Dynamic Observation of Colonic Lesions, Commensal Microbiome, and Mycobiome Variations in Trinitrobenzene Sulfonic Acid-Induced Experimental Crohn’s Disease in Rats

Introduction: Crohn’s disease (CD) is an inflammatory bowel disease characterized by chronic inflammation of the entire digestive lining. Although the pathogenesis of CD remains unclear, multiple factors, especially altered microbiota, are among its causes. Methods: In this study, an experimental CD model was established by trinitrobenzene sulfonic acid (TNBS) enema. Then the dynamic changes of colonic tissue lesions, tight junctions, inflammation response, and oxidative stress are respectively tested by hematoxylin and eosin staining, immunofluorescence staining, and commercial kits. 16S rRNA and ITS sequencing of colonic feces were applied to analyze the composition and diversity of the microbiome and mycobiome for lasting 5 weeks. Results: As a result, despite TNBS being applied only once time, the stimuli-caused injury reached a peak in the second week (the most severe period), after which symptoms began to gradually return to the normal stage. Additionally, consistent with the TNBS-caused colonic damage, deaths were also concentrated within 2 weeks after modeling, with only one death occurring in the subsequent period despite ongoing inflammation and other typical symptoms. In terms of gut bacteria, microbiome diversity decreased significantly while mycobiome diversity increased, along with the enrichment of harmful microbiota and shrinkage of probiotic microorganisms. Conclusion: Therefore, the data suggested that TNBS-induced CD can be roughly divided into two phases: the acute inflammatory phase (weeks 1–2) and the chronic inflammatory phase (weeks 3–5). However, the microbiome and mycobiome dysbiosis did not return to normal within the trial period. Hence, our findings may facilitate a better comprehension of the dynamic progress of experimental TNBS-induced CD.