Gut microbiota dysbiosis in a novel mouse model of colitis potentially increases the risk of colorectal cancer

This research investigates the gut microbiota profile in a novel mouse model of colitis with a specific knockout (KO) of the hnRNPI gene in intestinal epithelial cells. This KO mouse model is characterized by activation of the NF-κB pathway and early-onset colitis. Although the influence of gut microbiota on colitis pathophysiology is well established, its role in hnRNPI KO mice remains unexplored. To address this, we used 16S rRNA gene amplicon sequencing to compare the gut microbiota between hnRNPI KO and wild-type (WT) mice at baseline and following a dextran sodium sulfate (DSS) challenge. Untargeted metabolomics was also used to profile bacterial metabolites identified in the 16S rRNA analysis. Fecal DNA was extracted and analyzed to determine gut microbiota composition. Body weight and the disease activity index (DAI) were measured, while organ samples, including liver, spleen, and colon, were collected during necropsy for analysis. Representative bacteria identified from 16S-rRNA gene sequencing were cultured in designated media to further characterize their metabolite profiles. Initial findings on 16S-rRNA gene analysis revealed significant disparities in the gut microbiota between KO and WT mice. Notably, KO mice exhibited lower levels of Dubosiella sp. but higher levels of Paraclostridium bifermentans and Enterococcus faecalis compared with WT mice. The DSS challenge exacerbated colitis in KO mice and led to further alterations in gut microbiota diversity and composition. After DSS treatment, significant shifts were observed in five bacterial species. Specifically, Dubosiella sp. remained consistently low, whereas P. bifermentans persisted at high levels in DSS-treated KO mice. In addition, elevated levels of Clostridium paraputrificum and Lactococcus garvieae were detected in KO mice, whereas Malacoplasma muris was significantly higher in WT mice. The metabolomic analysis highlighted distinct bacterial metabolic profiles between P. bifermentans and Dubosiella newyorkensis. P. bifermentans were found to produce higher levels of glycocholate, urocanate, and deoxycholate, whereas D. newyorkensis predominantly produced N-formyltryptophan, indole-3-carboxaldehyde, and glycyl-L-norleucine. Importantly, an imbalance in the abundance of Dubosiella sp. and P. bifermentans was observed in KO mice, suggesting a potential role in colitis pathogenesis. Comprehensive pathway analysis based on 16S rRNA gene sequences revealed disturbances in several pathways, including those related to human diseases such as cancer, which were notably increased in hnRNPI KO mice after the DSS challenge. These findings underscore the disrupted microbiome balance in KO mice, particularly the altered levels of Dubosiella sp., which may play a pivotal role in gut health and colitis development.