1. Healthy mice fed with a resistance starch (HRS) diet showed upregulation in tryptophan and indole metabolism compared with CKD and CDK-RS groups. 2. RS diet reduced CKD progression compared with regular diet in CKD mice. 3. RS increased the abundance of beneficial bacteria (butyrate-producing bacteria) and decreased mucin-degrading bacteria. 4. Oscillibacter sp. 1–3 was the most abundant bacterium in healthy mice fed with RS. This evidence concerns the gene MUC5AC and chronic kidney disease.