The mouse microbiome, defined as all bacterial species found in or on the mouse, and their interactions among themselves and with their environment, are always present. Non-infective agents or pathogenicity of infective agents can lead to various diseases. The flora of mice in the will become more complex depending on their housing and rearing conditions, meaning that more bacterial species will colonize mice. The same strain may have different flora in different experimental animal breeders. Opportunistic pathogen is often referred to as ‘‘opportunistic’’ agent or even simply ‘‘opportunistic’’but it is a definition that blends both commensal flora and primary pathogens. Rats, the most commonly used species of experimental animals, are susceptible to a range of bacterial infections that can be enzootic or sporadic but can have high morbidity and motility rates leading to severe disease. When formulating differential diagnoses for sick or diseased animals, it must be recognized that diseases that were once common in animals imported in the 1960s and 1970s are now rare. It is also important to recognize that housing and sanitation conditions can affect exposure to potentially pathogenic bacteria. Animals raised in areas with biosecurity measures in place may be exposed to fewer pathogens than animals raised in mixed or free-range environments. Much of the available literature describing the clinical and epizoological features of bacterial infections of this type is dated and scientists should be encouraged to study the prevalence in rats and publish their results in more detail.