Background High throughput 16S rRNA gene sequencing and enhanced culture methods (e.g., expanded quantitative urine culture, EQUC) have established the existence of the human bladder microbiome. We aim to test the hypothesis that the bladder environment of patients with chronic kidney disease (CKD) differs from that of unaffected controls with associated consequences for the composition of the bladder microbiome. Methods and Materials Females (n=66) and males (n=66) diagnosed with CKD and age-BMI-matched healthy control (HC) females (n=22) and males (n=22) were recruited. Transurethral catheterized urine was collected for 16S rRNA gene sequencing and Expanded Quantitative Urine Culture (EQUC). Fecal samples also were sequenced. Urinary analysis, kidney function and serum cytokines were examined. Results Bladder microbiomes of CKD females and males versus HC females and males differed (FDR<0.05); however, the difference was more obvious in females. In CKD females, sequencing revealed depletion of 5 genera, including Lactobacillus, and enrichment of 14 genera, including Escherichia/Shigella, Bifidobacterium, and several clostridial genera (FDR<0.05), while EQUC detected increased Escherichia and decreased Lactobacillus CKDB(P<0.05). Escherichia-Shigella was positively, whereas Lactobacillus was negatively, associated with CKDB-female serum creatinine (r=0.285, P=0.020; r=-0.337, P=0.006, respectively). Lactobacillus was positively associated with eGFR (r=0.251, P=0.042). Some CKD-related serum cytokines were negatively associated with clostridial genera. In contrast, the fecal microbiomes of CKD and HC females and males did not significantly differ in bacterial diversity or composition. However, bladder and fecal microbiomes of CKD females resembled each other more than those of controls, as assessed by the Bray-Curtis Dissimilarity Index (FDR<0.05). Conclusions CKD bladder microbiomes were dysbiotic, which was more obvious in females. This dysbiosis was associated with kidney damage severity and dysregulation of serum cytokines. The increased similarity between bladder and fecal microbiomes of CKD females suggests possible gut-leakage.

The authors have declared no competing interest.

Wuxi Taihu Talents Program Medical and Health High-level Talents Project (THRCJH20200901); Wuxi key medical discipline construction Municipal Clinical Medical Center (municipal public health center) Project (LCYXZX202103); Wuxi Technological Project (N20192047); Zhejiang Provincial Natural Science Foundation of China (LXR22H160001); National Natural Science Foundation of China (81874142 and 82073041).

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