Microbiome and chronic pelvic pain in women: a mini-review

Chronic pelvic pain (CPP) is defined as noncyclic pain perceived in pelvic structures lasting at least 6 months and severe enough to cause functional disability or psychosocial distress ( Chronic Pelvic Pain, 2020 ; Lamvu et al. , 2021 ). It affects ∼5.7–26.6% of women of reproductive age worldwide, depending on the diagnostic criteria used and represents one of the leading indications for laparoscopy (∼40% of cases) and hysterectomy (∼12% of cases), most of which are probably unnecessary ( Chronic Pelvic Pain, 2020 ; Lamvu et al. , 2021 ). CPP often encompasses overlapping conditions such as endometriosis/adenomyosis, bladder-pain syndrome/interstitial cystitis (BPS/IC), irritable bowel syndrome (IBS), vulvodynia, and myofascial pain syndrome ( Chronic Pelvic Pain, 2020 ; Lamvu et al. , 2021 ). Despite their distinct clinical phenotypes, these syndromes converge on three interrelated biological axes that together sustain chronic pain: immune dysregulation, endocrine imbalance, and central sensitization ( Salliss et al. , 2021 ; Karp and Stratton, 2023 ; Cuffaro et al. , 2024 ; Cardaillac et al. , 2025 ). In recent years, the human microbiome has emerged as a potential upstream regulator of these pathways. Dysbiosis across the gut, vaginal, urinary, and endometrial microbiota may promote local and systemic inflammation, disrupt epithelial–barrier integrity, alter estrogen metabolism via the estrobolome and activate aberrant neuro-immune signalling along the gut–brain and hypothalamic–pituitary–ovarian axes ( Rahman-Enyart et al. , 2021 ; Cuffaro et al. , 2024 ; Hearn-Yeates et al. , 2024 ; Li et al. , 2025 ; Ren et al. , 2025 ). Recent studies revealed that dysbiosis rarely occurs in isolation within a single pelvic compartment ( Jimenez et al. , 2024 ). A systems-level overview of these interactions is presented in Fig. 1 . Microbiome-driven mechanisms linking epithelial barrier function, immune-endocrine signalling and central sensitization in chronic pelvic pain (CPP) . This schematic illustrates a systems-level model linking microbial homeostasis (left) to multi-site dysbiosis and CPP pathophysiology (right) across the gut, vaginal, urinary, and endometrial compartments. Homeostasis (left) : Lactobacillus-dominated and diverse commensal communities maintain mucus integrity and tight junctions, resulting in low epithelial permeability and low LPS tone. Short-chain fatty acids (SCFAs) derived from dietary fibre signal via GPR43 to promote regulatory T cell (Treg) expansion and immune tolerance. Microbial tryptophan metabolites activate the aryl hydrocarbon receptor (AhR), supporting epithelial repair and barrier protection (IL-22 pathways). Low β-glucuronidase activity preserves balanced estrogen signalling. Together, these mechanisms sustain endocrine balance, low neuroinflammatory tone, and physiological nociceptive processing. CPP dysbiosis (right) : Enrichment of anaerobic, Gram-negative, and BV-associated taxa is associated with barrier disruption and increased epithelial permeability. Elevated LPS activates TLR4/NF-κB signalling and pro-inflammatory cytokine production. Increased β-glucuronidase activity enhances estrogen recirculation, contributing to endocrine dysregulation. Altered bile acid and tryptophan metabolism engage FXR/TGR5 and AhR/kynurenine pathways, while TRPV1 activation contributes to peripheral sensitization. These converging immune, endocrine, and metabolic signals propagate along the gut–brain axis, including vagal afferent signalling and microbiota-derived neurotransmitters such as GABA, promoting neuroimmune activation and central sensitization, resulting in a pro-inflammatory state and persistent CPP. AhR, aryl hydrocarbon receptor; BV, bacterial vaginosis; FXR, farnesoid X receptor; GABA, gamma-aminobutyric acid; GPR43, free fatty acid receptor 2; IL, interleukin; LPS, lipopolysaccharide; SCFA, short-chain fatty acids; TGR5, Takeda G-protein-coupled receptor 5; TLR4, Toll-like receptor 4; Treg, regulatory T cell; TRPV1, transient receptor potential vanilloid 1. This narrative review synthesizes current evidence linking bacterial, viral, and fungal dysbiosis to CPP, highlighting mechanistic pathways, clinical implications, and emerging microbiome-targeted therapeutic strategies. The literature search strategy is detailed in Supplementary Materials and Methods .

