A healthy animal lives in harmony with many microorganisms that establish themselves on or in the body. The microorganisms that usually live on or in a particular body site are called the resident flora (or microbiota). The resident flora at each site include several, or even several hundred, different types of microorganisms. Environmental factors such as diet or sanitary conditions influence what microorganisms make up an animal’s resident flora. The resident flora are beneficial, often protecting the body against other organisms that can cause disease. Under normal conditions, if the resident flora are disturbed, they promptly reestablish themselves.
Under certain conditions, microorganisms that are part of an animal’s resident flora may cause disease. Such conditions include the use of antibiotics or a weakened immune system. When antibiotics used to treat an infection kill a large proportion of the resident flora of the skin or intestine, other bacteria or fungi can multiply without being held in check.