{"paper_id":"9baced8f-6e3e-4259-b694-f05cf1a39919","body_text":"Microbiota–metabolite axis in endometriosis: Pathogenic mechanisms and clinical implications\nMoyuan Li, Aiyuan Yue, Lingfeng Gu, Feiyang Li, Nuo Ye, Sujuan Xu, Zhen Gong, Dake Li, Pengfei Xu\nCite this article as:\nMoyuan Li, Aiyuan Yue, Lingfeng Gu, Feiyang Li, Nuo Ye, Sujuan Xu, Zhen Gong, Dake Li, Pengfei Xu. Microbiotametabolite axis in\nendometriosis:  Pathogenic  mechanisms  and  clinical  implications[J].  Journal  of  Biomedical  Research ,  In  press.  doi:\n10.7555/JBR.39.20250566\nView online: https://doi.org/10.7555/JBR.39.20250566\nArticles you may be interested in\nUnproofed\n\n \nMicrobiota–metabolite  axis  in  endometriosis:  Pathogenic\nmechanisms and clinical implications\nMoyuan Li1,2, Aiyuan Yue1, Lingfeng Gu1,2, Feiyang Li1, Nuo Ye1,2, Sujuan Xu3, Zhen Gong1,✉, Dake\nLi1,✉, Pengfei Xu2,✉\n1Department  of  Gynecology,  Women's  Hospital  of  Nanjing  Medical  University  (Nanjing  Women  and  Children's\nHealthcare Hospital), Nanjing, Jiangsu 210004, China;\n2Nanjing  Women  and  Children's  Healthcare  Institute,  Women's  Hospital  of  Nanjing  Medical  University  (Nanjing\nWomen and Children's Healthcare Hospital), Nanjing, Jiangsu 210004, China;\n3Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Women and Children's\nHealthcare Hospital), Nanjing, Jiangsu 210004, China.\nAbstract\nGrowing  evidence  highlights  the  role  of  microbiota,  including  those  of  the  gut,  reproductive  tract,  and\nendometrial tissue, as critical functional drivers in the pathogenesis of endometriosis (EM). Studies have revealed\na characteristic microbial imbalance in patients with EM, marked by a reduced abundance of beneficial bacteria\nand enrichment of opportunistic pathogens. These microbial communities exert their influence primarily through\nmetabolic activity, as demonstrated by metabolomic studies showing their capacity to modulate host immune and\nendocrine responses. This imbalance leads to multiple key metabolic disturbances, including decreased levels of\nshort-chain  fatty  acids,  particularly  butyrate;  a  shift  in  tryptophan  metabolism  toward  the  kynurenine  pathway;\nelevated  β-glucuronidase  activity;  increased  lipopolysaccharide  production;  and  altered  secondary  bile  acid\nprofiles.  Functionally,  these  metabolic  alterations  converge  to  promote  EM  by  disrupting  immune  homeostasis,\nenhancing  estrogen  signaling,  and  driving  systemic  inflammation,  collectively  creating  a  permissive\nmicroenvironment  for  ectopic  lesion  growth  and  invasion.  Targeted  interventions,  such  as  probiotics,  high-fiber\ndietary  strategies,  fecal  microbiota  transplantation,  and  selective  modulation  of  microbial  or  host  metabolic\nenzymes,  are  emerging  as  promising  non-hormonal  therapeutic  approaches.  Nonetheless,  further  studies\nincorporating  longitudinal  cohort  designs  and  integrative  multi-omics  approaches  are  essential  to  establish\ncausality and facilitate the development of precise diagnostic and personalized treatment strategies.\nKeywords: endometriosis, microbiota, metabolite\n \nIntroduction\nEndometriosis  (EM)  is  defined  as  the  presence  of\nendometrial-like glands and stroma outside the uterine\ncavity. Clinically, it presents as pelvic pain, infertility,\nor  pelvic  masses,  affecting  approximately  10%  of\nwomen  of  reproductive  age,  with  a  peak  incidence\nbetween  25  and  35  years[1].  Upon  estrogen\nstimulation,  ectopic  endometrial  glands  undergo\nhormone-dependent  cyclic  changes.  Depending  on\n✉Corresponding  authors:  Zhen  Gong,  Email:  gongzhen@njmu.\nedu.cn,  ORCID,  0000-0003-1421-5830;  Dake  Li,  Email:\ndkli@njmu.edu.cn;  ORCID,  0000-0001-6904-8529.;  Pengfei  Xu,\nEmail: pengfeixu@njmu.edu.cn, ORCID, 0000-0002-0389-1182.\nReceived:  15  December  2025;  Revised:  15  April  2026;  Accepted:\n20 April 2026;\nCLC number: R711.71, Document code: A\nThe authors reported no conflict of interests.\nThis is an open access article under the Creative Commons Attribu-\ntion (CC BY 4.0) license, which permits others to distribute, remix,\nadapt and build upon this work, for commercial use, provided the\noriginal work is properly cited.\n \nAvailable online at www.jbr-pub.org.cn\nOpen Access at PubMed Central\nJournal of Biomedical Research, 2026 40(0): 1–17  \n \nReview Article\n©  2026 by Journal of Biomedical Research. https://doi.org/10.7555/JBR.39.20250566\nUnproofed\n\ntheir  location,  such  as  the  ovaries,  fallopian  tubes,\npelvic  peritoneum,  or  ligaments,  they  can  cause  local\nbleeding,  pain,  fibrotic  nodule  formation,  or\ninfertility[2,3].  EM  pathogenesis  is  complex  and\nmultifactorial. The most widely accepted theory posits\nthat  retrograde  menstruation  facilitates  the\ntranslocation  of  viable  endometrial  cells  to  the  pelvic\ncavity  and  other  sites[4].  Although  some  degree  of\nretrograde  menstruation  occurs  in  most  women,  only\n1%–2%  develop  EM,  indicating  that  additional\npathophysiological  mechanisms  are  involved[5].\nVarious  factors  have  been  implicated  in  the  initiation\nand  progression  of  EM,  including  inflammatory\ncytokines[6],  alterations  in  the  immunopathological\nmicroenvironment[7],  environmental  factors[8],  and\nmicrobiota[9].\nIn  recent  years,  several  studies  have  suggested  a\nsignificant  role  for  the  microbiota,  including  the  gut,\nreproductive  tract,  and  tissue-resident  microbiota,  in\nthe  pathogenesis  and  progression  of  EM[9].\nFurthermore, Mendelian randomization analyses have\nprovided  novel  insights  into  the  potential  causal\nrelationship  between  the  gut  microbiota  and  EM.\nMembers  of  the  families  Christensenellaceae  and\nRuminococcaceae,  as  well  as  Eubacterium\nruminantium,  exhibit  protective  associations  against\nEM.  Conversely,  Anaerotruncus  and  Olsenella  have\nbeen  identified  as  risk-associated  taxa  that  increase\nsusceptibility to EM, whereas taxa such as those in the\norder  Bacillales  and  the  family  Prevotellaceae  have\nbeen  implicated  in  elevated  disease  risk[10–12].  