire system. That has the potential to cause harmful unnecessary inflammation in other parts of the body.