Naïve CD4+T cells differentiate into Treg or various helper T cell subsets (Th1, Th2, Th17 or Tfh). In the gut-associated lymphoid tissue, the process of differentiation occurs via presentation of antigens derived from gut microbiota by antigen presenting cells such as dendritic cells or M cells in Peyer´s patches. Typical process of an oral tolerance towards ingested food antigens can be described as continuous luminal sampling of antigens by DCs and their subsequent migration followed by priming of naïve T cells in mesenteric lymph nodes to become immunosuppressive T cells (Treg). Antigens received in this way ensure tolerance against them. Commensal microbiota activates immune response as well - in a way that protects host intestinal tissue from damaging it by immune cell reactions. The final outcome of T cell populations in healthy individuals differs from the spectrum of T cells resulting from acute infection or chronic inflammation. Inappropriate stimulation (typically by segmented filamentous bacteria - SFB) of chronic Th1 or Th17 cell response plays a crucial role in pathological damage to the host.