These\nmicrobial  communities  primarily  influence  EM\nprogression  through  their  metabolites,  which  regulate\nkey  processes  such  as  local  inflammation,  estrogen\nmetabolism, and neurogenesis. These findings provide\ngenetic  evidence  supporting  potential  causal  links\nbetween  the  gut  microbiota  and  EM.  Therefore,  this\nreview  systematically  summatise  and  integrates\ncurrent evidence on the roles of the gut, reproductive\ntract,  and  tissue-resident  microbiota  in  the\ndevelopment  and  progression  of  EM  from  the  dual\nperspectives of microbial composition and metabolite-\nmediated  mechanisms  and  explores  their  potential\nclinical implications. \nMicrobiome characteristics in EM\nDysbiosis, particularly that of the gut microbiota, is\nassociated  with  conditions  such  as  inflammatory\nbowel  disease[13],  arthritis[14],  and  certain  cancers[15],\nhighlighting  its  role  in  regulating  systemic\ninflammation  via  immune-mediated  mechanisms.\nGiven  the  importance  of  aberrant  inflammatory\nresponses in EM pathogenesis, a potential microbiota-\nEM link has been suggested[16]. Dysbiosis may elevate\nsystemic  estrogen  levels  by  influencing  hepatic\nmetabolism  and  intestinal  β-glucuronidase  activity[17],\nthereby  promoting  the  growth  of  ectopic  lesions  and\namplifying  inflammation[18].  In  addition  to  the  gut,\nalterations in the local microbiota of the reproductive\ntract and endometrial tissues have garnered increasing\nattention  in  EM  research.  Patients  with  EM  exhibit\nreduced  vaginal  microbiota  diversity  and  decreased\nrelative  abundance  of  Lactobacillus[19],  accompanied\nby  an  increase  in  the  abundance  of  opportunistic\npathogens  such  as  Gardnerella  and  Prevotella.  This\ndysbiotic state may promote the adhesion and survival\nof  ectopic  endometrial  tissues  by  altering  the  local\nimmune  microenvironment  and  enhancing  the\nsecretion of inflammatory factors[20]. The upper female\nreproductive  tract  is  now  recognized  as  non-sterile,\nand  the  microbiota  composition  of  the  endometrium\nand  peritoneal  fluid  exhibits  disease-specific\nalterations[21]. For instance, the enrichment of bacterial\ngenera such as Fusobacterium in ectopic lesions may\ndirectly  contribute  to  lesion  establishment  and\nprogression by activating growth factors and multiple\ninflammatory  pathways.  Furthermore,  bacterial\ntranslocation within the pelvic cavity, such as through\nretrograde  menstruation  or  intestinal  bacterial\ntranslocation,  may  further  interconnect  the  gut  and\nreproductive  tract  microenvironments,  forming  an\nintegrated  microbial-immune  regulatory  network.\nFigure 1  illustrates  the  compositional  changes  of  the\nmicrobiome  and  the  potential  inter-compartmental\nmicrobial  translocation  across  the  gut,  reproductive\ntract,  and  ectopic  tissue  in  EM.  Based  on  these\nmultifaceted  associations,  the  following  sections\nsystematically  explore  the  characteristics  of  these\nmicrobial alterations. \nGut microbiota\nThe  composition  of  the  gut  microbiota  in  patients\nwith EM is significantly altered compared with that in\nhealthy  individuals,  a  phenomenon  consistently\nobserved  in  both  human  clinical  samples  and  animal\nmodels[22–26].  In  human  studies,  comparative  analyses\nof  fecal  microbiomes  from  patients  with  EM  and\nhealthy  controls  have  revealed  significant  differences\nin  the  abundance  of  at  least  12  bacterial  genera[23].\nAnimal models provide robust and suportive evidence.\nFor instance, in a rhesus macaque EM model, distinct\nalterations  were  observed  in  the  shed  fecal  microbial\nprofiles of affected individuals[26]. In mouse models of\nEM,  although  some  studies  using  α-  and  β-  diversity\nanalyses  did  not  show  significant  changes  in  overall\ncommunity  diversity,  more  granular  taxonomic\n2 et al. J Biomed Res, 2026, 40(0)\nUnproofed\n\nanalyses  revealed  specific  compositional  and\nstructural alterrations in the gut microbiota[22,24]. These\nfindings support the conclusion that EM is associated\nwith disease-specific gut microbial dysbiosis.\nThe dysbiosis observed in EM does not manifest as\na  global,  unidirectional  shift  across  bacterial  taxa  but\npresents  a  heterogeneous  and  context-dependent\npattern.  At  the  phylum  level,  reported  trends  are\nhighly  variable,  potentially  due  to  differences  in\nexperimental  models,  host  species  or  strains,  dietary\ncomposition,  and  analytical  methodologies.  For\nexample, one mouse study identified an enrichment of\nthe  phyla  Firmicutes  and  Actinobacteria  in  the  EM\ngroup,  accompanied  by  a  significantly  elevated\nFirmicutes-to-Bacteroidetes  ratio,  a  metric  frequently\nregarded  as  an  indicator  of  gut  dysbiosis[22,27].  In\ncontrast,  another  study  reported  increased\nBacteroidetes  abundance  concomitant  with  reduced\nFirmicutes  in  EM  mice[28].  These  two  studies\nemployed  different  modeling  approaches\n(intraperitoneal  injection  of  endometrial  fragments\nversus  surgical  autotransplantation  combined  with\nantibiotic  intervention),  which  may  substantially\ninfluence microbial outcomes.\nAt  the  genus  level,  the  changes  were  more\npronounced  and  taxonomically  specific.  The  relative\nabundance  of  several  taxa  with  putative  protective  or\nhomeostatic  functions  was  reduced,  including\ndepletion  of  Lactobacillus  observed  in  rhesus\nmacaques  and  some  human  cohorts[23,26],  and  lower\nlevels  of  Alloprevotella  and  Turicibacter  in  patients\nwith  EM[23].  Conversely,  the  abundance  of  taxa\nassociated  with  pro-inflammatory  signaling  and\ndisease  progression  increased.  Representative\nexamples  include  a  higher  prevalence  of\nShigella/Escherichia-dominated  communities  in\nwomen  with  EM[25,29],  enrichment  of  Gram-negative\nbacteria  such  as  Escherichia  coli  (E.  coli)  and\nEnterobacter  in  a  rhesus  macaque  model[26],  and\nelevated  levels  of  Ruminococcaceae  UCG-014,\nBifidobacterium,  and  Parasutterella  in  murine  EM\nmodels[22].  Taxon-specific  microbial  alterations  are\nsummarized in Table 1.\nThese  distinct  microbial  alterations  may  contribute\nto  the  pathogenesis  and  progression  of  EM  via\nmultiple  interrelated  mechanisms.  