The aim of this article was to describe canine microbiome, which refers to the collection of genomes from all the microorganisms in the particular environment. Microbiota, sometimes used interchangeably, refers to specific microorganisms, including bacteria, viruses and fungi, that are found within a given environment. Dogs are colonized by trillions of microbes living on and within their body. The major phyla identified, are Bacteroidetes, Firmicutes, and Fusobacteria, with some differences related to animal age. Proteobacteria and Actinobacteria form a minor group in microbiome and metabolome in healthy dogs. The largest community of microorganisms, predominately made up of bacteria, can be found in the skin and within intestines. The gut microbiome contributes to host metabolism, protects against pathogens, educates the immune system and, through these basic functions, affects directly or indirectly most physiologic functions of its host. Different factors cause changes in the microbial communities. Canine microbiome is also shaped by long-term diet and certain medications, particularly antibiotics. Many diseases are related with disruptions of canine gut microbiome, referred as dysbiosis. Emerging research has found correlations between microbiome and behavioral traits such as aggression and sociability or work (explosive detection dogs, patrol and narcotics detection dogs, and vapor wake dogs).