While researching the negative effects of antibiotics and how bacteria might develop resistance to them, MIT and Harvard researchers discovered that the medications can actually operate against the body, reducing the immune system's ability to fight off infections. > span> According to research published in 2004 in the journal Nature Medicine, people who take antibiotics over a long period of time are at increased risk for developing inflammatory bowel disease and diabetes. The study also revealed that the antibiotics reduce the number of B cells - which make antibodies - as well as T cells, which work with B cells to fight infection and inflammation. This effect may last for months or years after you stop taking the drugs. In fact, studies have shown that people who have taken antibiotics are up to twice as likely to get sick from a cold or the flu. Doctors also report more severe cases from their patients who have been on these medications for an extended period of time. The best way to avoid weakening your immune system is to follow proper antibiotic use guidelines. Only give your doctor a list of all the medications you take, including generic names and doses. He or she will be able to tell if there are any interactions between your treatments.