Shifts  in  gut\nmicrobiota  composition  are  closely  associated  with\nperturbations in estrogen metabolism. Microbes, such\n \n \nEM\n↑ Tenericutes \n↑ Firmicutes\nGardnerella \n↑\nAtopobium \n↓\nBacteroides \n↑\nPrevotellaceae \n↓\nRuminococcus \n↑\nLactobacillus \n↓\nEscherichia \n↑\nShigella \n↑\nOthers\n  Reproductive Tract M\nicrobiota                                                                                                                  Gut M\nicrobiota\nEctopic Tissue\nFsetucimri                                                                Patodanomodues                                                                                                                                             Batodioretca                                                       Aatotecymonitc\n↑ Proteobacteria\n \n \nFig. 1     Microbiome characteristics in endometriosis (EM).  This  circular  schematic  illustrates  the  compositional  changes  and  potential\ninter-compartmental  microbial  translocation  across  three  anatomical  niches  in  EM.  The  central  gray  circle  denotes  the  disease  state  (EM),\nsurrounded  by  three  anatomical  modules  representing  distinct  microbiota  habitats:  gut  microbiota  (purple),  reproductive  tract  microbiota\n(green),  and  ectopic  tissue  microbiota  (yellow).  Triangular  arrows  between  modules  indicate  putative  migration  routes  of  microorganisms\namong  these  compartments.  The  outermost  ring  comprises  four  phylum-level  modules  and  one  \"Others\"  module.  Each  phylum  module\ndisplays  representative  genera  with  directional  arrows  indicating  increased  (↑)  or  decreased  (↓)  abundance.  Created  in  BioRender.  Xu,  P.\n(2025) https://BioRender.com/a51kabp.\nMicrobiota–metabolite axis in endometriosis 3\nUnproofed\n\nas  those  belonging  to  the  phyla  Firmicutes  and\nBacteroidetes and the genus Bifidobacterium, possess\ngenes  encoding  β-glucuronidase,  an  enzyme  that\ncatalyzes  the  deconjugation  of  estrogens  and\nfacilitates  their  reabsorption  into  the  systemic\ncirculation.  Consequently,  microbial  dysbiosis  may\nlead  to  elevated  in  circulating  bioactive  estrogen\nlevels,  thereby  establishing  a  permissive  hormonal\n \nTable 1   Characteristics of differentially abundant microbiota in endometriosis (EM)\nPhylum Bacterial name/Group Gram staining Abundance change (EM vs. Control) References\nGut microbiota\n　Actinomycetota Bifidobacterium G+ Up [22]\n　Bacteroidota\nBacteroidales S24-7 group G− Up [22]\nBacteroides G− Up [23]\nAlloprevotella G− Down [23]\nPrevotellaceae UCG-001 group G− Up [22]\nParabacteroides G− Up [23]\n　Firmicutes\nRuminobacter G+ Down [23]\nCoprococcus G+ Up [23]\nLachnospiraceae NK4A136 group G+ Up [22]\nOscillibacter G+ Up [23]\nRuminococcaceae UGG-014 group G+ Up [22]\nLactobacillus G+ Down [23,26]\nTuricibacter G+ Down [23]\n　Pseudomonadota\nParasutterella G- Up [22]\nUnclassified genus Typically G− Up [23]\nShigella/Escherichia G− Up [25,29]\nEscherichia coli G− Up [26]\nEnterobacter G− Up [26]\nReproductive tract microbiota\n　Actinomycetota\nGardnerella variable Up [19,25,34]\nAtopobium G+ Down [25]\nCorynebacterium G+ Up [25,32]\n　Bacteroidota Prevotella G− Up [19]\n　Firmicutes\nLactobacillus spp. G+ Down [19]\nStreptococcus G+ Up [25,32,34]\nEnterococcus G+ Up [34]\nVeillonellaceae (family) G− Up [19,25]\n　Pseudomonadota\nEscherichia coli/Shigella G− Up [25,29,34]\nEnterobacteriaceae (family) G− Up [25,32]\nPseudomonas G− Up [25,32]\n　Tenericutes Ureaplasma urealyticum G− Up [19,25]\nIn the ectopic tissue\n　Fusobacteria Fusobacterium nucleatum G−\nUp [38]\nIndifferent [42]\n　Firmicutes Faecalibacterium prausnitzii G+ Up [39]\n　Proteobacteria Pseudomonas G− Up (predominant in ascites) [41]\n4 et al. J Biomed Res, 2026, 40(0)\nUnproofed\n\nmilieu  that  supports  the  persistence,  growth,  and\nprogression  of  endometriotic  lesions[17].  Furthermore,\nthe enrichment of pro-inflammatory bacteria (Shigella\nand  Escherichia)  may  amplify  systemic  or  local\ninflammation,  whereas  the  depletion  of  protective\ncommensal taxa may compromise immune regulatory\ncapacity  and  inflammatory  resolution[25,26,29].\nAnatomical  factors,  such  as  a  shorter  anogenital\ndistance, may modulate these processes by increasing\nthe  likelihood  of  bacterial  translocation  between\nanatomical  compartments[30].  Collectively,  the  gut\nmicrobiota  has  emerged  as  a  critical  determinant  of\nEM  pathophysiology  and  represents  a  promising\ntarget  for  dietary  modulation  and  microbiota-based\ntherapeutic interventions[27]. \nReproductive tract microbiota\nStudies on the lower reproductive tract microbiome\nin  patients  with  EM  have  revealed  a  heterogeneous\nand  nuanced  microbial  landscape.  Some  studies  have\nreported  no  significant  differences  in  the  cervix\nbetween  patients  with  EM  and  healthy  controls[31],\nwhereas  others  have  identified  specific  microbial\nperturbations.  The  most  consistent  finding  observed\nwas  a  marked  reduction  in  protective  Lactobacillus\nspecies,  which  are  essential  for  preserving  a  healthy,\nacidic  vaginal  environment  and  cervicovaginal\nmicrobial  homeostasis[19].  At  the  phylum  level,  this\ndysbiosis  often  corresponds  to  a  decreased  relative\nabundance of Firmicutes (to which Lactobacillus spp.\nbelong)  and  an  increased  abundance  of  other  phyla\nsuch  as  Actinobacteria  and  Proteobacteria.\nConcurrently, there is a relative enrichment of a broad\nspectrum  of  genera,  many  of  which  are  associated\nwith  bacterial  vaginosis  (BV)  or  pro-inflammatory\nstates.  These  include  members  of  the  family\nEnterobacteriaceae,  genera  Streptococcus,\nPseudomonas,  and  Corynebacterium[25,32],  family\nVeillonellaceae,  genus  Gardnerella,  and  species  E.\ncoli/Shigella  and  Ureaplasma  urealyticum[19,25].\nInterestingly,  one  study  reported  absence  of\nAtopobium,  a  genus  associated  with  BV,  in  the\ncervical  and  vaginal  microbiota  of  patients  with\nEM[25].  In  contrast,  other  reports  indicate  that  non-\nLactobacillus-dominant  microbial  communities,\npaticularly  those  enriched  in  Gardnerella  and\nAtopobium,  frequently  colonize  the  cervicovaginal\nepithelium  in  women  with  BV[33].  