Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial.

Even though dietary fibers are often used as prebiotic supplements in dogs, the effect of individual types of fibers on canine microbiota composition is unknown. The objective of this study was to assess changes in fecal microbiota richness, diversity and taxonomic abundance with 3 different fiber supplements in dogs. These were psyllium husk, resistant starch from banana flour and methylcellulose. They were administered to 17 healthy dogs in a cross-over trial after transition to the same complete feed. Fecal scores and clinical activity indices were recorded, and fecal samples collected before and at the end of supplementation, as well as 2 weeks after each supplement (washout). Illumina NovaSeq paired-end 16S rRNA gene sequencing was performed on all samples. After quality control and chimera removal, alpha diversity indices were calculated with QIIME. Differences in specific taxa between groups were identified using Metastats. Methylcellulose significantly increased fecal scores but had no effect on microbiota. Psyllium resulted in minor changes of specific taxa abundance, but with questionable biological significance. Resistant starch reduced microbiota richness and resulted in the most abundant changes in taxa, mostly a reduction in short-chain fatty acid producing genera of the Bacillota phylum, with an increase in genera within the Bacteroidota, Pseudomonadota, Actinomycetota and Saccharibacteria. In conclusion, while psyllium and methylcellulose led to few changes in the microbiota composition, the taxonomic changes seen with resistant starch may indicate a less favorable composition. Based on this, the type of resistant starch used here cannot be recommended as a prebiotic in dogs.