Celiac disease (CD) is small intestinal chronic enteropathy triggered by wheat gluten protein in patients who are HLA-DQ2 or HLA-DQ8 positive. Although 20-30% individuals in the general population are genetically susceptible for CD and the majority of them consume wheat, ~ 1% of them develop the disease. Elimination of gluten containing food from the diet is only known cure for CD. Still, Celiac disease is becoming a public health issue, affecting almost 70 million individuals worldwide. We attempt to delineate the intestinal microbiota with respect to the pre-disease state that is in the first-degree relatives (FDRs) of CD patients along with the gut microbiome of patients with CD and controls. Notably, we found that the microbiota in pre-disease (FDR) and disease state (CD) has less ability of gluten metabolism as compared to the microbiota of control subjects. Similarly, other studies have shown that gluten digestive ability of oral bacteria by encoding endopeptidase specifically cleaves after proline leading to enzymatic detoxification of immunotoxic peptides during GI transit. This led us for the isolation and characterization of human gut microbiota involved in gluten metabolism to reveal the bacterial gene involved in detoxification of immunogenic gluten. We also aim to decode the underlying mechanism through whole genome analysis.