Vaginal and urinary microbiota in breast cancer survivors undergoing fractional CO2 laser therapy

Abstract Genitourinary syndrome of menopause (GSM) is common in breast cancer survivors (BCSs) receiving endocrine therapy, and non-hormonal treatment options remain limited. Fractional CO₂ laser therapy has been investigated as a non-hormonal treatment option, but its influence on the genitourinary microbiota remains unclear. We conducted a prospective study of BCSs with GSM undergoing five sessions of laser therapy. Vaginal swabs and midstream urine samples were collected before the first treatment and after the final treatment. Microbiota profiles (only bacteria here) were generated using Nanopore long-read 16 S rRNA gene sequencing targeting the V1–V8 region and temporal changes in alpha and beta diversity were evaluated. Twenty-six participants completed both sampling time points. The vaginal microbiota was predominantly Lactobacillus -dominated and showed no detectable change in alpha diversity or overall community composition after treatment. In contrast, the urinary microbiota displayed greater interindividual variability and a reproducible shift in overall community composition from baseline to follow-up. These urinary shifts persisted after adjustment for relevant clinical covariates and were not explained by consistent changes in individual taxa on differential abundance testing. Functional pathway profiles were unchanged in both vaginal and urinary samples. Overall, the vaginal microbiota remained largely stable between baseline and follow-up, whereas a modest temporal difference in urinary microbial community structure was observed. Further randomized controlled trials are needed, to elucidate whether these changes in urine microbiota are the result of laser therapy or are the results of other temporal changes in the women.