These  seemingly\nconflicting  findings  suggest  that  the  lower\nreproductive  tract  microbiota  in  EM  may  exhibit\ncontext-dependent  or  subtype-specific  dysbiosis\npatterns. Collectively, these observations indicate that\nthe lower reproductive tract in patients with EM exists\nin  a  state  of  disease-associated  microbial  imbalance,\nwhich  may  contribute  to  disease  progression  through\nmodulation  of  local  immune  responses  and\ninflammatory signaling.\nThe  existence  of  distinct  endometrial  microbiota\nremains  controversial,  as  microbial  detection  may\npartially  reflect  contamination  by  cervicovaginal  or\nintestinal bacteria. Studies have reported an increased\nabundance  of  Gardnerella,  Streptococcus,\nEnterococcus,  and  E.  coli  in  the  endometrium  of\npatients  with  EM[34],  which  have  previously  been\nassociated  with  menopause  and  estrogen-depleted\nstates[35]. As Enterococcus and E. coli are common gut\ncolonizers,  these  findings  raise  the  possibility  of\nintestinal  bacterial  carryover  or  contamination  in\ncertain  samples.  However,  other  investigations  have\nyielded  contrasting  results,  identifying  an  enrichment\nof  Prevotella,  Veillonellaceae,  and  Atopobium  in  the\nendometrium  of  women  with  EM;  these  genera  are\nfrequently  detected  in  women  with  BV[19].  Such\ninconsistencies  likely  reflect  disease  heterogeneity,\nmethodological  variability,  or  differences  in  disease\nstage or sampling strategies.\nIn summary, the current evidence indicates a higher\nprevalence  of  BV-associated  bacteria  in  the\ncervicovaginal  and  endometrial  microbiota  of  women\nwith EM. Functionally, this shift reflects the depletion\nof protective Lactobacillus alongside an enrichment of\npro-inflammatory  taxa  (Gardnerella  and  E.  coli),\nwhich  may  facilitate  disease  progression  by\nmaintaining  a  chronic  inflammatory\nmicroenvironment  that  favors  ectopic  lesion\nestablishment.  Despite  inter-study  variability  in\nspecific bacterial compositions, certain BV-associated\nmicrobiota  have  consistently  been  associated  with\nEM. \nTissue-resident microbiota\nIn  recent  years,  microbial  communities  in\npathological  tissues  have  attracted  increasing\nattention. In human tumor tissues, bacteria have been\nidentified as intratumoral residents within both cancer\nand  infiltrating  immune  cells[36].  Fusobacterium,  a\ncommon  commensal  bacterium  found  in  the  oral\ncavity  and  gastrointestinal  tract,  is  considered  an\nopportunistic  pathogen.  Species  within  the  genus\nFusobacterium, such as Fusobacterium nucleatum (F.\nnucleatum),  participate  in  the  development  of\nperiodontitis and may facilitate tumorigenic processes\nby eliciting the production of inflammatory cytokines,\nincluding  interleukin-6,  interleukin-8,  and  tumor\nnecrosis  factor[37].  The  presence  of  tissue-resident\nmicrobiota  within  tumors  has  prompted  a  broader\nMicrobiota–metabolite axis in endometriosis 5\nUnproofed\n\nreconsideration  of  how  microbes  may  influence  non-\nmalignant tumor-like pathological conditions. Despite\nits  histologically  benign  nature,  EM  shares  several\nhallmark  features  with  neoplastic  diseases,  including\nsustained  proliferation,  resistance  to  apoptosis,  local\ninvasiveness,  angiogenesis,  and  immune  evasion.\nThese  tumor-like  characteristics  suggest  that  ectopic\nendometrial  lesions  may  provide  a  permissive  niche\nfor microbial colonization or persistence analogous to\nthat observed in malignant tissues.\nEmerging  evidence  indicates  that  the  endometrium\nand  ectopic  lesions  of  patients  with  EM  show\nsignificant  enrichment  of  F.  nucleatum[38]  and\nFaecalibacterium  prausnitzii[39]  compared  with\nhealthy controls. Among these, F. nucleatum activates\ntransforming  growth  factor  beta  (TGF-β)  signaling,\nthereby  promoting  the  transformation  of  fibroblasts\ninto  myofibroblasts  with  enhanced  proliferative,\nadhesive,  and  migratory  capabilities,  ultimately\ncontributing  to  the  progression  of  endometrial\nlesions[38].  Under  certain  conditions,  this  enrichment\nmay  be  associated  with  vaginal  dysbiosis[40].\nAccordingly,  these  bacteria  may  gain  access  to  the\nupper  female  reproductive  tract  via  mechanisms  such\nas retrograde menstruation from the dysbiotic vaginal\nmicroenvironment,  leading  to  the  colonization  of\nectopic  lesions.  Furthermore,  one  study  reported  that\nPseudomonas  is  the  predominant  bacterial  genus  in\nthe  peritoneal  fluid  of  patients  with  EM,  with\napproximately  95%  originating  from  the  intestine[41].\nThis  phenomenon  is  often  accompanied  by  elevated\nlipopolysaccharide  (LPS)  levels  and  disruption  of\nintestinal  barrier  integrity.  Through  fecal  microbiota\ntransplantation  in  a  mouse  model,  researchers\nexperimentally demonstrated the translocation process\nof  bacteria  along  the  \"gut-peritoneal  cavity-lesion\"\naxis, providing mechanistic evidence for the intestinal\norigin  of  the  microbiota  within  the  ectopic\nendometrium[41].\nHowever,  a  recent  study  revealed  no  significant\ndifference  in  the  presence  of  Fusobacterium  spp.  in\nthe  normal  endometrium  between  patients  with  EM\nand  healthy  individuals[42].  This  contradiction  with\nprevious findings is likely due to the heterogeneity of\nthe  study  populations.  Moreover,  differences  in  host\nfactors,  such  as  geographical  location,  dietary  habits,\nand ethnic background, may account for the divergent\nconclusions  regarding  F.  nucleatum  enrichment,\nsuggesting  that  its  potential  diagnostic  or  prognostic\nutility in EM warrants further investigation. \nMicrobiota-derived metabolites in EM\nFollowing  the  identification  of  gut  microbiota,  the\nreproductive tract, and ectopic tissue dysbiosis in EM,\na  central  question  arises:  how  do  these  microbial\nperturbations influence host physiology? Women with\nEM exhibit gut dysbiosis and significant differences in\nstool  metabolites[43].  The  microbiota  functions  as  an\nactive,  metabolically  integrated  biological  unit  that\ngenerates  metabolites  that  enter  the  systemic\ncirculation  and  modulate  immune,  endocrine,  and\nmetabolic  processes.  