Advances in Clinical Applications of Intestinal Microbiome Analysis in Dogs and Cats

The intestinal microbiome is the sum of all microorganisms present within the gastrointestinal tract (GIT).The term includes the presence of microbes (eg, bacteria, archaea, fungi, and viruses), and their function.It is estimated that the entire community in the GIT totals trillions of microorganisms, with bacteria constituting the majority.This vast number illustrates that it is not easy to change microbial composition.However, when severe microbiome shifts are recognized, this indicates that major changes in the function of the microbiome and host are present within the GIT [1].A normal microbiome is beneficial to the host, as microbes act as a metabolic system that influences nutrition and immune responses.Bacteria convert dietary compounds (eg, carbohydrates, proteins, fats, and micronutrients) and host molecules such as bile acids into secondary and even tertiary metabolites, thereby affecting the function of GIT and other organ systems.Multiple interacting pathways from the host and the intestinal microbiome act together in normal GIT physiology.Nutrients from the diet are broken down into small molecules by mechanical and enzymatic host processes, and these are then absorbed by active and passive transport in the small intestinal brush border.Dietary substrates (eg, fatty acids, proteins, and carbohydrates) are in part also metabolized by resident bacteria, resulting in the production of microbial-derived metabolites [2].Metabolites provide benefits for the