Illustration of the bacteria Clostridioides difficile. These rod shaped bacteria have flagella, which are used for motility. Clostridioides difficile (formerly known as Clostridium difficile) are anaerobic bacteria prevalent in soil. In humans, the bacteria can become established in the colon and disrupt the normal gut microbiota, particularly in people taking antibiotics. Toxins released by Clostridioides difficile can produce diarrhoea and inflammation.