The canine microbiome

Microbiome refers to the population of microorganisms (bacteria, viruses, protozoa and fungi) that inhabit the entire gastrointestinal (GI) tract, more particularly the colon whose role it is to maintain the integrity of the intestinal mucosa and control the proliferation of pathogenic bacteria. The term microbiome refers to the total number of microorganisms and their genetic material and is contrasted from the term microbiota, which is the microbial population present in different ecosystems in the body. Alteration in the composition of the gut microbiome is called dysbiosis. It has been shown that dysbiosis predisposes to inflammatory bowel diseases such as ulcerative colitis, Crohn's disease and indeterminate colitis (Tomasello et al, 2016).

Identification of bacteria within the canine GI tract has traditionally been achieved by culture of faecal samples. This method has, however, now been recognised as being ineffective with large numbers of bacteria remaining undetected (Suchodolski, 2011). Faecal cultures yield useful results when trying to detect specific enteropathogens such as Salmonella and Campylobacter jejuni, which is useful in a clinical setting as these bacterial infections are commonly seen in practice. However, it is thought that only 30% of GI bacteria have been able to be cultured (Fraher et al, 2012), and this does not take into consideration the rest of GI microbiome (protozoa, fungi or viruses).