How does the use of antibiotics affect the interaction between the immune system and the healthy human microbiome?

Antibiotics kill many bacteria in the gut, so the normal microbial community shrinks and its diversity drops. This loss removes the microbes that normally train the immune system to distinguish harmless bacteria from threats, so the immune system may become overactive or underreactive. With fewer microbes to produce signals like short‑chain fatty acids, the gut lining can become inflamed and immune cells may attack the body’s own tissues. Over time, the weakened microbial signals also reduce the immune system’s ability to fight new infections, making people more prone to illness. For example, a child who takes a broad‑spectrum antibiotic may later develop eczema or allergies because the gut bacteria that normally calm the immune response were wiped out.