Abstract
Chronic pelvic pain (CPP) is defined as the persistent or recurrent pain in the pelvic region lasting for six months or longer. It is a heterogeneous and multifactorial condition, with endometriosis representing one of its major gynecological causes. However, diagnosing endometriosis as the root cause of CPP remains challenging due to its variable presentation and limitations in current non-invasive detection methods. Although the reproductive microbiome has been proposed as a promising tool to distinguish endometriosis-associated CPP from other CPP etiologies, clinically validated microbial biomarkers have not yet been established. In this study, we investigated whether the taxonomic and predicted functional diversity of the vaginal and rectal microbiomes could differentiate CPP patients with endometriosis (CPP Endo) from those without endometriosis (CPP Only) using a 16S rRNA sequencing dataset. Microbial diversity did not distinguish CPP Endo from CPP Only at either body site as there was a lack of disease-associated separation. Furthermore, our core microbiome analysis only identified one amplicon sequence variant (ASV) that was unique to the core rectal or vaginal microbiome of CPP Endo patients, and we failed to identify indicator species by Indicator Species Analysis (ISA) that could reliably distinguish CPP Endo. Although there were many differentially enriched taxa found by DESeq and predicted functional pathways found by PICRUSt2 between CPP Endo and CPP Only patients at both body sites, many of these features were also observed in healthy controls, suggesting an overall lack of CPP Endo specific microbial signatures. Consistent with these findings, our random forest model trained on microbial taxon abundance was unable to accurately predict CPP Endo status. Together, our data show that the community-level composition and function of the microbiome of CPP patients with endometriosis did not differ from CPP patients without endometriosis despite small differences in predicted functional profiles. These findings suggest that microbial dysbiosis may not be a reliable diagnostic indicator for endometriosis-associated CPP.