After ovulation estrogen is joined by progesterone from the corpus luteum making the endometrium denser and mature. Estrogen is not only metabolized by the liver but also re-circulated between the gut and the liver (entero-hepatic circulation). Antibiotics can affect estrogen metabolism in two ways. Most antibiotics are metabolized in the liver and their presence can affect the rate of metabolism of estrogen (and progesterone). This can change the supply of estrogen available in the blood and that can cause irregularity of the cycle. Some antibiotics cause diarrhea like symptoms as they change the gut flora.