The pelvic microbiota forms an interconnected ecological network and disruptions within these niches are associated with CPP ( Salliss et al. , 2021 ). In the vagina, Lactobacillus species dominate and maintain epithelial homeostasis through acidification ( France et al. , 2022 ). Dysbiosis, marked by reduced Lactobacillus spp. and overgrowth of Prevotella , Gardnerella , and Atopobium , is repeatedly linked to increased pain intensity, elevated interleukin-8 (IL-8) concentrations, and a heightened inflammatory milieu among women with endometriosis or severe dysmenorrhea ( Salliss et al. , 2021 ; Jimenez et al. , 2024 ). Additional alterations in endometriosis- and adenomyosis-related CPP include increased Clostridium butyricum , Clostridium disporicum , Alloscardovia omnicolens , and Veillonella sp. ( Chao et al. , 2021 ), suggesting a more complex vaginal signature in hormonally responsive pelvic pain disorders. The endometrium harbours a low-biomass microbial community, whose composition and physiological role is still debated ( Pelzer et al. , 2018 ; Wessels et al. , 2021 ; Reschini et al. , 2022 ). Although evidence supports the concept that the endometrial microbiome is biologically relevant to endometriosis, no robust, reproducible disease-specific microbial signature has been identified, with associations remaining inconsistent across studies ( Facciotti et al. , 2025 ). This likely reflects methodological and biological confounding rather than absence of a microbiome-disease link. Small and underpowered cohorts, inadequate control for menstrual cycle phase, hormonal treatments, diet, and geography, contamination in low-biomass samples, heterogeneous sequencing platforms, inconsistent bioinformatic pipelines, and differences between central or commercial analytical platforms undermine comparability and reproducibility ( Gajer et al. , 2012 ; Yatsunenko et al. , 2012 ; Brooks et al. , 2018 ; Knight et al. , 2018 ; Fierer et al. , 2025 ). Findings from studies relying on non-standardized analytical approaches should therefore be interpreted with appropriate caution. Reported enrichments in endometrial samples include Streptococcus , Gardnerella , and Prevotella genera, but vary across studies. Given the low bacterial biomass and contamination risk, these genus-level signals remain fragile. Genus-level taxonomic resolution is therefore insufficient to infer causality or mechanistic relevance. Many genera reported as differentially abundant encompass both commensal and potentially pathogenic species, as well as strains with profoundly divergent metabolic and immunomodulatory capacities. As a result, taxonomic associations at the genus level frequently obscure functionally relevant variation and may explain the poor reproducibility observed across studies. The case of Fusobacterium nucleatum is illustrative in this regard. Muraoka et al. reported its enrichment in the endometrial cavity of women with endometriosis, with antibiotic treatment reducing lesion burden in a murine model ( Muraoka et al. , 2023 ). However, these findings have not been consistently reproduced, highlighting the difficulty of validating low-biomass endometrial signatures. Key studies examining vaginal and endometrial microbiota in relation to CPP are summarized in Table 1 . Lower and upper female reproductive tract (FRT) microbiome studies. Summary of studies examining vaginal and endometrial microbiota in relation to CPP conditions. BV, bacterial vaginosis; endo, endometriosis; VMT, vaginal microbiota transplantation. Abbreviations: AUB, abnormal uterine bleeding; BV, bacterial vaginosis; CA125, cancer antigen 125; CPP, chronic pelvic pain; CXCL1/GRO, C-X-C motif chemokine ligand 1/growth-regulated oncogene; EM/AM, endometriosis/adenomyosis; FRT, female reproductive tract; IBS, irritable bowel syndrome; IL, interleukin; MDC, macrophage-derived chemokine; TNF, tumour necrosis factor; VEGF, vascular endothelial growth factor; VMT, vaginal microbiota transplantation. The urinary tract harbours a specific resident microbiota ( Whiteside et al. , 2015 ; Palumbo et al. , 2025 ). Spatial profiling demonstrates that urine and urothelium contain related but distinct microbial communities, with Lactobacillus spp. dominating urine and Staphylococcus spp. more abundant in the urothelium ( Wolfe et al. , 2023 ). Studies investigating BPS/IC show heterogeneous results, with some reporting differences in alpha diversity, Lactobacillus spp. relative abundance or urinary metabolites ( Walton and Nickel, 2021 ; Fu et al. , 2024 ). Etiocholanolone sulphate, an excretory product of testosterone metabolism, was identified in the urinary metabolome as a highly discriminatory metabolite for BPS/IC, separating patients from controls with >90% accuracy. Importantly, its