Abstract: Background–Shotgun DNA sequencing is an untargeted approach for identifying changes in relative microbiota abundances, while qPCR allows reproducible quantification of specific bacteria. The canine dysbiosis index (DI) is a mathematical model based on the obtained qPCR data designed to evaluate shifts in the global microbiota. Objectives–To correlate results between qPCR assays included in the DI and DNA shotgun sequencing. Animals–Fecal samples from 296 dogs (112 healthy, 150 with various enteropathies, 34 dogs with non-gastrointestinal diseases). Methods–Correlations between relative proportions of bacteria obtained by sequencing or qPCR were evaluated by Spearman tests. Samples were classified into four groups based on the DI interpretation: normal (DI< 0 with all evaluated bacterial taxa within the reference interval, RI), minor changes (DI< 0 but with at least one bacterial taxa out of RI), mild-moderate changes (02). Microbiota shifts were evaluated based on Bray-Curtis distances and statistics were performed with ANOSIM. Results–Significant correlations (P < .001) were found for all bacterial taxa quantified by qPCR and sequencing. A significantly lower alpha diversity (P < .001) was found in dogs with DI>2 (median[range]: 148[70-280]) than in dogs with a normal DI (192[89-329]). The DI classification correctly predicted microbiota shifts obtained by sequencing with increasing size effects (higher R-values indicate larger size effects): minor changes (R=.19), mild-moderate changes (R=.24), and significant dysbiosis (R=.62), compared to dogs with a normal DI (P < .001 for all). Conclusions and clinical importance–The DI correlates with results obtained by DNA shotgun sequencing in dogs.
.jpg "Chi-Hsuan Sung, DVM photo")