Therefore,  metabolomics,  which\nenables  the  comprehensive  profiling  of  small-\nmolecule  metabolites,  provides  critical  insights  into\nupstream  microbial-host  interactions[44].  Accordingly,\nmicrobial  dysbiosis  in  EM  likely  drives  significant\nremodeling of the host metabolite landscape.\nIn  the  context  of  EM,  gut  microbiota  imbalance\nleads  to  pronounced  changes  in  microbiota-derived\nmetabolites, which primarily fall into three categories.\nFirst, dietary components are abnormally transformed\nby gut microbes. For example, short-chain fatty acids\n(SCFAs),  including  acetate,  propionate,  and  butyrate,\nare major fermentation products of undigested dietary\nfibers generated by colonic bacteria and play essential\nroles in maintaining intestinal homeostasis[45]. In EM,\nreduced  SCFA  levels  may  impair  anti-inflammatory\nand immunoregulatory functions, thereby promoting a\npro-inflammatory  microenvironment  conducive  to\nlesion  establishment  and  growth.  Tryptophan  (Trp)\nmetabolism  in  the  gastrointestinal  tract  is  highly\ndependent on the microbiota, which converts Trp into\nvarious  bioactive  compounds[46].  Altered  Trp\nmetabolites  in  EM  can  modulate  immune  responses\nand  affect  pain  perception,  thereby  eliciting\nneurological  symptoms  associated  with  the  disease.\nSecond,  host-synthesized  molecules  undergo\nmicrobial  modification  in  the  gut.  A  key  example  is\nsecondary  bile  acids  (SBAs).  Primary  bile  acids\nproduced in the liver are converted into SBAs, such as\ndeoxycholic  acid  (DCA)  and  lithocholic  acid  (LCA),\nby  specific  gut  bacteria  (Clostridium  spp.)  through\ndehydroxylation  reactions,  a  process  tightly  regulated\nby  the  microbial  composition[47].  In  EM,  SBAs  may\ncontribute  to  inflammation  and  cellular  proliferation,\npotentially  exacerbating  the  development  of  ectopic\nlesions.  Third,  certain  metabolites  originate  directly\nfrom  the  microorganisms  themselves.  LPS,  a  major\ncomponent  of  the  outer  membrane  of  Gram-negative\nbacteria,  can  translocate  into  the  circulation  during\ndysbiosis  and  act  as  a  potent  inflammatory  activator,\ntriggering  systemic  inflammation  via  Toll-like\nreceptor 4 (TLR4) signaling[48]. Elevated LPS levels in\nEM are believed to drive chronic pelvic inflammation\nand  pain  while  promoting  the  adhesion  and  invasion\nof endometrial cells. Simultaneously, β-glucuronidase\n6 et al. J Biomed Res, 2026, 40(0)\nUnproofed\n\nproduced  by  certain  gut  bacteria  hydrolyzes\nconjugated  estrogen  into  its  free,  biologically  active\nform, enabling its reabsorption and disrupting normal\nenterohepatic  estrogen  cycling[49].  The  microbial\nreactivation  of  estrogen  in  EM  increases  local  and\nsystemic  estrogen  levels,  which  are  key  factors  in\nstimulating  endometrial  tissue  growth  and  survival\noutside the uterus.\nThese  three  dysbiosis-driven  metabolic  alterations\nconstitute  the  critical  biochemical  basis  for  EM.\nHence,  we  propose  the  microbiota–metabolite  axis  as\na  pathological  framework  to  systematically  elucidate\nthe  mechanisms  underlying  dysbiosis  in  the  gut  and\nvaginal microbiota through the modulation of specific\nmetabolic  pathways,  thereby  reshaping  local  and\nsystemic  immune  microenvironments,  thereby\npromoting the initiation and progression of EM. In the\nfollowing  section,  drawing  on  the  five  metabolic\nreprogramming  pathways  (SCFAs,  Trp,  SBAs,  LPS,\nand  estrogen  metabolism)  outlined  in  Figure  2,  we\nexplore  the  mechanisms  of  microbiota-derived\nmetabolites  in  EM  from  the  perspective  of  altered\nmetabolic profiles. \nSCFA dysregulation\nThe production of SCFAs is critically dependent on\n \nDietary\nfiber\nSCFA\nSCFAs Dysregulation\nPromote M2 Polarization,\nSuppress M1 and Limit\nTreg Expansion\nTrp\nIndole\nAhR\nKYNAhR\nIL-6\nTNF-α\nIL-22\nTreg\nTrp Metabolic Imbalance\nInhibit Teff function and\nexpand Tregs Pro-inflammatory Pro-inflammatory\nDCA,LCA\nPrimary\nbile acids\nTGR5\ncAMP PKA\nNF-κB\nTNF-α\nIL-17\nIL-1β\nSBAs-Related\nMetabolism \nTLR4\nNF-κB\nTNF-α\nIL-17\nIL-1β\nLPS\nLPS-Related\nMetabolism\nReprogramming of\nE2 Metabolism\nGnRH‑Mediated E2\nSecretion and Promote\nlesion growth\nPituitary\ngland\nIDO-1\nSCFA\nTreg\nMe\nAc\nFoxp3\nIL-6\nTNF-α\nGPR15\nGPR43\nCD4+T \nGPR109a\nDC\nmø\nConjugated\nestrogen\nUnconjugated\nestrogen\nUnconjugated\nglucuronic acid\nFacilitation Inhibition\n Receptor G protein-coupled\nreceptor\nIntestinal/Vaginal\nEpithelium\nBlood vessel Increase Reduce\nA B C D E\n \n \nFig.  2     Microbiota  dysbiosis  drives  metabolic  reprogramming  in  endometriosis  (EM).  This  schematic  illustrates  five  interconnected\npathways  through  which  microbial  imbalance  disrupts  host  metabolism,  immune  function,  and  estrogen  homeostasis  in  EM.  Panels  are\narranged  horizontally.  (a)  SCFAs  dysregulation:  Reduced  SCFA-producing  bacteria  decrease  SCFAs,  impairing  Treg/M2  polarization  and\nenhancing  NF-κB-mediated  inflammation.  (b)  Tryptophan  metabolic  aberration:  Altered  microbiota  shifts  tryptophan  toward  kynurenine\npathway, expanding Tregs while suppressing Teffs. Reduced AhR ligands (IPA, IAA) increase IL-6/TNF-α, fostering immune tolerance. (c)\nSBA-related  metabolic  alteration:  Reduced  SBA-producing  bacteria  lower  DCA/LCA,  diminishing  TGR5-cAMP/PKA  signaling,  which\ndisinhibits  NF-κB  and  promotes  pro-inflammatory  cytokines.  (d)  LPS-related  metabolic  perturbation:  Gram-negative  bacterial  overgrowth\nelevates  LPS,  activating  NF-κB  via  TLR4  and  driving  TNF-α/IL-17/IL-1β  secretion,  contributing  to  chronic  pelvic  inflammation.  (e)\nReprogramming  of  estrogen  metabolic  imbalance:  Microbial  β-glucuronidase  increases  free  E2  reabsorption,  elevating  local/systemic\nestrogen. Altered neuroactive metabolites disrupt the hypothalamic-pituitary-ovarian axis, creating a self-reinforcing cycle of estrogen excess\nand  inflammation.  