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The Canine Inflammatory Bowel Disease Activity Index (CIBDAI) and Canine Chronic Enteropathy Clinical Activity Index (CCECAI) are key tools for monitoring chronic enteropathies (CE) in dogs. Despite their widespread use, concerns persist regarding their intra-observer repeatability and inter-observer reproducibility, which may impact clinical and research applications. This study evaluated the reliability of these indices through a two-phase approach using anonymized clinical records. In Phase 1, two observers independently scored 41 consultation forms twice, one month apart, to assess repeatability and reproducibility. Phase 2 involved four observers with varying expertise who scored 59 forms using a standardized guide addressing Phase 1 inconsistencies. Statistical methods included Lin's concordance correlation coefficient and Bland-Altman plots. High intra-observer repeatability was observed for most variables, but inter-observer reproducibility was limited for CIBDAI, CCECAI, and fluctuating parameters like stool consistency and defecation frequency. The standardized guide marginally improved consistency but did not resolve discrepancies. Expert evaluators did not consistently outperform non-experts. Reproducibility declined in more clinically severe cases. These findings highlight the need for standardized training, dynamic scoring systems, and digital tools to enhance reliability. Addressing these limitations is critical to improve clinical decision-making and research outcomes in canine CE.

Background The gut microbiota and derived metabolites play a key role in regulating host physiology. Diet is identified as a key regulatory factor of the microbiota composition and, potentially, of subsequent functionalities. Demonstrating the role of diet may be complex as most human studies are cross-sectional and dietary intervention is often accompanied by hygienic changes. The objective of the present study was to investigate the impact of an industrial diet on the modulation of the microbiota and targeted functionalities using a canine “natural” model. Results We carried out a controlled dietary trial in a cohort of Tunisian semi-stray dogs. We made a transition from a natural diet to an industrial kibble diet and monitored the composition of the fecal microbiota, the concentration of short-chain fatty acids (SCFA) and bile acids (BAs), and protease activities. We demonstrated that dietary change significantly decreased fecal primary bile acids levels and protease activities. Interestingly, correlation analyses demonstrated that variation of specific microbial genera were associated with modulated physiological parameters. Conclusions Our study reveals that an industrial diet induces beneficial changes in microbial composition and functions characterised by increased diversity, synthesis of SCFA and secondary bile acids production, stressing the key role of the diet-microbiota-dog crosstalk.

Chronic inflammatory enteropathies (CIEs) in dogs are currently classified based on response to sequential treatment trials into food-responsive (FREs); antibiotic-responsive (AREs); immunosuppressant-responsive (IREs); and non-responsive enteropathies (NREs). Recent studies have reported that a proportion of NRE dogs ultimately respond to further dietary trials and are subsequently misclassified. The FRE subset among CIEs is therefore probably underestimated. Moreover, alterations in the gut microbiota composition and function (dysbiosis) have been shown to be involved in CIE pathogenesis in recent research on dogs. Metronidazole and other antibiotics that have been used for decades for dogs with AREs have been demonstrated to result in increased antimicrobial resistance and deleterious effects on the gut microbiota. As a consequence, the clinical approach to CIEs has evolved in recent years toward the gradual abandonment of the use of antibiotics and their replacement by other treatments with the aim of restoring a diverse and functional gut microbiota. We propose here to refine the classification of canine CIEs by replacing the AREs category with a microbiota-related modulation-responsive enteropathies (MrMREs) category.

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterised isolates between laboratories has parallelised research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the genetics that underpins it. Campylobacter jejuni strain NCTC11168, deposited at the National Collection of Type Cultures in 1977, has been widely adopted as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C. jejuni NCTC11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates previously identified to have aberrant phenotypes varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37oC, invasion of chicken and human cell lines and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. Footnotes * https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467 * https://doi.org/10.6084/m9.figshare.7849268 * https://microreact.org/project/NCTC11168