Bacterial and fungal communities in feces from healthy dogs and cats analyzed by massive parallel 16S rRNA gene FLX-titanium amplicon pyrosequencing

This study evaluated the fecal microbiota of 12 healthy pet dogs and pet cats using bacterial and fungal tag-encoded FLX-titanium amplicon pyrosequencing and group specific 16S rRNA gene clone libraries for Lactobacillus and Bifidobacterium spp. The most abundant bacterial phyla in dogs and cats were Firmicutes, Bacteroidetes, and Actinobacteria. The most prevalent bacterial class was Clostridia, dominated by Clostridium (clusters XIVa and XI) and Ruminococcus. At 5% dissimilarity, 106 Operational Taxonomic Units (OTUs) were identified in dogs and 132 OTUs in cats. Diversity indices and principal component analysis (PCA) based on the Unifrac distance metric indicated that cats and dogs harbor species specific microbiota. The Unifrac distance metric further showed that animals cluster together according to age, body condition and diet. Ascomycota was the only fungal phylum detected in cats, while Ascomycota, Basidiomycota, Glomeromycota, and Zygomycota were identified in dogs. Nacaseomyces was the most abundant fungal genus in dogs, while Saccharomyces and Aspergillus were predominant in cats. At 5% dissimilarity, 66 different OTUs were observed in dogs and 16 OTUs in cats. In conclusion, this study indicates that dogs and cats harbor species specific microbiota and that age, diet and body condition might influence the fecal microbiota.