Microbial Gene Profiling and Targeted Metabolomics in Fecal Samples of Dogs With Chronic Enteropathy With or Without Increased Dysbiosis Index

Background: In previous studies, only a subset of dogs with chronic enteropathy (CE) had an increased dysbiosis index (DI) or altered fecal metabolites or both, suggesting differences in underlying intestinal pathophysiology between these subsets. Objectives: To compare microbial functional genes and fecal metabolites between healthy dogs with DI < 0 (HC) and dogs with CE and DI > 0 (increased DI‐CE) or DI < 0 (normal DI‐CE).AnimalsRetrospective cross‐sectional study including 78 HC and 138 CE dogs. Methods: Fecal microbiome was assessed by DNA shotgun sequencing. Dysbiosis index was quantified by qPCR. Targeted fecal metabolites, long‐chain fatty acids, sterols, bile acids (BAs), and carbohydrates were measured using gas chromatography–mass spectrometry (GC–MS). Results: In permutational analysis of variance (PERMANOVA), functional gene profiles showed larger shifts in increased DI‐CE (median R$^{2}$ [95% confidence interval (CI)] = 0.12 [0.08–0.17]) than normal DI‐CE (0.02 [0.01–0.04]) compared with HC (adjusted‐p < 0.02), characterized by increased counts of carbohydrate and lipid degradation genes. Similarly, increased DI‐CE (PERMANOVA, median R$^{2}$ [95% CI] = 0.23 [0.14–0.34]) had larger shifts in fecal metabolome than normal DI‐CE (0.10 [0.04–0.20]; adjusted‐p < 0.02). Increased DI‐CE had lower fecal unconjugated secondary BAs percentage (95% CI; HC, 88.4%–96.4%; normal DI‐CE, 79.8%–99.0%; increased DI‐CE, 28.1%–64.1%) and transporter‐independent carbohydrates (combined ribose, xylose, rhamnose, and arabinose) concentrations (1.6–2.6; 0.7–1.8; 0.3–1.3 ng/mg; adjusted‐p < 0.01). Conclusions: Results indicate differences in fecal microbial gene profiles and metabolome in increased DI‐CE versus normal DI‐CE and HC, suggesting dogs with an increased DI have more severe intestinal changes in metabolic functions.