levels correlated with pelvic pain intensity and these alterations remained stable over 3-6 months, suggesting a persistent biochemical endophenotype in severe BPS/IC ( Parker et al. , 2016 ). Subtype-specific differences are increasingly apparent, with Hunner-type IC, defined by the presence of characteristic inflammatory Hunner lesions on cystoscopy, being associated with increased levels of Pseudomonas and Gardnerella , whereas non-Hunner IC shows a higher relative abundance of Lactobacillus spp. and Enterococcus spp. ( Zhu et al. , 2025 ). Integrated urine microbiome–metabolome profiling highlights a distinct BPS/IC urinary microenvironment, with shifts in community structure (notably altered β-diversity) and dozens of differentially abundant genera and metabolites ( Zheng et al. , 2023 ). These paired signatures include depletion of potentially protective taxa, like Lactobacillus spp., alongside changes in inflammation-relevant compounds, most notably reduced theophylline, supporting microbe–metabolite interactions as plausible contributors to symptom-associated inflammatory pathways ( Zheng et al. , 2023 ). Interventional evidence suggests microbial plasticity: dextrose prolotherapy appears to shift urinary profiles towards more favourable compositions and improve symptoms ( Chen et al. , 2025 ). Key studies examining the urinary microbiota and metabolome in relation to CPP are summarized in Table 2 . Urinary microbiome and metabolome studies. Summary of studies examining the urinary microbiota and metabolome in relation to IC/BPS and CPP. Abbreviations: BPS, bladder pain syndrome; CPP, chronic pelvic pain; HIC, Hunner interstitial cystitis; IC, interstitial cystitis; IC/BPS, interstitial cystitis/bladder pain syndrome; NHIC, non-Hunner interstitial cystitis; β-diversity, between-sample microbial diversity. The gut contains various receptors and ion channels involved in nociceptive signalling, including transient receptor potential (TRP) channels, serotonergic, and cannabinoid pathways. Gut dysbiosis is one of the most consistent findings in pelvic pain disorders and gut microbiota can activate these receptors directly or indirectly ( Rea et al. , 2019 ). These pathways involve Toll-like receptors, TRP channels, opioid receptors, and serotonergic signalling ( Guo et al. , 2019 ). Women with endometriosis, IBS, or mixed-phenotype CPP frequently exhibit reduced microbial diversity and enrichment of Gram-negative anaerobes, particularly members of the Bacteroidetes phylum, such as members of Prevotella , Bacteroides , Alistipes , and Parabacteroides genera ( Li et al. , 2022 ; Hearn-Yeates et al. , 2024 ; Ren et al. , 2025 ). Environmental factors strongly modulate gut dysbiosis risk. Post-infectious IBS develops in ∼21% of individuals following Campylobacter infection, particularly in women, younger individuals and those with severe initial symptoms ( Berumen et al. , 2021 ). Antibiotic use further contributes to dysbiosis, nearly doubling the odds of IBS development ( Krogsgaard et al. , 2018 ). Functionally, gut dysbiosis is accompanied by metabolic alterations, including elevated primary and conjugated bile acids that correlate with pain severity and differ across IBS subtypes ( Dior et al. , 2016 ), as well as reduced short-chain fatty acids (SCFAs), particularly butyrate. SCFA depletion contributes to barrier dysfunction, increased cytokine production and nociceptive sensitization ( Chadchan et al. , 2021 ; Li et al. , 2022 ; Ustianowska et al. , 2022 ; Hearn-Yeates et al. , 2024 ; Ren et al. , 2025 ). In murine models of endometriosis, antibiotic-mediated depletion of the gut microbiota significantly reduces lesion number, volume, angiogenesis, and macrophage infiltration, whereas restoration via faecal microbiota transfer from diseased donors rescues lesion growth ( Chadchan et al. , 2019 , 2023 ). Furthermore, transplantation experiments using germ-free donor tissue show that uterine-associated microbiota is dispensable for lesion development, implicating intestinal microbial communities as dominant regulators of pelvic inflammatory tone ( Yuan et al. , 2018 ; Chadchan et al. , 2023 ). Mechanistic studies in pain biology support a role for the gut microbiota in nociceptive modulation. Depletion of the gut microbiota in germ-free or antibiotic-treated mice reduces mechanical hypersensitivity in neuropathic pain models. Restoration of microbiota normalizes microglial maturation and re-establishes pain behaviour, in parallel with increased pro-inflammatory cytokine production and Toll-like receptor-dependent NF-κB signalling in spinal microglia ( Lin et al. , 2020 ). Key studies examining gut microbiota in relation to CPP and related conditions are summarized in Table 3 . Gut microbiome studies in CPP-related