We recently read with great interest the study by Raj et al. titled “Prebiotic Administration to CKD Patients Modifies Their Microbiome and Metabolism”.1 The research offers compelling insights into prebiotic-mediated gut microbiota and metabolic modulation in chronic kidney disease (CKD), and we highly commend the authors for integrating shotgun metagenomics and multi-tissue metabolomics to unravel host-microbe interactions. However, we would like to share some perspectives and suggestions to further strengthen the study's implications and translational value.