Frainey, B. T. | Search bioRxiv

bioRxiv2026

Urobiome Analysis in Interstitial Cystitis/Bladder Pain Syndrome Reveals Nuanced Differences Associated with Localized Pain

PurposeInterstitial cystitis/bladder pain syndrome (IC/BPS) is a prevalent chronic pain syndrome associated with functional urinary disorders. IC/BPS symptoms can be localized to the pelvic-region or have co-occurring widespread pain. Importantly, response to treatment depends on pain localization phenotype. The etiology of IC/BPS remains elusive, and whether bacteria contribute to IC/BPS pathophysiology remains uncertain. Materials and MethodsWe used urine samples collected from a longitudinal randomized controlled trial of individuals with IC/BPS to study the association of the urobiome and IC/BPS symptoms over time. Individuals provided urine samples at baseline, post-treatment, and at five months. We performed a secondary analysis on urine samples applying 16S rRNA sequencing and assigned bacterial taxonomy to amplicon sequence variants (ASVs) to characterize the urobiome. We then compared urobiome bacterial diversity, stability, and its association with IC/BPS symptoms over time. We also assessed the relationship between pain localization and the urobiome. ResultsAs validation of this dataset, we noted a strong influence of menopausal status and recent urinary tract infection on the composition of the urobiome. We did not detect widespread differences in the urobiome that correlated with subjects pain localization or severity. Instead, we observed specific bacterial sequences that were altered in abundance in relation to symptomatology, such as reduced abundance of a Dialister ASV in persons with localized pelvic pain. ConclusionsTogether, this dataset advances our understanding of the urobiome in interstitial cystitis/bladder pain syndrome and sets the stage for future studies on the urobiome and interstitial cystitis/bladder pain syndrome symptoms.

microbiology↗

bioRxiv2025

Unmasking Pathogen Traits for Chronic Colonization in Neurogenic Bladder Patients

Individuals with neurogenic bladder are particularly susceptible to both chronic bacterial colonization of the bladder and urinary tract infections (UTIs). Neurogenic bladder can arise from a variety of diseases such as diabetes, spinal cord injuries, and spina bifida. To study the ecological and evolutionary dynamics of the microbiome in neurogenic bladder, we developed a longitudinal cohort of 77 children and young adults with spina bifida from two medical centers. We used enhanced urine culture, 16S rRNA sequencing, and whole genome sequencing to characterize the microbial composition of urine and fecal samples. In addition to prospective sample collection, we retrieved prior bacterial isolates from enrolled patients from Vanderbilts clinical microbial biobank, MicroVU. This allowed us to compare bacterial isolates from the same patients over a period of five years. Urine samples were characterized by high abundance of urinary pathogens, such as E. coli and Klebsiella. From longitudinal isolates from individual patients, we identified two common patterns of urinary tract colonization. We observed either the rapid cycling of strains and/or species, often following antibiotic treatment, or we observed the persistence of a single strain across timepoints. Neither persistence of a strain nor colonization with a new strain or species was associated with increased antibiotic resistance. Rather, in paired longitudinally collected strains from the same patients, mutations were identified in genes that code for cell envelope components associated with immune or phage evasion. Experimental testing revealed that O-antigen/LPS biosynthesis mutations confer protection from the immune system while altering susceptibility to phage predation, reflecting a fitness trade-off. We argue that this unparalleled cohort offers the opportunity to identify mechanisms of bacterial adaptation to the urinary tract that can be exploited in future therapeutic approaches.

microbiology↗