conditions. Summary of clinical and preclinical studies examining the gut microbiota in relation to endometriosis, IBS, and CPP. Abbreviations: CPP, chronic pelvic pain; FMT, faecal microbiota transplantation; GI, gastrointestinal; IBS, irritable bowel syndrome; IBS-C, constipation-predominant irritable bowel syndrome; IBS-D, diarrhoea-predominant irritable bowel syndrome; LPS, lipopolysaccharide; NP, neuropathic pain; SCFA, short-chain fatty acid; S-CPP, sensitized chronic pelvic pain; α-diversity, within-sample microbial diversity. Dysbiosis across pelvic compartments destabilizes epithelial barriers and drives pro-inflammatory immune reprogramming. Lipopolysaccharide (LPS) and other microbial components activate Toll-like receptor 4 (TLR4), triggering nuclear factor kappa B (NF-κB), and cyclooxygenase-2 (COX-2) signalling, increasing IL-6, IL-1β, and TNF-α levels while weakening tight-junction integrity ( Li et al. , 2022 ; Ustianowska et al. , 2022 ; Guo and Zhang, 2024 ; Ren et al. , 2025 ). In a rat model of vaginal dysbiosis, loss of Lactobacillus spp. and anaerobes overgrowth triggered mucosal inflammation with increased IL-1β and TNF-α expression, which could be reversed by vaginal microbiota transplantation or selected probiotics ( Chen et al. , 2021 ). Fungal dysbiosis may further modulate symptom severity. Recurrent vulvovaginal candidiasis is strongly associated with vulvodynia, consistent with β-glucan signalling ( De Seta et al. , 2022 ) through Dectin-1 and Toll-like receptor 2 (TLR2) pathways ( Ren et al. , 2025 ). These mechanisms may impair Lactobacillus persistence and epithelial homeostasis ( De Seta et al. , 2022 ). Endometriosis itself is characterized by broad immune dysregulation involving macrophages, dendritic cells, mast cells, regulatory T cells, and natural killer (NK) cells, which synergize with microbial cues to maintain chronic inflammation ( Garmendia et al. , 2025 ). In animal models, microbiota depletion reduces mechanical and visceral hypersensitivity, whereas recolonization with a complex microbiota restores pain behaviour alongside microglial maturation and pro-inflammatory cytokine production in the spinal cord ( Lin et al. , 2020 ). Consistent with this, mice with impaired detoxification of LPS develop exaggerated pelvic pain that is reversible following microbiota transfer ( Rahman-Enyart et al. , 2021 ). Together, these findings suggest that gut microbiota-derived immune signals can amplify peripheral pelvic nociception while reinforcing central sensitization, thereby contributing to pain persistence independently of lesion burden. The estrobolome, defined as the repertoire of gut microbial genes encoding β-glucuronidase (GUS) activity, regulates systemic estrogen recirculation by deconjugating hepatic estrogen glucuronides in the intestine, allowing their reabsorption into the enterohepatic circulation and subsequent distribution to peripheral target tissues. This is particularly relevant in estrogen-sensitive disorders such as endometriosis and adenomyosis, where estrogen-dependent signalling sustains inflammation and nociception ( Hu et al. , 2023 ). Dominant GUS-producing taxa include Escherichia , Bacteroides , and Clostridium , along with other members of the Firmicutes lineage ( Ervin et al. , 2019 ; Hu et al. , 2023 ). Subsequent experimental studies confirmed that enhanced microbial GUS activity increases the pool of deconjugated estrogens and promotes pro-inflammatory cytokine release, including IL-6 and IL-1β, thereby linking estrogen recycling to immune activation ( Baker et al. , 2017 ; Alghetaa et al. , 2023 ; Pai et al. , 2023 ). In women with endometriosis, gut microbiome studies suggest an increased abundance of GUS-producing bacteria, particularly Escherichia and Bacteroides members ( Jiang et al. , 2021 ). However, direct evidence linking dysbiosis to circulating estrogen levels remains limited. Whether aromatase inhibitors or progestins modulate microbiome-driven estrogen reactivation remains largely unknown. In a small prospective before–after cohort of women with endometriosis, dienogest therapy was associated with changes in gut microbial composition, including a reduced Bacillota/Bacteroidota ratio, decreased Staphylococcus spp. and increased Lactobacillus spp. and Collinsella aerofaciens, suggesting that progestin therapy may influence intestinal microbial communities. However, this study did not assess vaginal microbiota, microbial estrogen reactivation or direct pain–microbiome correlations ( Pronina et al. , 2025 ). This represents an important mechanistic gap warranting prospective investigation integrating microbial, hormonal, and pain phenotyping. Exogenous hormonal contraception modestly modulates the vaginal microbiome in a method-dependent manner: