Table 3.

Microbial changes in cats and dogs with gastrointestinal disease¹

Species	Sampling location	Tissue type	Disease	Method	Microbial changes in diseased animals	Reference
Cats	Small intestine	Biopsies	IBD	FISH	Increase in Enterobacteriaceae	Janeczko et al., 2008
Dogs	Duodenum	Biopsies	IBD	16S rRNA gene clone libraries	Increase in Proteobacteria; decrease in Clostridia	Suchodolski et al., 2010
Dogs	Duodenum	Mucosal/luminal brushings	IBD	16S rRNA gene clone libraries	Increase in Enterobacteriaceae (Escherichia coli); reduction in biodiversity	Xenoulis et al., 2008
Dogs	Duodenum	Mucosal/luminal brushings	Chronic enteropathies (FRD, ARD)	16S rRNA gene clone libraries	Increase in Lactobacillales (Streptococcus and Abiotrophia)	Allenspach et al., 2010
Dogs	Duodenum	Biopsies	IBD	454-pyrosequencing of the 16S rRNA gene	Increase in Proteobacteria; decrease in Faecalibacterium, Ruminococcus, and Dorea spp. within the Clostridium clusters IV and XIVa	Jergens et al., 2010
Dogs	Duodenum	Biopsies	Chronic enteropathies (SRD, FRD, ARD)	454-pyrosequencing of the 16S rRNA gene	Reduced biodiversity	Craven et al., 2009
Cats	Feces	Fecal samples	Small and large bowel IBD	FISH	Decreased total bacteria, Bifidobacterium spp. and Bacteroides spp.; increase in Desulfovibrio spp.	Inness et al., 2007
Dogs	Feces	Fecal samples	Chronic diarrhea	FISH	Increase in Bacteroides	Jia et al., 2010
Dogs	Feces	Fecal samples	Diarrhea	T-RFLP	Increases in Clostridium perfringens, Enterococcus faecalis, and Enterococcus faecium	Bell et al., 2008
Dogs	Colon	Biopsies	Granulomatous colitis of Boxer dogs	FISH	Intracellular translocation of adherent and invasive E. coli	Simpson et al., 2006

¹IBD = inflammatory bowel disease; FISH = fluorescence in situ hybridization; ARD = antibiotic responsive diarrhea; FRD = food-responsive diarrhea; SRD = steroid-responsive diarrhea; T-RFLP = terminal RFLP.