Alterations of gut microbiota composition and function in CKD may be due to ureamic state, metabolic acidosis, slow colonic transit, dietary restrictions and pharmacological therapies. These alterations induce microbial fermentation of protein in the colon and formation of ureamic toxins. Ureamic toxins can normally be excreted by the kidney, but may contribute to inflammation and impaired nephron function in patients with chronic kidney disease. Dietary restriction of potassium-rich fruits and vegetables which are common sources of fermentable dietary fiber inhibit the conversion of dietary fiber to short chain fatty acids (SCFA) which are the primary nutrient source for the symbiotic gut microbiota. Reduced consumption of fermentable dietary fiber limits the population of SCFA-forming bacteria and causes disbiosis of the gut microbiota. It may also cause reduction of the regulatory T lymphocyte (T-reg) population and function and result in systemic inflammation. The use of prebiotics may be a therapeutic choice to modulate gut microbiota and reduce ureamic toxin formation that aggravates the progression of chronic kidney disease.