Abundance and short-term temporal variability of fecal microbiota in healthy dogs

Temporal variations of the intestinal microbiota have been investigated in humans, but limited information is available for other animal species. The study aim was to evaluate the abundance and short-term temporal variability of fecal microbiota in dogs. Two fecal samples were collected (15 days apart) from six healthy dogs. The microbiota was evaluated using fluorescent in situ hybridization (FISH) and 454-pyrosequencing targeting the 16S rRNA and its gene. Pyrosequencing revealed 15 families comprising >80% of all microbiota, with intra-individual coefficients of variation (%CV) ranging from 2 to 141% (median: 55%). In contrast, the inter-individual %CV ranged from 62% (Ruminococcaceae) to 230% (Lactobacillaceae) (median: 145%). Relative proportions of Faecalibacterium and Subdoligranulum were low (two dogs harbored 4-7% of Subdoligranulum, the remaining dogs had <1% of sequences of either genus). Conversely, FISH revealed that Faecalibacterium comprised a median of 5% of total counts (range: 0-8%, probe Fprau645). A novel FISH probe (Faecali 698) was tested that, compared to Fprau645, can detect in silico a similar percentage of Faecalibacterium but higher proportions of Subdoligranulum. This probe revealed a high percentage of Faecalibacterium-Subdoligranulum (median: 16% of DAPI counts). The results should be considered when evaluating changes on the canine intestinal microbiota.