Basic clinical characteristics
A total of 166 patients were enrolled in the study, with 17 in CKD group, 47 in CT group, 49 in HD group, and 53 in PD group. No significant differences in age, gender, and body weight were found among the four groups (p > 0.05). Renal function tests, including uric acid, blood urea, nitrogen, and serum creatinine in the healthy control group were significantly lower than those in the other three groups (p < 0.001). Metabolic status, including the expression levels of albumin and TC, were significantly higher in CT group (p < 0.001), while FBG showed no difference among groups (p = 0.29) (Table 1). Primary kidney diseases were altered among three groups of CKD patients, cases of chronic nephritis in CKD, HD, and PD was 4(23.5%), 2716 (32.7%) and 1321(39.6%), the number of hypertensive nephropathy in CKD, HD, and PD was 10(58.8%), 27(55.1%) and 1322 (4124.5%)， chronic renal failure only observed in PD group with 9 (17.0%) patients (p = 0.002). In inflammatory conditions, CRP and IL–6 were significantly higher in CKD patients (p < 0.001) while WBC showed no difference among four groups (p = 0.18). CKD patients with PD showed a trend of longer dialysis vintage compared to those with HD (39.85±39.44 month vs. 35.35±32.33 month, p = 0.532). Comorbidities including coronary disease and hypertension showed no difference between PD and HD populations (p = 0.305 and p = 0.327). No significant difference was found on distribution of NYHA classifications (P = 0.117). (Table 1).
Alpha-beta diversity analysis of intestinal flora
Alpha and beta diversity analysis showed that the intestinal flora structure diversity (including Sob index, Chao index, Ace index, Shannon index, and Simpson index) and species diversity distance in PD group was significantly lower than CKD, CT, and HD groups under the same measurement depth (p < 0.001) (Fig. 1). Further analysis showed that the express of albumin affects the alpha diversity, patients showed with lower albumin level present lower intestinal flora structure diversity and vice visa (Fig. 2).
Different relative abundance level of bacterial taxa
A total of 20 intestinal flora phyla were detected in 166 fecal samples, namely Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Verrucomicrobia, Fusobacteria, Cyanobacteria, Synergistetes, Tenericumtes, TM7, Chloroflexi, Lentisphaerae, Euryarchaeota, Acidobacteria, Chlamydiae, Spirochaetes, OD1, Elusimicrobia, Parvarchaeota, and unclassified, mostly abundance in Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Verrucomicrobia (Fig. 3A). All samples were divided into 3 dominant intestinal types including Bacteroides-dominant gut type, Firmicutes-dominant type and Proteobacteria-dominant gut type, which displayed significantly different distributions among the four treatment groups (p < 0.01). The relative abundance of bacteria within the phylum Bacteroidetes and Firmicutes were significantly decreased, while relative abundance of the phylum Proteobacteria was increased in PD group (Fig. 3B-D).
The genus level composition of each group of intestinal flora
Further analyses found 198 genera, the abundance of 86 genera were significantly different (Fig. 3B). 42 genera belong to the Bacteroidetes (7), Proteobacteria (7), Firmicutes (17), and Actinobacteria (11) phyla were significantly different in PD group, 20 genera belonging to Bacteroidetes (5), Proteobacteria (4), Fusobacteria (5), and Firmicutes (6) were significantly different in HD group, 21 genera belonging to Bacteroidetes (3), Proteobacteria (7), and Firmicutes (11) were significantly different in CT group and 3 genera in CKD group belonging to Bacteroidetes (1), Firmicutes (1), Actinobacteria (1) were significantly different (Fig. 4). 4 dominant genera among four groups were: Bacteroides, Faecalibacterium, Escherichia and Salmonella. Bacteroides and Faecalibacterium were dominant genus in CT, CKD, and HD groups, while Escherichia and Salmonella was dominated genus in PD group (Fig. 5).
Relative abundance of indole and p-cresol producing taxa in family level
Bifidobacteriaceae and Prevotellaceae was significantly decreased, while Enterobacteriaceae, Enterococcaceae were significantly increased in patients with PD compared with the other groups. A trend of increased level was found in the relative abundance of Verrucomicroblaceae (Fig 6).
Analysis of intestinal microbial function
High-abundance bacteria KEGG level 1 pathways in the four groups were significantly enriched in metabolism, genetic information processing, and environmental information processing. The following KEGG level 2 pathways were significantly enriched in carbohydrate metabolism, amino acid metabolism, energy metabolism, translation, and membrane transport. Number of differential expressed genes in KEGG enrichment pathways: starch and sucrose metabolism, alanine aspartate and glutamate metabolism, arginine and proline metabolism, oxidative phosphorylation, ribosome, aminoacyl tRNA biosynthesis, and ABC transporters were significantly different in PD group compared with CT, CKD, and HD groups (Fig. 7 & Table S1).