Collectively,  these  dysbiosis-driven  metabolic  shifts  promote  ectopic  lesion  survival,  proliferation,  and  invasiveness  in\nEM. Abbreviations: AhR, aryl hydrocarbon receptor; DC, dendritic cell; DCA, deoxycholic acid; E2, Estradiol; IAA, indole-3-acetic acid;\nIDO-1,  indoleamine  2,3-dioxygenase  1;  IPA,  indole-3-propionic  acid;  KYN,  kynurenine;  LCA,  lithocholic  acid;  LPS,  lipopolysaccharide;\nSBAs, secondary bile acids; SCFA, Short-chain fatty acids; TGR5, Takeda G protein-coupled receptor 5; TLR4, Toll-like receptor 4; Treg,\nregulatory T cell; Trp, Tryptophan; mø, macrophage. Created in BioRender. Xu, P. (2025) https://BioRender.com/a51kabp.\nMicrobiota–metabolite axis in endometriosis 7\nUnproofed\n\nthe  composition  of  the  gut  microbiota.  Key  SCFA-\nproducing  genera  include  Bacteroides,\nBifidobacterium,  Ruminococcus,  Lactobacillus,\nFaecalibacterium,  Prevotella,  and  Eubacterium[50].  In\nthe context of EM, a dysbiotic state characterized by a\nreduced  abundance  of  specific  beneficial  taxa,\nparticularly  Ruminococcus  and  Eubacterium  species,\nis  the  primary  cause  of  impaired  SCFA  generation.\nBeneficial bacteria, such as Eubacterium ruminantium\n(family  Ruminococcaceae),  are  positively  correlated\nwith  SCFA  production  in  EM[51],  and  species  such  as\nRuminococcus  faecis  play  a  pivotal  role  in\nbutyrogenesis[52].\nSCFAs,  principally  acetate  (60%),  propionate\n(20%),  and  butyrate  (20%),  are  produced  by  the  gut\nmicrobiota  through  anaerobic  fermentation  of  dietary\nfibers[45].  These  potent  SCFAs  exert  systemic\nimmunomodulatory  effects  through  distinct\nmechanisms. Their primary immunoregulatory actions\nare mediated by activating specific G protein-coupled\nreceptors (GPCRs) and inhibiting histone deacetylases\n(HDACs)[53].  Butyrate,  the  main  energy  source  for\ncolonocytes[45]  and  recognized  for  its  anti-\ninflammatory  and  anticancer  properties[54,55],  acts  as  a\nkey  regulator  of  colonic  regulatory  T  cell  (Treg)\ngeneration by directly promoting histone acetylation at\nthe FOXP3 locus to drive naïve CD4+ T cells toward a\nTreg  phenotype[56]  or  by  indirectly  inducing  Treg\ndifferentiation  via  dendritic  cell  activation  through\nGPR109a[57].  Furthermore,  butyrate  enhances  Treg\nfunction  and  Foxp3  expression  by  inhibiting  HDACs\n(HDAC9)  [64],  thereby  promoting  FOXP3+  Treg\nexpansion[58].  Propionate  and  acetate  recruit\nextraintestinal  Tregs  to  the  colon  via  GPR15  and\nGPR43,  respectively[59].  Beyond  Tregs,  SCFAs\nsuppress  nuclear  factor  (NF)-κB-mediated\ninflammatory  responses  in  macrophages[60]  and\npromote  macrophage  polarization  toward  the  anti-\ninflammatory M2 type over the pro-inflammatory M1\nphenotype.\nSCFA deficiency resulting from gut dysbiosis plays\na  significant  role  in  the  pathogenesis  of  EM.  The\nconsequent  reduction  in  systemic  anti-inflammatory\ncapacity and compromised immunoregulation create a\npermissive environment for ectopic lesions. Decreased\nbutyrate  levels  stemming  from  a  reduced  abundance\nof  key  producers  weaken  the  suppression  of  NF-κB-\nmediated  inflammation[60]  and  impair  Treg\ndifferentiation  and  function[56,61].  One  study  revealed\nthat  experimental  depletion  of  Tregs  in  mice\nexacerbated  lesion  growth  and  inflammation[62].\nMoreover, butyrate supplementation in mouse models\nsignificantly  reduced  the  endometriotic  lesion\nburden[63,64]. Butyrate exerts bidirectional regulation of\nsteroidogenesis,  and  its  deficiency  may  impair  the\ncorrection  of  the  hyperestrogenic  state  in  EM[65].\nAltogether,  gut  dysbiosis-induced  SCFA  deficiency\nimpairs  systemic  anti-inflammatory  capacity  and\nintestinal barrier integrity, thereby facilitating immune\nimbalance,  the  diffusion  of  inflammatory  mediators,\nand  the  establishment  and  persistence  of  ectopic\nendometrial tissue[66]. \nAberrations in tryptophan metabolism\nThe dysbiotic gut microbiota profile is a key driver\nof the metabolic imbalance of Trp in EM. Dysbiosis is\ncharacterized  by  reduced  levels  of  Lactobacillus  and\nBacillus species and an increase in that of E. coli. This\nreduction  affects  known  commensal  bacteria  capable\nof  producing  aryl  hydrocarbon  receptor  (AhR)\nligands,  which  are  limited  to  Lactobacillus  species[67]\nand  Peptostreptococcus  russellii[68].  Concurrently,  an\nincrease in the abundance of E. coli, which, along with\nsome  Lactobacillus  species,  increases  tryptophanase\nexpression  to  convert  Trp  into  indole[69],  thereby\nredirecting  the  metabolic  flux.  The  decrease  in  the\nnumber  of  Bacillus  species  that  generate  tryptamine\nvia  decarboxylation[70]  further  contributes  to  the  loss\nof  bioactive  molecules.  This  dysbiosis  is  reflected  by\nreduced  levels  of  the  bacterial  metabolite  4-\nhydroxyindole  (4HI)  in  feces,  which  correlates  with\nspecific  microbial  shifts:  positively  with  beneficial\ngenera  such  as  Faecalibacterium  and\nLachnospiraceae  and  negatively  with  the  commensal\nbacterium  Dorea[43].  This  specific  microbial  shift\nfundamentally  disrupts  the  homeostasis  of  host  Trp\nmetabolism.\nTrp  metabolism  in  the  gastrointestinal  tract  occurs\nmainly  through  three  pathways[46]:  (1)  direct\nconversion  of  Trp  by  the  gut  microbiota  into  AhR\nligands and other bioactive molecules; (2) catabolism\nvia  indoleamine  2,3-dioxygenase  1  (IDO-1)  in\nimmune  and  epithelial  cells,  forming  the  kynurenine\n(KYN)  pathway;  and  (3)  synthesis  of  serotonin  by\nenterochromaffin  cells.  Microbial  metabolism  is  the\nprimary source of AhR activation in the gut[71]. During\nmicrobial  tryptophan  metabolism,  the  oxidation  and\nreduction  pathways  yield  indole-3-acetic  acid  (IAA)\nand  indole-3-propionic  acid  (IPA),  both  of  which\nmodulate  intestinal  permeability  and  immune\nfunction[72]. Indole, a key intermediate metabolite, acts\nas  an  interspecies  signaling  molecule  that  influences\nbacterial  physiology[73].  Thus,  by  shaping  Trp  flux\nacross these pathways, gut microbes critically regulate\nhost  barrier  integrity,  local  immunity,  and  systemic\nphysiology.\n8 et al. J Biomed Res, 2026, 40(0)\nUnproofed\n\nIn  EM,  dysbiosis-driven  disruption  manifests  as  a\npivotal  imbalance  between  the  KYN  and  indole\npathways,  which  play  a  decisive  role  in  disease\nprogression.  The  altered  microbiota  specifically\nenhances  the  KYN  pathway  while  suppressing  the\nindole  pathway.  