The intestinal microbiome composition and its interactions with the host are important elements in the pathogenesis of gastrointestinal disorders. In small animals, several studies have demonstrated that acute and chronic gastrointestinal diseases are associated with alterations in fecal microbial communities. The aim of this study was to evaluate possible taxonomic biomarkers of inflammatory bowel disease (IBD) using 16S rDNA amplicon sequencing in dogs. Inclusion criteria were histological evidence of intestinal inflammatory cellular infiltration on endoscopy biopsies according to the WSAVA parameters, availability of the clinical activity index (CCECAI) and the microbiota profile. Exclusion criteria included treatment with anti-inflammatory or antimicrobials drugs within 2 months before presentation. We included in the study 360 samples: 326 from dogs with IBD and 34 from control dogs that were clinically healthy and had no gastrointestinal disease in the last year. Microbiome DNA of aliquots were extracted, six hypervariable regions of the 16S genes (V2, V3, V6+V7, V8, V9) were amplified and sequenced on Ion Torrent. The sequences were processed to separate the regions and then analyzed with Mothur to find operational taxonomic units (OTUs), their abundances and taxonomies by using relational database (RDP) as a reference. Alpha and beta diversity for V4 was calculated by using the Phyloseq R. OTUs were significantly different in the two groups of dogs by DESeq2 analysis. There was no significant difference in alpha diversity between IBD and healthy dogs, and it was not possible to discern them in ordination plots. DESeq2 analysis resulted in 34 differentially abundant OTUs belonging to phyla Bacteroidetes, Firmicutes and Proteobacteria. Bacteroidetes were significantly more abundant in IBD dogs, with Bacteroides and Prevotella as the most represented genera. Among Proteobacteria, larger abundances of Enterobacteriaceae, Anaerobiospirillum, Sutterella and Helicobacter were observed in IBD dogs, while Burkholderia was more abundant in healthy dogs. Taxa within the Firmicutes phylum, including Clostridium-XIVb, Streptococcus and Enterococcus were also more abundant in IBD dogs compared to healthy dogs. Lachnospiraceae data were conflicting as OTUs were significantly abundant in both healthy and IBD dogs. As previously reported, Collinsella was found more abundant in IBD dogs. Our data are consistent with previous studies suggesting intestinal microbial dysbiosis in dogs with IBD. As new finding, we identified further gut microbial taxa significantly increased in dogs with IBD that might be useful to better understand the etiology of chronic gastrointestinal diseases and might represent diagnostic markers for IBD.

Disclosures

No disclosures to report.