Specifically, we discuss the modulation of CKD-MBD by uremic toxins of bacterial origin, the impact of dietary phosphate and phosphate binders on the gut microbiota, the interaction between vitamin D and parathyroid hormone (PTH) with the microbiota and the potential therapeutic use of microbiota in CKD-MBD through the concepts of optimization of phosphorus utilization and phosphate accumulating organisms. Here, PTH is linked to chronic kidney disease.