The  KYN  pathway  is  markedly\nupregulated in patients with EM due to elevated IDO-\n1  activity,  leading  to  increased  KYN  levels.  KYN\npromotes immune tolerance by suppressing effector T\ncells  and  expanding  Tregs,  thereby  facilitating  the\nimmune evasion of ectopic lesions[74]. In contrast, the\nmicrobial  indole  pathway  was  suppressed.  Fecal\nmetabolomic  analyses  revealed  significantly  reduced\nlevels of beneficial metabolites, such as IPA. As a key\nAhR  ligand,  IPA  exerts  anti-inflammatory  and\nantioxidant  effects  by  activating  this  receptor  and\ninhibiting the production of pro-inflammatory factors,\nsuch  as  IL-6  and  TNF-α,  thereby  contributing  to  its\nanti-inflammatory  role[75].  The  decrease  in  the  levels\nof other immunomodulatory derivatives, such as IAA,\nindole-3-lactic  acid,  and  4HI,  further  weakens  host\ndefense[43].  Quinic  acid  is  a  key  fecal  metabolite  that\npromotes lesion growth in EM[76]. This dual alteration,\nan enhanced immunosuppressive KYN pathway and a\ndeficient  protective  AhR  pathway,  generates  an\nimmunotolerant  microenvironment  conducive  to\nlesion survival and proliferation.\nThe functional significance of AhR signaling in EM\nis  supported  by  direct  cellular  evidence  at  multiple\nlevels.  Mechanistically,  AhR  is  expressed  in  mast\ncells  that  infiltrate  endometriotic  lesions;  upon  AhR\nactivation, these mast cells produce IL-17 and reactive\noxygen  species,  contributing  to  a  pro-inflammatory\nmicroenvironment that sustains lesion development[77].\nFurthermore,  AhR  may  interact  with  other  receptors,\nincluding  classical  estrogen  receptors,  thereby\nmodulating the course of estrogen-dependent diseases,\nsuch  as  EM[78].  Environmental  AhR  ligands,  such  as\n2,3,7,8-tetrachlorodibenzo-p-dioxin,  exert  their  toxic\neffects  by  binding  to  AhR,  forming  an  activated\nheterodimer  with  transcriptional  activity  that  may\npromote an inflammatory state and facilitate menstrual\nprocesses  relevant  to  EM  pathogenesis[79].  These\nfindings  provide  a  direct  mechanistic  link  between\ntryptophan metabolic disturbances and EM pathology.\nConsequently,  therapeutic  strategies  targeting  the\nTrp-AhR  axis,  such  as  probiotics,  prebiotics,  IDO-1\ninhibitors,  and  AhR  modulators,  are  emerging  as\npromising  approaches  for  microbiota-based  immune\nmodulation in EM[80]. \nSecondary bile acid-related metabolic alterations\nThe  production  of  SBAs  in  the  intestine  is  directly\ngoverned by the gut microbiota. Primary bile acids are\nconverted into SBAs, such as DCA and LCA, through\nmicrobial  transformations,  particularly\ndehydroxylation,  mediated  by  bacteria  such  as\nClostridium  difficile[47].  DCA  and  LCA  are  the  most\nprevalent SBAs. The abundance of specific beneficial\nbacteria  determines  SBA  levels.  A  previous  study\nindicated  a  significant  positive  correlation  between\nRuminococcus abundance and SBA levels[66], whereas\nEubacterium species have been shown to regulate bile\nacid  metabolism  and  mitigate  inflammation[51].\nTherefore,  dysbiosis,  which  involves  a  decline  in  the\nabundance of these key genera, is the primary cause of\nreduced SBA production.\nAs  important  signaling  molecules,  SBAs  can\nsystemically  modulate  immune  balance  and\ninflammatory  responses  by  significantly  reducing  the\nproduction  of  multiple  inflammatory  chemokines  and\ncytokines, including TNF-α and IL-17[81]. Their potent\nanti-inflammatory effects are predominantly mediated\nby  the  activation  of  Takeda  G  protein-coupled\nreceptor  5  (TGR5).  TGR5  inhibits  NF-κB  activation\nby modulating the cAMP/PKA signaling pathway. For\ninstance, in a murine model of Staphylococcus aureus-\ninduced  endometritis,  DCA  exerts  protective  effects\nby  significantly  upregulating  TGR5  and  PKA\nexpression;  this  effect  is  abolished  by  TGR5  or  PKA\ninhibitors,  which  block  the  production  of  TNF-α  and\nIL-1β  and  suppress  NF-κB  activation[82].  LCA  and\nDCA  suppress  pro-inflammatory  cytokine  production\nby  human  peripheral  blood-derived  macrophages  via\nTGR5 activation[83].\nIn  the  context  of  EM,  gut  dysbiosis-induced  SBA\ndeficiency  creates  a  permissive  pro-inflammatory\nmilieu  that  fuels  disease  progression.  A  reduction  in\nthe  abundance  of  beneficial  bacteria,  such  as\nRuminococcus  and  Eubacterium,  leads  to  decreased\nSBA  levels.  This  deficiency  impairs  the  vital  TGR5-\nmediated  suppression  of  the  NF-κB  pathway  and  the\nproduction  of  pro-inflammatory  cytokines  (TNF-α,\nIL-1β,  and  IL-17)[81–83].  The  consequent  loss  of\nsystemic anti-inflammatory signaling disrupts immune\nhomeostasis,  allowing  unchecked  inflammation  that\npromotes  the  survival,  implantation,  and  growth  of\nectopic  endometrial  tissue.  Direct  evidence  from\nhuman  endometriotic  stromal  cells  supports  the\nprotective  role  of  TGR5  activation.  Activation  of\nTGR5  by  its  specific  agonist  INT-777  protects\nendometriotic  stromal  cells  from  TNF-α-induced\ninflammation and oxidative stress, reducing the levels\nof pro-inflammatory cytokines (IL-6, IL-8, and MCP-\n1),  adhesion  molecules  (ICAM-1  and  VCAM-1),  and\nNADPH oxidase 4 (NOX4) expression. These effects\nMicrobiota–metabolite axis in endometriosis 9\nUnproofed\n\nare mediated through the inhibition of JNK/AP-1 and\nNF-κB  signaling[84].  Thus,  dysbiosis-driven\nsuppression  of  SBA  production  represents  a  key\nmechanistic  link  between  gut  microbiota  alterations\nand the inflammatory pathogenesis of EM. \nLPS  and  endotoxemia-related  metabolic\nperturbations\nLPS, a major component of the outer membrane of\nGram-negative bacteria, acts as a potent inflammatory\nactivator  by  binding  to  TLR4  on  immune  cells,\nthereby  triggering  downstream  signaling  pathways,\nsuch  as  NF-κB.  This  cascade  activates  macrophages\nand  induces  the  release  of  pro-inflammatory\ncytokines,  including  IL-6  and  TNF-α[48].  In  EM,  an\nincreased  abundance  of  Gram-negative  bacteria,  such\nas those from the Prevotellaceae family, in the gut or\nreproductive  tract,  leads  to  elevated  systemic  LPS\nlevels.  