Multi‐Omic Analysis of the Microbiome and Fecal Metabolome in Mice with Experimentally Induced Chronic Colitis

Abstract

Ulcerative Colitis (UC) is characterized by chronic inflammation of the colon and results from an interplay of genetic and environmental factors that trigger an inappropriate immune response. Gut microbiota has emerged as a critical factor in UC pathogenesis. It is hypothesized that the gut microbiota exerts its effects on the host via production, utilization, or alteration of local and circulating metabolites. However, functional interactions of gut microbiota and metabolites in a chronic colitis model has not been systematically evaluated and was the focus of this study. Methods Chronic colitis was induced with 5 cycles of 2.5% dextran sulfate sodium (DSS) alternating weekly with water in C57BL/6J mice (7-9 wks M). The cecal samples were used for microbiome analysis (ZymoBIOMICS® Targeted Sequencing Service). Fecal metabolic profile was analyzed by “Metabolon” (NC). Interactions between microbes and metabolites were determined by Pearson correlation coefficients (p <0.05) in R. Results Chronic DSS treatment resulted in altered ecological structure of gut microbiota with a significant decrease in alpha diversity (rarefaction curve), beta diversity (Bray-Curtis and UniFrac plots), and Shannon diversity index. On a taxonomic level, LEfSe analysis showed an increase in the composition of Phylum (p) Verrucomicrobia (0.53% water vs 7.3% DSS) and p-Tenericutes (0.012% water vs 0.17% DSS). Differentially abundant species were also observed in p-Firmicutes and Genus g-Turicibacter. Principal Component Analysis showed a strong separation between metabolites detected from mice given water or DSS. We shortlisted significant metabolites belonging to nucleotides and energy metabolism by summing the normalized and imputed values of individual metabolites and further investigated their correlation with differential abundance of microbiota observed in chronic colitis. Purines and Pyrimidines perform many important functions including serving as monomeric precursors of nucleic acids. Under chronic colitis, Guanosine (possesses anti-inflammatory and anti-oxidative properties) was decreased (0.51 fold), while N1-Methyladenosine (m1A-important for RNA methylation and biomarker of tumors) was significantly increased (2.75 fold). The changes in m1A were positively correlated with p-Tenericutes (r 0.929). Also, guanosine showed a significant negative correlation (-0.861 and -0.857) with both p-Verrucomicrobia and g-Turicibacter. UMP and CMP were also decreased (0.5 and 0.64 fold) and negatively correlated with p-Verrucomicrobia (r -0.83 and -0.816). Aconitate and Itaconate (anti-inflammatory and anti-microbial), products of the TCA cycle, were increased (2.92 and 8.87 fold) and positively correlated with p-Tenericutes (r 0.915 and 0.978). Conclusion The dysbiosis associated with chronic colitis affects specific metabolic pathways that may contribute to the pathogenesis of UC. These pathways could be targeted for microbial based therapeutics for UC.