Our objective was to determine the effects of feeding raw meat–based diets with or without inulin or yeast cell wall extract (YCW) on fecal microbial communities of dogs using 454 pyrosequencing. Six healthy female adult beagles (5.5 ± 0.5 years; 8.5 ± 0.5 kg) were randomly assigned to six test diets using a Latin square design: (1) beef control; (2) beef + 1.4% inulin; (3) beef + 1.4% YCW; (4) chicken control; (5) chicken + 1.4% inulin; and (6) chicken + 1.4% YCW. Following 14 days of adaptation, fresh fecal samples were collected on day 15 or day 16 of each period. Fecal genomic DNA was extracted and used to create 16S rRNA gene amplicons, which were subjected to 454 pyrosequencing and qPCR. Predominant fecal bacterial phyla included Fusobacteria, Firmicutes, Bacteroidetes, and Proteobacteria. Beef-based diets increased (P < 0.05) Escherichia, but decreased (P < 0.05) Anaerobiospirillum vs. chicken-based diets. Inulin decreased (P < 0.05) Enterobacteriaceae. Inulin increased (P < 0.05) Megamonas vs. control. Inulin also decreased (P < 0.05) Escherichia vs. YCW. qPCR data showed that YCW increased (P < 0.05) Bifidobacterium vs. inulin and control and inulin increased (P < 0.05) Lactobacillus vs. YCW. Although a few changes in fecal microbiota were observed with inulin or YCW consumption, a strong prebiotic effect was not observed.