Abstract: The intestinal mucus layer is mainly composed of mucin 2 (MUC2), a highly glycosylated protein secreted by goblet cells. The Muc2^‒/‒ mice are a spontaneous colitis model, due to intestinal mucus barrier defects, gut microbes directly contact with intestinal epithelial cells and induce intestinal inflammation. Nevertheless, how gut microbes affect the intestinal epithelium and trigger inflammation in the absence of mucus remains unknown. This study analyzed histopathological changes, colonic transcriptome and gut microbiome of Muc2^‒/‒ mice to elucidate the role of gut microbes in inducing intestinal inflammation. Animal experimentations were approved by the Institutional Animal Care and Use Committee of Nanjing University of Chinese Medicine, Ethical Review No. 202302A007. Pathological analysis showed that Muc2^‒/‒ mice manifested considerable intestinal mucosal damage accompanied by inflammatory cell infiltration and goblet cell exhaustion. Transcriptomic analysis showed that mucus synthesis, endoplasmic reticulum stress, and autophagy-related gene expressions were altered in Muc2^‒/‒ mice. Kyoto Encyclopedia of Genes and Gene Ontology pathway enrichment analyses showed considerable enrichment of inflammation and immune-related pathways, and pathways in response to bacteria derived molecules were upregulated. Microbial gene sequencing revealed dysbiosis of the gut microbiome in Muc2^‒/‒ mice, with Akkermansia muciniphila expansion being the characteristic profile. The expansion of Akkermansia muciniphila was confirmed in Il10^‒/‒ mice, which also displayed mucus barrier defects. Correlation analysis showed that the disturbed gut microbes of Muc2^‒/‒ mice was positively correlated with intestinal inflammation and immune-related differentially expressed genes, which were enriched in pathways such as MAPK cascade and chemokine production. In conclusion, in the absence of intestinal mucus layer, gut microbes can induce immune response by affecting the colonic gene transcription, leading to sustained secretion of inflammatory cytokines and intestinal inflammation. This study investigated the mechanism by which gut microbiota induces colonic inflammation in the absence of the intestinal mucus layer through integrated analysis of colonic transcriptomic profiles and gut microbiota dynamics. The findings aim to identify therapeutic targets for colitis treatment and drug discovery.