Background: Patients with end-stage renal disease (ESRD) have extremely high risks of mortality and morbidity, as well as altered gut microbiota and impaired intestinal barrier function. The translocation of gut-derived molecules in ESRD contributes to systemic complications. In this study, we evaluated the gut microbiome difference in ESRD patients compared to age- and gender-matched subjects without kidney disease in discovery and validation cohorts.Results: Compared to controls with normal renal function, an increased α-diversity and distinct β-diversity were found in ESRD subjects. The increase in α-diversity was correlated with protein-bound uremic toxins, particularly hippuric acid. A higher microbial dysbiosis index (MDI) was found in ESRD patients with the following enriched genera: Facealibacterium, Ruminococcus, Fusobacterium, Dorea, Anaerovorax, Sarcina, Akkemansia, Streptococcus, and Dysgonomonas. MDI at the genus level demonstrated highly differentiated accuracies between ESRD and control subjects in the discovery cohort (area under the curve [AUC] of 81.9%) and between ESRD and control subjects in the validation cohort (AUC of 83.2%). On functional enrichment analysis with gut metabolic modules, ESRD subjects presented with increased saccharide and amino acid metabolism when compared with matched controls.Conclusions: An enriched but dysbiotic gut microbiota was presented in ESRD patients, in which the bacteria that were present increase amino acid metabolism linked to the production of protein-bound uremic toxins.