Mycobacteria, namely Mycobacterium avium subsp. paratuberculosis (MAP), have long been suspected as being a possible etiological agent of Crohn's disease. A similar animal disease, paratuberculosis (Johne's disease), has a high prevalence in dairy cattle herds in the European Union, USA and Canada. Animals with paratuberculosis produce enormous numbers of MAP cells, containing known triggers of autoimmune diseases. Infected milk, dairy products and meat are not eliminated from the food chain because paratuberculosis is not considered a zoonosis. Thus, consumers are exposed to bacterial triggers (peptidoglycans, muramylpeptides etc.) from killed MAP cells. Moreover, MAP is very resistant to heat treatment and about 2% of heat treated retail milk contains cultivable MAP. Mycobacteria can also contaminate drinking water. The present knowledge, resulting from different scientific fields, will be discussed; not only around a table between the direct participants, but everybody can send opinions to be discussed and published in the Proceedings.