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, while Staphylococcaceae 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 36 respond (i.e., increase or decrease in its relative abundance) to prebiotic administration.37 Prebiotic administration was associated with a good acceptance and no side effects (e.g. 38 diarrhea) were reported by the owners. A low dose of FOS and inulin (50 mL total regardless of 39 body weight with the end product containing 0.45% of prebiotics) revealed a significantly lower 40 abundance of Gammaproteobacteria and higher abundance of Veillonellaceae during prebiotic 41 administration in cats, while Staphylococcaceae showed a higher abundance during prebiotic 42 administration in dogs. These differences were not sufficient to separate bacterial communities 43 as shown by analysis of weighted UniFrac distance metrics. A predictive approach of the fecal 44 bacterial metagenome using PICRUSt also did not reveal differences between the period before 45 and during prebiotic administration. A second trial using a higher dose of FOS and inulin (3.2 46 mL/kg body weight with the end product containing 3.1% of prebiotics) was tested in dogs and 52 This study shows a high interindividual variation of fecal bacterial communities from pet cats 53 and dogs, that these communities are relatively stable over time, an...