estrogen-containing rings promote Lactobacillus spp. dominance ( Crucitti et al. , 2018 ), whereas long-term use of depot medroxyprogesterone acetate may reduce it ( Mitchell et al. , 2014 ), with little net effect observed across injectable and intrauterine methods ( Jacobson et al. , 2014 ; Achilles et al. , 2018 ). Tryptophan metabolism constitutes another bidirectional pathway linking dysbiosis to immune activation and nociception. Indole derivatives such as indole-3-acetate, indole-3-lactate, and indolepropionic acid signal through the aryl hydrocarbon receptor (AhR) to enhance IL-22-mediated epithelial barrier integrity ( Escorcia Mora et al. , 2025 ). In inflammatory states, diversion towards the kynurenine pathway is associated with immune activation and N-methyl-D-aspartate receptor-dependent pain sensitization ( Ren et al. , 2025 ). Yet this pathway is not exclusively pro-inflammatory, as certain kynurenines can activate G protein-coupled receptor 35 and exert antinociceptive and immunomodulatory effects ( Li et al. , 2022 ). Overall, gut microbiota-dependent tryptophan metabolism—particularly the balance between the serotonin and kynurenine pathways—may exert context-dependent effects on gut–brain signalling and neuroimmune regulation ( Qu et al. , 2024 ). In addition, gut microbiota can modulate neurotransmitters including dopamine, glutamate, gamma-aminobutyric acid (GABA), and neurosteroids like allopregnanolone that may be linked to pain ( McCurry et al. , 2024 ). Microbiome-derived signals interact with neural pathways via the gut–brain axis to drive visceral and pelvic pain. Gut dysbiosis enhances microglial activation and increases central IL-6 and IL-1β levels in experimental mouse models ( Griffiths et al. , 2024 ; Ren et al. , 2025 ). Advanced tracing and chemogenetic tools used to map and selectively activate enteric neurons in mice demonstrate that perturbation of gut–neural circuits reshapes mucosal immunity, microbial metabolite profiles, and host–microbiome signalling, providing causal evidence for bidirectional neuroimmune communication ( Griffiths et al. , 2024 ). Human neuroimaging studies in IBS consistently demonstrate hyperactivation of key pain-processing regions, including the anterior cingulate cortex, insula, prefrontal cortex, and thalamus, alongside impaired descending pain modulation ( Hubbard et al. , 2015 ; Wang et al. , 2017 ). Experimental suppression of cingulate cortical activity in murine models attenuates visceral hypersensitivity and anxiety-like behaviours ( Brenner et al. , 2021 ). Neuromodulation strategies may alleviate pelvic and visceral pain partly through microbiota-dependent mechanisms. In a single-blind randomized controlled trial (RCT) in constipation-predominant irritable bowel syndrome (IBS-C) (n = 40), transcutaneous auricular vagus nerve stimulation (taVNS) significantly improved abdominal pain, bowel habits, and psychological scores, while increasing vagal tone ( Liu et al. , 2024 ). Consistently, psychobiotics such as Bifidobacterium breve and Bifidobacterium longum have been shown to modulate central stress and emotional circuits via modulation of the hypothalamic–pituitary–adrenal (HPA) axis ( Dinan and Cryan, 2017 ; Ķimse et al. , 2024 ). However, microbiota-mediated analgesic effects are strain- and context-dependent. While L. reuteri restores peripheral opioid receptor expression and reduces visceral hypersensitivity in distension models ( Hegde et al. , 2020 ), other strains fail to produce analgesia in neuropathic or inflammatory pain, with no effect on microglial activation ( Huang et al. , 2019 ). Microbial metabolites link microbial community structure to epithelial integrity, immune regulation, and neural sensitization in CPP. SCFAs, mainly butyrate, acetate, and propionate, promote regulatory T-cell differentiation, suppress pro-inflammatory cytokines such as IL-6, TNF-α, and IL-17A, and attenuate microglial activation by inhibiting TLR4–MyD88–NF–κB signalling, thereby limiting neuroinflammation along gut–brain pain circuits in experimental models ( Huuskonen et al. , 2004 ; Du et al. , 2024 ; Facchin et al. , 2024 ; Zhao et al. , 2025 ). Bile acids modulate visceral sensitivity and are altered in IBS with increased primary and conjugated bile acids correlating with pain severity ( Dior et al. , 2016 ). Tryptophan-derived metabolites influence both immune and neural processes. Multi-omics analyses identified several indole derivatives, including 4-hydroxyindole, as reduced in endometriosis and functional experiments demonstrated that 4HI exerts anti-inflammatory and anti-nociceptive effects while suppressing lesion initiation and progression in murine and human xenograft models ( Talwar et al. , 2025 ). In a recent single cohort metabolomic