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Anthropomorphism of dogs has affected feeding and the choice of components present in diets for dogs. Conflicting trends are present: raw or vegetarian appear more prevalent. Animal-derived proteins seem to have unfavourable impacts on intestinal microflora by decreasing the presence of <i>Bacteroidetes</i>. This preliminary study evaluates whether effects of diets with animal proteins on intestinal microbiota can be compensated by the addition of certain carbohydrates to dog diet. Eight female beagles were included in a cross-over study and fed a vegetarian diet or the same diet supplemented with feather meal (2.7%) and either 20% of cornmeal, fermented or non-fermented rye (moisture content of the diets about 42%). A 16S rRNA gene amplification was performed within the hypervariable region V4 on faecal samples and sequenced with the Illumina MiSeq platform. The <i>Firmicutes</i>/<i>Bacteroidetes</i> ratio tended to shift to the advantage of <i>Firmicutes</i> when feather meal and cornmeal were added (<i>Firmicutes</i>/<i>Bacteroidetes</i> ratio of 5.12 compared to 2.47 when offered the vegetarian diet) and tended to switch back to the advantage of <i>Bacteroidetes</i> if rye: fermented (2.17) or not (1.03) was added. The addition of rye might have the potential to compensate possible unfavourable effects of diets with animal proteins on intestinal microbiota of dogs.