Conventional urine culture methods may fail to identify the appropriate microbial species or achieve an effective treatment response in patients with cystitis. Therefore, this study aimed to utilize microbiome analysis to identify microbial species associated with current cystitis.

Midstream samples of voided urine were obtained from 99 outpatients presenting with lower urinary tract symptoms suggestive of cystitis between April 2022 and March 2023. Cystitis was defined as symptoms accompanied by pyuria (WBC > 9/HPF) or bacteriuria (> 10^2 CFU/mL). Patients who received antibiotic treatment within one month or had urological abnormalities due to surgeries or injuries were excluded. Alpha-diversity was calculated using the ACE, Chao1, Shannon, and Simpson indices to assess microbial diversity in the urine samples. Beta-diversity analysis using weighted normalized UniFrac distance and PERMANOVA analysis was performed to measure the similarity of microbial composition between samples.

We analyzed samples from 44 patients with cystitis, 49 patients with non-infectious lower urinary tract symptoms, and 6 patients with other pelvic-genital infections. Although beta-diversity analysis showed a tendency for differences in microbial composition between groups, it did not reach statistical significance (p = 0.192, PERMANOVA). Alpha-diversity analysis of microbial species composition within each group revealed significant differences, with the non-cystitis group showing lower microbial diversity compared to the other groups (ACE index: p = 0.004, Shannon index: p = 0.001, Simpson index: p = 0.000). Additional analysis of microbial species at the phylum level using the Kruskal-Wallis test showed that Proteobacteria dominated in cystitis and pelvic-genital infections, though without significant differences. At the genus level, Escherichia, Finegoldia, Streptococcus, and Facklamia were significantly increased in cystitis patients compared to the other groups (p = 0.000, p = 0.009, p = 0.007, p = 0.001).

In addition to Escherichia and Streptococcus, microbiome analysis revealed the presence of underreported microbial species, such as Facklamia and Finegoldia, in outpatient cystitis patients. These microorganisms are not adequately reported by conventional culture methods for various reasons, including multiple species growth, contamination, or trace amounts. Facklamia and Finegoldia could be considered potential target microorganisms for the treatment of recurrent or treatment-refractory cystitis.