study, Proteobacteria-associated alterations in glycerophospholipids, particularly phosphatidylcholine PC(40:8), achieved near-perfect discrimination between women with endometriosis/adenomyosis and controls ( Li et al. , 2025 ), supporting the diagnostic potential of integrated microbial–metabolite signatures. Together, these findings suggest that dysbiosis may not merely correlate with pelvic pain, but may contribute to shaping immune, metabolic, and neural pathways. Experimental manipulations in preclinical models provide mechanistic evidence for bidirectional interactions between microbiome and chronic pain, although direct causal evidence in humans remains limited. Beyond endometriosis, systems-biology analyses in women with sensitized CPP (S-CPP), including mixed-phenotype CPP, demonstrate a consistent depletion of Lactobacillus genera and ASVs across the gut, vaginal, and urinary microbiomes. In parallel, taxonomic modules dominated by Peptostreptococcales-Tissierellales and Christensenellaceae_R-7 correlate with pain intensity, anxiety, and gastrointestinal symptoms, supporting coordinated microbial networks as potential drivers of pelvic sensitization ( Cardaillac et al. , 2025 ). Multi-omics frameworks integrating taxonomic, functional, and metabolite data can identify disease-associated modules and link them to host immune-metabolic pathways, supporting precision-medicine applications ( Muller et al. , 2024 ; Yang et al. , 2025 ). Among pelvic pain disorders, endometriosis provides the most experimentally tractable model to investigate microbiota–pain interactions, with well-established systems allowing manipulation of both microbial communities and nociceptive outcomes. Induction of endometriosis in mice alters gut microbiota composition, including shifts in the Firmicutes/Bacteroidetes ratio and increased Bifidobacterium abundance at later disease stages ( Yuan et al. , 2018 ). Integrated metabolomic analyses further reveal reduced microbial diversity and coordinated alterations in secondary bile acid biosynthesis and α-linolenic acid metabolism, suggesting that dysbiosis reshapes bioactive lipid and bile acid pools ( Ni et al. , 2020 ). In a murine model, broad-spectrum antibiotics reduce lesion burden and inflammatory status, whereas faecal microbiota transfer from mice with endometriosis restores disease activity, supporting a causal contribution of the gut microbiota ( Chadchan et al. , 2019 ). At the genital level, preliminary evidence from a murine preprint, not yet peer-reviewed, suggests that endometriosis-associated vaginal dysbiosis may be sufficient to induce pain ( Pratt et al. , 2025 ). In the same model, intravaginal antibiotic treatment and vaginal microbiome transplantation (VMT) from healthy donors transiently alleviate mechanical allodynia and ongoing pain in endometriosis mice, while VMT from endometriosis donors induces allodynia and spontaneous nociceptive behaviours in otherwise healthy recipients ( Pratt et al. , 2025 ). These findings suggest a potential role for vaginal microbiota-driven pain transmission, but should be interpreted with appropriate caution until confirmed in peer-reviewed and translational studies. Preclinical models consistently demonstrate that microbiome-targeted interventions can reduce lesion burden, visceral hypersensitivity and inflammatory tone. However, clinical evidence remains limited: only a small number of RCT have been conducted, most in IBS rather than CPP specifically, and effect sizes are modest with substantial heterogeneity across studies. No intervention has yet demonstrated sufficient efficacy and safety to be recommended as standard-of-care in CPP management. A structured summary of these interventions by level of evidence is provided in Table 4 . Therapeutic interventions targeting the microbiome in CPP and related conditions. Summary of studies evaluating microbiome-targeted interventions, including probiotics, diet, faecal or vaginal microbiota transplantation, antibiotics, SCFAs and microbiota-related neuromodulation. Abbreviations: BV, bacterial vaginosis; CPP, chronic pelvic pain; DB, double-blind; endo, endometriosis; FMT, faecal microbiota transplantation; FODMAP, fermentable oligosaccharides, disaccharides, monosaccharides and polyols; FU, follow-up; GPR, G-protein-coupled receptor; HDAC, histone deacetylase; HPA, hypothalamic–pituitary–adrenal; IBS, irritable bowel syndrome; IBS-C, constipation-predominant irritable bowel syndrome; IBS-D, diarrhoea-predominant irritable bowel syndrome; NK, natural killer; RCT, randomised controlled trial; SCFA, short-chain fatty acid; taVNS, transcutaneous auricular vagus nerve stimulation; VMT, vaginal microbiota transplantation. Probiotics demonstrate anti-inflammatory and analgesic effects in preclinical