Gut microbes ferment dietary fibers, producing beneficial short-chain fatty acids (SCFAs). Often, individuals with inflammatory bowel disease (IBD) and multiple sclerosis (MS) have altered gut microbiota, reduced SCFAs, and fiber sensitivity. The Armstrong lab demonstrated that unfermented β-fructan fibers induce inflammation via TLR2 and the NLRP3 inflammasome in IBD. Chronic inflammation can promote colorectal cancer (CRC), suggesting that diet-induced inflammation may promote IBD progression to CRC. Similar changes in the gut microbiome, SCFAs, and TLR2 are involved in gut-brain axis diseases, suggesting that fiber-induced inflammation may impact other autoimmune diseases. Therefore, I hypothesized that unfermented β-fructans promote inflammatory processes related to IBD progression to IBD-CRC and affect other gut-brain axis diseases, specifically MS. To examine tumorigenic responses, cell migration (scratch wound assay with Mitomycin C) and barrier integrity (TEER) were examined in human gut epithelial cells (Caco2, T84) treated with β-fructans. Intestinal biopsies (non-IBD/IBD) were cultured ex vivo with β-fructans. Changes in IBD-CRC markers (p53, villin, axin2, NLRP3) were examined with TLR2 (β-fructan receptor) using microscopy. Barrier integrity and cell migration were not impacted by β-fructans, but an inability to polarize cells affected TEER measurements. Pro-tumorigenic markers were positively associated with TLR2 in colonic biopsies. To examine how unfermented β-fructans impact the gut-brain axis beyond IBD, we used the experimental autoimmune encephalomyelitis (EAE) mouse model of MS in germ-free (unable to ferment) mice. Mice began a β-fructan (5%) or control (5% cellulose) diet at day 14 (symptom onset). EAE scores and weight were recorded daily. Tissues were examined for gut damage and demyelinating lesions (H&E, Luxol Fast Blue-Hematoxylin). EAE mice consuming β-fructan displayed worsened CNS symptoms following symptom peak (day 20-28; P<0.05) with increased CNS demyelinating lesions in the brain and spine (P<0.001). While dietary fibers form interactions in the gut, EAE mice had no gut damage. This suggests that unfermented β-fructan promotes disease-specific organ damage in the gut-brain axis, such as IBD progression to IBD-CRC or CNS damage in an MS mouse model. Gut microbiota changes and reduced fermentation increase unfermented fiber, likely altering the immune system (TLR2 pathways), leading to detrimental effects of β-fructan in the gut-brain axis.