Differences in the Intestinal Microbiome and Lipidome of Dogs Diagnosed with Idiopathic Inflammatory Bowel Disease and Food-Responsive Diarrhea before and after the Induction Phase of Treatment

Background: Idiopathic inflammatory bowel disease (IBD) and food-responsive diarrhea (FRD) are common categories of chronic inflammatory enteropathy (CIE) in dogs. The intestinal microbiota is considered a major contributing factor to the pathogenesis of IBD. Intestinal dysbiosis has been identified in dogs with IBD, but only little information is available on differences in the mucosal microbiota of dogs diagnosed with IBD and FRD. In humans, dyslipidemia has also been described in patients with IBD. However, studies on the lipid profile in dogs with IBD or FRD are currently lacking. Objectives: This is the first study to (1) compare the intestinal mucosal microbiota of dogs with IBD and FRD in the duodenum and the colon, (2) evaluate differences in the mucosal microbiota of each dog before and after the induction phase of treatment, and (3) evaluate the systemic phospholipid profile of dogs with IBD or FRD also both prior to and after the induction phase of treatment. Materials and Methods: Duodenal and colonic mucosal biopsies from 24 dogs with CIE (15 FRD, 9 IBD) and EDTA-plasma and whole blood from 32 dogs (16 FRD, 16 IBD) were retrieved from a former study on canine CIE. All client-owned dogs were prospectively enrolled in the study. All dogs received a standardized diagnostic work-up and treatment including a dietary trial. Dogs that responded to the elimination diet within 14 days were classified as FRD; the remaining dogs requiring additional immunosuppressant treatment were classified as IBD. Biopsy specimens of duodenum and colon were obtained endoscopically both before and after standard therapy. DNA was extracted from these biopsies and the intestinal mucosal microbiota of the duodenum and colon were evaluated by Illumina sequencing of the bacterial 16S rRNA gene. The phospholipids in whole blood and EDTA plasma, collected both before and after treatment, were analyzed by hydrophilic interaction liquid chromatography (HILIC). Differences in the composition were statistically assessed by alpha diversity indices, principal coordinate analysis, analysis of similarities (ANOSIM) and linear discriminant (LDA) analysis effect size (LEfSe) for the microbiota and by principal component analysis (PCA), analysis of variance (ANOVA) and random forest analysis for the phospholipid profile. Results: All differences in the microbial composition and phospholipid profile described below are statistically confirmed with significance set at p-value 2.0. No difference in the global bacterial composition was identified neither between the two disease groups of dogs nor with the treatment status. However, abundances of several bacterial taxa varied between disease groups and also with the treatment status. When comparing disease groups, an unclassified genus of Neisseriaceae was more abundant in the duodenum in the IBD group, whereas Bilophila spp. occurred more frequently in the duodenum of the FRD group. Comparison before and after treatment revealed Enterococcus spp., Corynebacterium spp. and Proteobacteria to be enriched in the duodenum of FRD dogs before treatment. Bacteroides spp. was more abundant in the colon in the FRD group post-treatment. In the IBD dogs, Unclassified_Neisseriaceae was more abundant in the duodenum and mainly Proteobacteria (Burkholderia spp., Citrobacter spp.) in the colon prior to treatment. Bacteroides spp. was significantly more abundant in the colon after treatment. The phospholipidome differed dependent on the type of specimen (whole blood vs. plasma). In addition, treatment and disease severity presented the most significant factors determining the variance of the phospholipid profile. An increase in lysolipids and a significant shift of the phosphatidylcholine (PC) species from PC 38:4 (18:0 / 20:4) to mainly lysophosphatidylcholine 18:0 was observed after treatment. Conclusions: Some differences in individual bacterial taxa were identified both between disease groups of dogs and with regard to treatment status. The role of these bacterial groups in the pathogenesis of IBD and FRD is still unknown. However, Bacteroides spp. might be of importance, and this species could potentially serve as marker of treatment response. Furthermore, significant variances were identified in the phospholipid profiles of dogs with IBD and FRD, which were particularly associated with the type of specimen used, disease severity, and treatment status. These alterations in the phospholipid profile could potentially aid in monitoring the response to treatment. Subsequently, specific modulation of the intestinal microbiota and the phospholipid profile might also present novel therapeutic strategies in dogs with CIE