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

Abstract

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&#x2009;<&#x2009;0 (HC) and dogs with CE and DI&#x2009;>&#x2009;0 (increased DI-CE) or DI&#x2009;<&#x2009;0 (normal DI-CE). ANIMALS: Retrospective cross-sectional study including 78 HC and 138&#x2009;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[95% confidence interval (CI)]&#x2009;=&#x2009;0.12 [0.08-0.17]) than normal DI-CE (0.02 [0.01-0.04]) compared with HC (adjusted-p&#x2009;<&#x2009;0.02), characterized by increased counts of carbohydrate and lipid degradation genes. Similarly, increased DI-CE (PERMANOVA, median R[95% CI]&#x2009;=&#x2009;0.23 [0.14-0.34]) had larger shifts in fecal metabolome than normal DI-CE (0.10 [0.04-0.20]; adjusted-p&#x2009;<&#x2009;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&#x2009;ng/mg; adjusted-p&#x2009;<&#x2009;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.