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Inflammatory bowel disease (IBD) is associated with an inappropriate immune response to the gut microbiota. Notably, patients with IBD reportedly have alterations in fecal microbiota. However, the colonic microbiota occupies both the gut lumen and the mucus covering the epithelium. Thus, information about mucus-resident microbiota fails to be conveyed in the routine microbiota analyses of stool samples. Further, studies analyzing microbiota in IBD have mainly focused on stool samples taken after onset of inflammation. Our objective was to investigate both temporal and spatial changes in colonic microbiota communities preceding the onset of colitis.We studied mucus and stool microbiota using a spontaneous model of colitis, the mdr1a−/− mouse, and their respective wild-type littermate controls in a time series mode.Using this approach we have shown that microbial dysbiosis was evident in the mucus but not stools, with reduced abundance of Clostridiales evident in the mucus but not stools, of colitis-prone mice mdr1a−/−- mice 12 weeks before the onset of detectable inflammation. This altered microbial composition was coupled with a significantly thinner mucus layer. On emergence of inflammation, dysbiosis was evident in the stools and at this time point, the spatial segregation between microbiota and host tissue was also disrupted, correlating with worsened inflammation. Our results reveal that microbial dysbiosis is detectable before changes in the stools. Importantly, dysbiosis in the mucus layer preceded development of colitis.Our data reveal the importance of mucus sampling for understanding the underlying etiology of IBD and fundamental processes underlying disease progression.