endometriosis and IBS models, including reduced stress-induced visceral hypersensitivity via HPA-axis modulation and suppression of ectopic lesion growth via IL-12-dependent NK-cell activation ( Itoh et al. , 2011 ; Ait-Belgnaoui et al. , 2018 ; Zhou et al. , 2020 ). In a small pilot randomized trial in women with stage III–IV endometriosis (n = 37), oral multi-strain Lactobacillus spp. supplementation was associated with greater short-term reductions in dysmenorrhea and overall pain scores, although sample size and follow-up were limited ( Khodaverdi et al. , 2019 ). A recent meta-analysis of 82 RCTs in IBS (n = 10 332) reported modest, strain-specific benefits of selected Bifidobacterium and Lactobacillus formulations on global symptoms and abdominal pain, but with low certainty of evidence and substantial heterogeneity across strains and combinations ( Goodoory et al. , 2023 ). Among individual strains, excellent tolerability and clinically meaningful reductions in abdominal pain in IBS have been demonstrated for Lactobacillus acidophilus DDS-1 and Bifidobacterium lactis UABla-12 in a large multicentre RCT (n = 330) ( Martoni et al. , 2020 ). Whether probiotic or prebiotic interventions can durably reverse established dysbiosis remains unclear, as colonization resistance may limit sustained engraftment and long-term microbiome recovery is rarely demonstrated ( Suez et al. , 2018 ; Zmora et al. , 2018 ). Dietary interventions modulate the gut microbiome function through converging mechanisms. Low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diets (dietary approaches that reduce intake of specific fermentable carbohydrates) reduce abdominal pain and bloating in IBS while altering fermentation patterns and SCFA profiles, although evidence remains modest ( Bertin et al. , 2024 ). Fibre- and polyphenol-rich interventions, ranging from targeted additions (nuts, legumes, cocoa, and berries) to whole-diet patterns, consistently enrich SCFA-producing genera such as Faecalibacterium , Roseburia , Eubacterium , and Blautia , and shift circulating and faecal metabolites towards anti-inflammatory profiles ( Meiners et al. , 2025 ;  Rodríguez-Daza et al. , 2021 ). Emerging data in endometriosis suggest that diet-induced shifts in the gut microbiota, particularly with Mediterranean/anti-inflammatory and low-FODMAP patterns, may contribute to pain relief via effects on inflammation, mast-cell activation, and estrogen signalling, although mechanistic evidence remains largely indirect and based on small or uncontrolled studies ( Moore et al. , 2017 ; Nirgianakis et al. , 2022 ; Abulughod et al. , 2024 ; Türkoğlu et al. , 2025 ). Postbiotic SCFAs act as signalling molecules with direct G protein-coupled receptor and histone deacetylase-mediated anti-inflammatory and neuromodulatory effects ( Du et al. , 2024 ; Zhao et al. , 2025 ). Other strategies target the hormonal–microbiome interface, notably selective inhibitors of gut microbial β-glucuronidases, which modulate enterohepatic estrogen cycling ( Ervin et al. , 2019 ; Hu et al. , 2023 ). Psychobiotics, encompassing specific probiotics and prebiotics targeting the gut–brain axis, modulate HPA-axis activity, systemic inflammation, and neurotransmitter pathways, with preclinical models and small clinical trials suggesting improvements in mood and stress-related symptoms and a possible reduction in visceral hypersensitivity, although clinical evidence remains heterogeneous ( Dinan and Cryan, 2017 ; Ķimse et al. , 2024 ). Microbiota transplantation approaches represent ecosystem-level interventions with variable translational signals across indications. Preclinical data suggest that microbial communities can drive pain independently of lesion burden. In murine endometriosis models, vaginal dysbiosis can induce pain: while antibiotics and VMT from healthy donors alleviate allodynia, VMT from diseased donors transfers pain phenotypes ( Pratt et al. , 2025 ). By contrast, clinical translation in IBS has been disappointing. In a rigorously designed double-blind, randomized, placebo-controlled crossover trial of faecal microbiota transplantation capsules in diarrhoea-predominant IBS (N = 48), no significant difference in symptom severity was observed between faecal microbiota transplantation and placebo at 12 weeks ( Aroniadis et al. , 2019 ). These findings highlight strong placebo responses, methodological heterogeneity, and the need for improved patient stratification and mechanism-based endpoints. By contrast, VMT shows promise in recurrent bacterial vaginosis, with early data supporting feasibility and microbiome restoration ( Chen et al. , 2021 ; Martinelli et al. , 2023 ). Next-generation strategies are moving towards defined synthetic microbial consortia and engineered bacteria designed