The intestinal microbiota is defined as the collection of all living microorganisms (i.e., bacteria, fungi, protozoa, and viruses) that inhabit the gastrointestinal tract. With the development of novel molecular analysis tools (based commonly on sequencing of the bacterial 16S rRNA gene), it is now appreciated that the gastrointestinal microbiota of animals is highly complex, comprising several hundred to thousand bacterial phylotypes.1'2 It is estimated that the mammalian intestine harbors a total of 1010-1014 microbial cells, approximately 10 times more than the number of host cells. It is, therefore, obvious that this highly complex microbial ecosystem will play a crucial role in health and disease. Gut microbes are useful to the host by acting as a defending barrier against transient pathogens, they aid in digestion, and help to harvest energy from the diet. Furthermore, they provide nutrition for enterocytes and play an important role in the development and regulation of the host immune system. However, in the last few years convincing evidence has been gathered associating alterations in the composition of the intestinal microbiota with acute and chronic enteropathies of dogs and cats.
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