If alterations in the human microbiome are linked to increased susceptibility to autoimmune diseases, what underlying mechanism could explain this relationship?

Changes in the microbiome can reduce the production of anti‑inflammatory metabolites such as short‑chain fatty acids that normally help train the immune system to tolerate self‑antigens. When these metabolites are low, regulatory T cells decline, while pro‑inflammatory Th17 cells expand. This shift creates a chronic, low‑grade inflammatory state that encourages the immune system to attack the body's own tissues. For example, a loss of butyrate‑producing bacteria in the gut can lower Treg cell numbers, increasing the risk of conditions like inflammatory bowel disease. Thus, microbiome imbalance can tip the immune balance toward autoimmunity.