to restore specific metabolic pathways, or to deliver inducible anti-inflammatory effectors, sometimes combined with phage-based approaches ( Lynch et al. , 2025 ; Mkilima, 2025 ). These live biotherapeutic approaches will nevertheless require rigorous manufacturing, strain-level characterization, antimicrobial-resistance surveillance, and long-term pharmacovigilance frameworks to ensure safety and regulatory acceptability ( Lynch et al. , 2025 ). Antibiotics occupy a paradoxical role in the microbiome-CPP landscape: preclinical models demonstrate that broad-spectrum gut microbiota depletion reduces endometriosis lesion burden and visceral hypersensitivity, and intravaginal antibiotics transiently alleviate pain in vaginal dysbiosis models ( Chadchan et al. , 2019 ; Pratt et al. , 2025 ). However, clinical use carries significant risks—disruption of commensal communities, worsening dysbiosis, post-infectious IBS, and antimicrobial resistance—and no adequately powered trials support their use for CPP-associated dysbiosis. Antibiotics should therefore be reserved for documented infections rather than empirical dysbiosis management.

A systems perspective reframes CPP as a modifiable network, enabling more personalized care. However, evidence for microbiome-targeted interventions remains largely preclinical and human data are limited and heterogeneous. These approaches should not be considered standard of care without robust randomized trials demonstrating efficacy and safety. Given the high disease burden, rigorous evidence generation is both scientifically and ethically essential before clinical adoption.

This review highlights substantial heterogeneity and variable quality in the existing evidence base. Most human studies are small, cross-sectional, and rely on variable case definitions, sampling strategies, and sequencing methodologies, often with incomplete metadata on key confounders such as antibiotic exposure, hormonal therapies, diet, menstrual cycle phase, and menopausal status. Low-biomass pelvic sites, including the endometrium and bladder, are particularly vulnerable to contamination and current research remains largely bacteria-centric, with sparse and preliminary data on the virome and mycobiome. Collectively, these factors constrain causal inference and limit direct comparability across studies, in addition to generally low participant numbers. Correlation with pain symptoms remains limited, as most studies investigate the microbiome primarily as a disease signature rather than in relation to symptomatology. This pattern is frequently observed in endometriosis research. It is also worth noting that dysbiosis across gut, vaginal, and endometrial compartments is also observed in asymptomatic women, suggesting it is insufficient alone to drive CPP. Additional host factors—immunological, neurological, or genetic—likely shape clinical expression. Moreover, most human evidence remains associative, with causal insights largely derived from preclinical models. Future research should prioritize longitudinal and interventional designs that sample multiple pelvic compartments, gut, vagina, bladder, and endometrium, within the same individuals and integrate microbiome data with immune, endocrine, neural, and psychosocial phenotyping. Harmonized protocols and reporting standards, ideally aligned with STORMS (Strengthening The Organization and Reporting of Microbiome Studies) recommendations, together with multi-omics approaches, will be essential to identify robust microbial and metabolite signatures that cut across CPP syndromes. Mechanism-based trials of dietary, probiotic/psychobiotic, postbiotic, and microbial transfer interventions should embed predefined microbial and host biomarkers alongside pain outcomes, enabling patient stratification, on-target effect monitoring, and safer, more rational development of microbiome-targeted therapies. Validated, standardized patient-reported outcome measures (PROMs) should be pre-specified as primary endpoints, alongside harmonized standard operating procedures (SOPs) for sampling and microbiome profiling, with early integration of robust safety monitoring. CPP is best understood as a systems disorder in which microbial, immune, endocrine, and neural circuits form a tightly coupled network across the gut–vagina–endometrium–bladder axis. Given that most women with CPP are of reproductive age, the potential impact of pelvic dysbiosis on fertility and pregnancy outcomes warrants consideration. Emerging evidence suggests that vaginal and endometrial dysbiosis may impair implantation and increase adverse perinatal risks ( Moreno et al. , 2016 ; Fettweis et al. , 2019 ). Integrating reproductive outcomes into future CPP microbiome research would enhance its translational relevance.