Abstract

Background : Crohn's disease (CD) is characterized by impaired epithelial barrier function and dysregulated gut microbiota, particularly characterized by a reduced abundance of short-chain fatty acid (SCFA)-producing bacteria such as Ruminococcus . Time-restricted feeding (TRF), which limits daily food intake to specific feeding windows, has been demonstrated to restore microbial balance, enrich SCFA-producing bacteria, and enhance gut homeostasis. Nevertheless, the extent to which TRF confers protection against CD, as well as the mechanisms underlying this effect, remains largely unexplored. Methods : Fecal samples were obtained from patients with active CD and from healthy control subjects to quantify the abundance of Ruminococcus . Using 16S rRNA sequencing, we examined the impact of TRF regimens with varying fasting/feeding cycles (12/12, 16/8, and 20/4) on Ruminococcus . In preclinical CD models, we systematically evaluated the protective effect of TRF by analyzing colonic inflammation and fibrosis using histopathological techniques. RNA-seq and epigenetic analyses were performed to elucidate the underlying mechanisms. Results : Fecal Ruminococcus abundance was significantly reduced in patients with CD and inversely correlated with disease activity indices. Among the tested regimens, only the 12/12 fasting/feeding regimen (TRF_12h), but not regimens with shorter feeding windows, robustly increased the Ruminococcus abundance and potently stimulated mitochondrial β-oxidation and lactate generation. Preemptive administration of TRF_12h markedly protected against colitis severity and fibrosis in CD models, as evidenced by marked reductions in F4/80 + /MPO + inflammatory cell infiltration and decreased extracellular matrix deposition. RNA-seq analysis revealed that TRF-mediated epithelial protection was predominantly driven by SCFA-dependent activation of hypoxia-inducible factor-1α (HIF-1α) signaling. IEC-specific knockout of HIF-1α largely abrogated the protectiv