Diagnosis and interpretation of intestinal dysbiosis in dogs and cats.

The intestinal tracts of dogs and cats harbor a highly complex microbiota, which consists of bacteria, fungi, viruses and protozoa. Until recently, traditional bacterial culture was commonly used to identify bacteria present in the gastrointestinal tract, but it is now well recognized that standard plating techniques do not have enough resolution for identification of the mostly anaerobic bacteria that reside within the gut. Molecular methods are now established for assessing intestinal dysbiosis in dogs and cats with gastrointestinal disease, but these approaches are not yet widely available for routine diagnosis. The loss of normal commensal bacterial microbiota (i.e. Lachnospiraceae, Ruminococcaceae, and Faecalibacterium spp.) in acute and chronic intestinal diseases has been linked to metabolic changes, for example alterations in immunomodulatory bacterial metabolites, such as short chain fatty acids and secondary bile acids. This highlights the importance of dysbiosis in the pathophysiology of gastrointestinal diseases. Development of molecular based assays for specific bacterial groups, calculations of microbial dysbiosis indices and assays for microbial functional metabolites are currently underway to help assess dysbiosis. These will yield a better understanding of the pathophysiology of gastrointestinal diseases and may also lead to new diagnostic and therapeutic approaches to dysbiosis.