Chemotherapy and radiation therapy upset the healthy balance of bacteria in the mouth. There are many different kinds of bacteria in the mouth. Some are helpful and some are harmful. Chemotherapy and radiation therapy may cause changes in the lining of the mouth and the salivary glands, which make saliva. This can upset the healthy balance of bacteria. These changes may lead to mouth sores, . This can upset the healthy balance of bacteria. These changes may lead to mouth sores, infections, and tooth decay., and tooth decay.