Prebiotics are selectively fermentable dietary compounds that result in changes in the composition and/or activity of the intestinal microbiota, thus conferring benefits upon host health. In veterinary medicine, commercially available products containing prebiotics have not been well studied with regard to the changes they trigger on the composition of the gut microbiota. This study evaluated the effect of a commercially available nutraceutical containing fructo-oligosaccharides (FOS) and inulin on the fecal microbiota of healthy cats and dogs when administered for 16 days. Fecal samples were collected at two time points before and at two time points during prebiotic administration. Total genomic DNA was obtained from fecal samples and 454-pyrosequencing was used for 16S rRNA gene bacterial profiling. The linear discriminant analysis (LDA) effect size (LEfSe) method was used for detecting bacterial taxa that may respond (i.e., increase or decrease in its relative abundance) to prebiotic administration. Prebiotic administration was associated with a good acceptance and no side effects (e.g. diarrhea) were reported by the owners. A low dose of prebiotics (50 mL total regardless of body weight with the end product containing 0.45% of prebiotics) revealed a lower abundance of Gammaproteobacteria and a higher abundance of Veillonellaceae during prebiotic administration in cats, whileStaphylococcaceae showed a higher abundance during prebiotic administration in dogs.These differences were not sufficient to separate bacterial communities as shown by analysis of weighted UniFrac distance metrics. A predictive approach of the fecal bacterial metagenome using PICRUSt also did not reveal differences between the period before and during prebiotic administration. A second trial using a higher dose of prebiotics (3.2 mL/kg Guard et al., 2015; Hand et al., 76 2013; Handl etal., 2013;Junginger et al., 2014;Kieler et al., 2016;Minamoto et al., 2014; 77 Minamoto et al.,2015;Song et al., 2013;Suchodolski et al., 2015). These studies are supported 78 by meta'omic analytic techniques (Morgan and Huttenhower, 2014) and powerful freely-79 available computational resources to analyze the generated data (Navas- Molina et al., 2013 106 Moreover, prebiotics should theoretically increase the abundance of certain bacterial groups (e.g.107 Lactobacillus and Bifidobacterium) in the gut in order to be considered a prebiotic, given current 108 definitions of these dietary compounds (Gibson et al., 2010). 175 from all fecal samples as described elsewhere . Primers specific for 16S176 rRNA genes were used to amplify the variable V4-V5 region as described previously et al., 2009). Fecal bacterial communities were evaluated using 454-178 pyrosequencing before and during prebiotic administration using a bacterial tag-encoded FLX-179 titanium 16S rRNA gene amplicon pyrosequencing (bTEFAP) as described previously for canine 180 and feline fecal samples Handl et al., 2011 Garcia-Mazcorro et al., 2016; 219 that contained normal as a category. As pe...