Characterization of the Fecal and Mucosa-Associated Microbiota in Dogs with Chronic Inflammatory Enteropathy

Abstract

Canine chronic inflammatory enteropathy implicates multifactorial pathogenesis where immunological dysregulation and gut microbiota changes have a central role. Most sequencing-based taxonomic studies have been focused on the fecal microbiota. However, the analysis of these samples does not provide complete information regarding the composition of the small intestine affected by this canine disease. Therefore, in this study, we aimed to characterize the intestinal bacterial microbiota in dogs with inflammatory bowel disease (IBD) (n = 34) by means of duodenal biopsies and fecal samples collected at the time of the diagnosis and to compare those to a group of healthy dogs (n = 12) using the 16S ribosomal RNA (16S rRNA) gene-targeted sequencing (Illumina MiSeq platform). Our study showed that IBD dogs presented differences in the fecal bacterial communities when compared with healthy dogs, with a lower relative abundance of Prevotellaceae (p = 0.005), Prevotella (p = 0.002), and Prevotellaceae Ga6A1 group (0.006); Erysipelotrichales (p = 0.019), Candidatus Stoquefichus (p < 0.001), Erysipelotrichaceae (p = 0.011), and Allobaculum (p = 0.003); Lachnospiraceae NK4A136 group (p = 0.015), Sellimonas (p = 0.042), Oscillospirales (p = 0.037), Oscillospiraceae UCG–005 (p < 0.001), Faecalibacterium (p = 0.028), and Fournierella (p = 0.034); Acidaminococcales, Acidaminococcaceae, and Phascolarctobacterium (p = 0.001); Aeromonadales (p = 0.026), Succinivibrionaceae (p = 0.037), and Succinivibrio (p = 0.031). On the other hand, a higher relative abundance of Enterococcaceae (Enterococcus; p = 0.003), Streptococcaceae (Streptococcus, p = 0.021), Enterobacterales (p = 0.027), Enterobacteriaceae (p = 0.008), and Escherichia–Shigella (p = 0.011) was detected. Moreover, when evaluating α–diversity, the dogs with IBD showed lower diversity in terms of richness and abundance of species (observed species [p = 0.031] and Shannon index [p = 0.039]). Furthermore, fecal microbiota in dogs with IBD was significantly different from healthy dogs (p = 0.006). However, only a few taxa relative abundance shifts (lower Rubrobacteria, Rubrobacterales, Rubrobacteriaceae, and Rubrobacter [p = 0.002]; Cyanobacteria [p = 0.010], Vampirivibrionia, Obscuribacterales, and Obscuribacteraceae [p = 0.005]; Neisseriaceae [p = 0.004] and Conchiformibius [p = 0.003]) were observed when assessing duodenal-associated microbiota of dogs with IBD. Thus, even if the bowel inflammation mainly affects the small intestine in the IBD-affected dogs of the study, fecal specimens may constitute a better sample due not only to their easy availability but also in terms of searching for bacterial taxa as biomarkers for canine IBD. The use of different diets in the study can also have a partial influence on the microbiota composition. Future studies encompassing multi-omics approaches should evaluate the functionality in both levels to unravel the pathophysiology of canine IBD.

A dynamics association study of gut barrier and microbiota in hyperuricemia

“…The short chain fatty acids secreting genus Parabacteroides was showed reduce neutrophil infiltration and exert anti-proinflammatory signaling ( Wu T. et al, 2019 ; Lei et al, 2021 ; Cui et al, 2022 ). Depletion of Erysipelotrichales has also been reported previously in inflammatory bowel disease dog ( Díaz-Regañón et al, 2023 ) and crohn disease ( Gevers et al, 2014 ). Notably, the reduction of key bacterial populations at the early stages of hyperuricemia, although not directly linked to abnormal uric acid levels and intestinal barrier function, may initiate a cascade of events that hinder immune development, exacerbate microbiota disruption, and lead to various long-term adverse outcomes.…”

Relationship between sheep feces scores and gastrointestinal microorganisms and their effects on growth traits and blood indicators

“…Cellvibrionales flora, Caproiciproducens-s_uncultured_bacterium , and Caproiciproducens were the key flora influencing growth performance. Acidaminococcales, and Acidaminococcaceae were identified to carry antibiotic resistance genes, and their relative abundance in the feces of the healthy group was significantly higher than that of the diarrhea group, which is in agreement with our findings ( Díaz-Regañón et al, 2023 ). Gammaproteobacteria include Enterobacteriales, Pseudomonas , etc., which are the hallmark flora of intestinal inflammation and diarrhea ( Williams et al, 2010 ).…”

Grape seed proanthocyanidin improves intestinal inflammation in canine through regulating gut microbiota and bile acid compositions

“…Specifically, Faecalibacterium , Fusobacterium , Chiranonis , Blautia , and Turicbacter are commonly decreased, whereas Streptococcus and Escherichia coli show an increase during dysbiosis 42,43,45 . Consistent with our research findings, the reduction in Faecalibacterium abundance is a common characteristic of gastrointestinal diseases in several species, including dogs, and is associated with chronic constipation, celiac disease, irritable bowel syndrome, and IBD 7,41 . In the genus Faecalibacterium , Faecalibacterium prausnitzii has been found to exhibit anti‐inflammatory actions through the induction of IL‐10 and inhibition of TNF‐α, IL‐6, and IL‐12, as well as the promotion of tight junction protein expression to alleviate intestinal hyperosmolarity 46 .…”

“…Studies have found that polyphenol intake can elevate Bacteroidetes abundance in the gut and then lead to a decline in the Firmicutes to Bacteroidetes ratio, which has been linked to reduced serum cholesterol and fat weight through regulation of lipid metabolism 38,39 . Studies on dogs afflicted with acute diarrhea showed similar microbial changes in this study, in which the abundance of Faecalibacterium , Ruminococcaceae, and Bacteroidetes was decreased, but Clostridiaceae was increased 7,40,41 . Due to the inconsistency in the abundance of a single taxon for distinguishing between health and disease, the dysbiosis index (DI) based on quantitative PCR analysis of canine fecal samples serves as a reliable indicator for assessing gastrointestinal diseases 42 .…”