The knowledge of canine and feline intestinal microbiota is relatively scarce and based mainly on data from laboratory animals, on responses to dietary interventions, or on animals suffering from chronic intestinal disorders believed to be of bacterial nature. Most of the studies are performed on quite low numbers of animals that were often sacrificed and samples of intestinal material collected post-mortem (1,2).

As obtaining fecal samples is much more feasible than sampling the contents of upper intestinal tract, most of the papers have focused on fecal microbiota, which may not be considered to represent the whole intestinal microecology. In addition, observations based on the cultivation of luminal contents may not reflect the microbiota adhered to mucosa.

Most of the bacterial studies have been performed with traditional cultivation and characterization methods, which may have biased the identification and taxonomy of microbiota. In humans, it is estimated that only 40% of intestinal bacteria are culturable (3); a similar outcome can be expected also in dogs and cats. In addition, the bacterial taxonomy and nomenclature have changed during time, so bacteria identified in earlier studies may currently be re-classified under a different name. For a more in-depth description on the analysis of the intestinal microbiota, see the chapter by Ben-Amor and Vaughan in this book.

Proximal small intestine harbors total bacteria of 106-8 CFU/ml of luminal content. The number of intestinal bacteria increases distally, reaching up to 1014 CFU/g in feces. In the small intestine aerobic and facultative aerobic bacteria outnumber anaerobic bacteria (4). When moving aborally in the gut, anaerobic bacteria start to dominate and finally gain numbers as high as 1010 of CFU anaerobic bacteria/g fecal material (5).

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