Dysbiosis of urine microbiota in obstructive urinary retention patients revealed by next-generation sequencing

Abstract

Background Urinary retention (UR) is a common urinary system disease can be caused by urinary tract obstruction with numerous reasons, however, the role of urine microbes in these disorders is still poorly understood. The aim of this study was to identify the urine microbial features of two common types of obstructive UR, caused by urinary stones or urinary tract tumors, with comparison to healthy controls. Methods Urine samples were collected from a cohort of 32 individuals with stone UR, 25 subjects with tumor UR and 25 healthy controls. The urine microbiome of all samples was analyzed using high-throughput 16S rRNA (16S ribosomal RNA) gene sequencing. Results We observed dramatically increased urine microbial richness and diversity in both obstructive UR groups compared to healthy controls. Despite different origins of UR, bacteria such as Pseudomonas, Acinetobacter and Sphingomonas were enriched, while Lactobacillus, Streptococcus, Gardnerella, Prevotella and Atopobium were decreased in both UR groups in comparison with healthy controls, exhibited an approximate urine microbial community and functional characteristics of two types of obstructive UR. Furthermore, disease classifiers were constructed using specific enriched genera in UR, which can distinguish stone UR or tumor UR patients from healthy controls with an accuracy of 92.29% and 97.96%, respectively. Conclusion We presented comprehensive microbial landscapes of two common types of obstructive urinary retention and demonstrated that urine microbial features of these patients are significantly different from that of healthy people. The urine microbial signatures would shed light on the pathogenesis of these types of urinary retention and might be used as potential classification tools in the future.

Role of microbiome in kidney stone disease

“…Likewise, they observed an increase in opportunistic pathogens such as Acinetobacter , Enterococcus , Comamonas and Delftia in patients with KSD and also an increase in Lactobacillus , which authors speculated was a self-protective response of the urobiota of these patients. Jiang et al [22 ▪ ] found, unlike these previous studies, an increase in Bacteroidetes in bladder urine microbiota of KSD patients, although Proteobacteria was the majority phylum. Likewise, increases in potential pathogens such as Pseudomonas , Proteus or Acinetobacter and decreases in Lactobacillus and Prevotella were observed.…”

“…Infection was more conclusive in OA1 patients as they showed greater leukocyturia. Jiang et al [22 ▪ ], compared the bladder urine microbiota in patients with obstructive uropathy and healthy controls. Patients with obstructive uropathy had tumors or stones.…”

Impact of coexisting type 2 diabetes mellitus on the urinary microbiota of kidney stone patients

“…The bacteria discovered in this study, such as Sphingomonas , Propionibacterium , and Corynebacterium , have been reported in several previous studies on urinary microbiota ( Ahn et al, 2022 ; Cappelli et al, 2023 ; Nickel et al, 2022 ; Perovic et al, 2022 ; Popovic et al, 2018 ; Kim & Park, 2018 ). However, Methylophilus , identified in this study, has only been reported in earlier studies on human skin and gut microbiota ( Dekio et al, 2005 ; Jiang et al, 2021b ; Jiang et al, 2021b ; Lee et al, 2021 ; Zheng et al, 2023 ). It is necessary to conduct large-scale studies in the future to further clarify the bacterial composition in human urine, which will play a crucial role in redefining urinary tract infections.…”

Characterization of the urogenital microbiome in Miniature Schnauzers with and without calcium oxalate urolithiasis

“… 59 This genus is also overrepresented in the urine of humans with obstructive urinary retention secondary to both uroliths and uroepithelial tumors, and even has been directly isolated from nephroliths of humans. 65 , 66 The independent association of specific organisms with urolithiasis across species supports a potential role of core taxa, such as Acinetobacter , in disease pathogenesis. Acinetobacter secretes oxalic acid during experimental lecithin degradation and can contribute to mineralization of organic compounds in soil, but whether these properties translate into lithogenic risk in the urine remains unclear.…”