- Vitamin D deficiency reduces microbiota diversity and exacerbates inflammation in IBD and was associated with a worse prognosis. - Increases IL2 levels, modulates T cell cytokine production, improves the function of Foxp3+ Treg cells, inhibits NF-κB activation, and controls the IBD risk gene ATG16L1 and, therefore, can attenuate colon inflammation by regulating JAK/STAT pathway. Here, ATG16L1 is linked to vitamin D deficiency.