Abstract Background and Aims The human intestinal tract contains 100 trillion microorganisms, and 500–1000 microbial strains exist in each individual, classified into two main phyla: Firmicutes and Bacteroidetes. The gut bacterial microbiota is altered in patients with chronic kidney disease (CKD). However, the bacterial composition at each stage of CKD is unclear in these patients, including those receiving renal replacement therapy. In this report, we present the changes in the gut microbiota among patients with CKD. Method A total of 93 individuals were recruited for the study. Seventy-three patients had stage 3–5 CKD, including those receiving renal replacement therapy (CKD group), and 20 were age- and sex-matched controls (CKD stage 1–2). Gut microbiome composition was analyzed using a 16S ribosomal RNA gene-based sequencing protocol. Results The beta diversity of the samples was evaluated via principal coordinates analysis (PCoA). The unweighted and weighted UniFrac distances revealed a tendency toward separation of microbiota in the samples according to the CKD stage 1–2 and CKD stage 3–5, 5D groups. At the genus level, the butyrate-producing bacteria Lachnospira, Blautia, Coprococcus, Anaerostipes, and Roseburia were more abundant in the control group (Linear Discriminant Analysis score of >3) than in the CKD group. Lachnospira was more abundant in the control group than in patients with CKD stage 3a. Compared to the control group, multiplex butyrate-producing bacteria were deficient in patients with CKD stage 3b–5D, including in patients receiving renal replacement therapy. Conclusion Our findings highlight that the gut bacterial composition, including butyrate-producing bacteria, deteriorates from CKD stage 3b. Even after renal replacement therapy, the bacterial composition did not change.