Sustained  endotoxemia  drives  chronic\ninflammation  in  the  pelvic  and  systemic\ncompartments, creating a favorable microenvironment\nfor  the  adhesion,  proliferation,  and  progression  of\nectopic  endometrial  cells[85].  In  the  context  of  EM,\nLPS enhances TLR4 expression and activates the NF-\nκB  pathway,  exacerbating  peritoneal  inflammation\nand promoting the development of endometriotic-like\nlesions  in  mouse  models[86].  Moreover,  menstrual\nblood  is  frequently  contaminated  with  high  levels  of\nE.  coli,  and  microbial  colonization  within  the\nendometrium  has  been  documented,  both  of  which\nmay serve as significant sources of systemic LPS and\ncontribute to endotoxemia[87]. \nReprogramming of estrogen metabolic imbalance\nEstrogen plays a pivotal role in the pathogenesis of\nEM,  and  its  homeostasis  is  regulated  by  the  gut\nmicrobiota.  First,  during  gut  dysbiosis,  which  is\ncharacterized by reduced microbial diversity, microbe-\nderived  β-glucuronidase  is  abnormally  upregulated.\nThis  enzyme  deconjugates  estrogen,  which  is\ninactivated by hepatic glucuronidation, and converts it\nback  to  its  biologically  active  free  form[49].  These\nreactivated  estrogens  are  reabsorbed  via  the\nenterohepatic  circulation,  leading  to  abnormally\nelevated  circulating  estrogen  levels,  which  directly\npromote  the  growth,  shedding,  and  inflammatory\nactivity of ectopic endometrial tissue[87].\nSecond, gut dysbiosis can influence the function of\nthe  hypothalamic–pituitary–ovarian  axis  by  altering\nneuroactive  metabolites.  Dysbiosis-induced  changes\nin the metabolome can elevate the circulating levels of\nneurotransmitter-like  substances,  such  as  serotonin,\nglutamate,  SCFAs,  and  γ-aminobutyric  acid.  These\nmetabolites  can  cross  the  blood–brain  barrier  and  act\non  various  receptors,  including  those  expressed  on\ngonadotropin-releasing hormone neurons, triggering a\ncascade  of  hormonal  signals  that  lead  to  increased\novarian  estrogen  secretion[9].  Furthermore,  shifts  in\nmicrobial composition can modulate the production of\nSCFAs  and  LPS  in  response  to  estrogen  imbalance,\nwhereas  fluctuations  in  estrogen  levels  can\nreciprocally influence microbial community structure.\nThis bidirectional interaction contributes to the altered\nimmune  microenvironment  observed  in  patients  with\nEM[49,88]. \nOther metabolic alterations\nIn addition to the metabolites discussed previously,\nmany other metabolites are associated with alterations\nin  the  gut  microbiota  in  EM.  Using  correlation\nanalysis,  a  mouse  model  study  confirmed  that  L-\nmethionine  and  L-cysteine  levels  were  increased  in\nthe feces of mice with adenomyosis. Their abundance\nis  negatively  correlated  with  that  of  Bacteroides  but\npositively  correlated  with  Desulfovibrio,  suggesting  a\nstatistical  association  between  specific  amino  acid\nmetabolism  and  microbiota  composition[89].\nFurthermore,  other  studies  using  the  same  disease\nmodel have depicted a broader landscape of metabolic\ndysregulation,  identifying  the  differential  expression\nof various metabolites, including quinic acid, cytosine,\nand L-methylhistidine, in the feces of affected mice[76].\nAmong  these,  quinic  acid  levels  increased\nsignificantly.  Functional  experiments  confirmed  the\nability  of  quinic  acid  to  effectively  promote  the\nproliferation  of  immortalized  human  endometrial\nepithelial  cells,  providing  a  potential  molecular\nexplanation  for  the  direct  involvement  of  microbial\nmetabolites  in  the  growth  of  ectopic  lesions[76].  The\neffects of this metabolic reprogramming were evident\nin  lipid  and  primary  bile  acid  metabolism.  For\ninstance,  in  the  feces  of  EM  model  mice,  the\nabundance  of  bile  acids,  such  as  chenodeoxycholic\nand  ursodeoxycholic  acids  is  increased,  whereas  the\nlevels of alpha-linolenic acid and its metabolite 12,13-\nepoxyoctadecatrienoic  acid  are  decreased.  This  shift\nleads  to  significant  perturbations  in  enriched\npathways,  including  secondary  bile  acid  biosynthesis\nand  alpha-linolenic  acid  metabolism[90].  Altered\nabundance  of  specific  metabolites  has  been  observed\nin  the  fecal  samples  of  women  with  EM.  These\nbiomarkers  include  linoleic  acid,  adenine,  cytosine\nand  adenosine  (Table  2)[43].  Although  these  studies\nillustrate  extensive  alterations  in  the  gut  microbial\nmetabolic  network  under  disease  conditions,  most\nanalyses  remain  descriptive  and  have  yet  to  elucidate\n10 et al. J Biomed Res, 2026, 40(0)\nUnproofed\n\nthe causal relationship between microbial changes and\nspecific alterations in metabolite levels. \nClinical  applications  of  microbiota  and  their\nmetabolites in EM\nOur  proposed  \"microbiota–metabolite\"  axis  has\nbeen substantiated, providing a systematic framework\nfor understanding the underlying mechanisms of EM.\nThis  model  highlights  how  microbial  dysbiosis  acts\nsynergistically  across  multiple  levels,  including\nimmune  regulation,  inflammatory  responses,  and\nhormonal  balance,  by  driving  disturbances  in  key\nmetabolic  pathways  to  promote  disease  development\nand  persistence.  Given  the  central  role  of  the\n\"microbiota–metabolite\" axis in EM pathogenesis, the\ndevelopment  of  novel  diagnostic  and  therapeutic\nstrategies  targeting  this  axis  has  emerged  as  a\npromising  research  direction.  These  translational\napproaches aim to address the critical unmet needs in\ncurrent  clinical  practice,  namely  delayed  diagnosis\nand limited treatment options. \nDiagnostic strategies\nCurrently,  the  gold  standard  for  diagnosing  EM  is\ninvasive  laparoscopic  surgery,  which  has  an  average\ndiagnostic  delay  of  7–10  years[91].  Although  most\nbiomarkers  are  still  in  the  exploratory  stage,\nmetabolomics and microbiome profiling offer a robust\nfoundation  for  developing  noninvasive  or  minimally\ninvasive liquid biopsy approaches. Fecal microbiome-\nbased diagnostic methods have been successfully used\nin  the  clinical  diagnosis  of  various  diseases[92],\nsuggesting  that  fecal  microbial  markers  have  the\npotential for cross-disease diagnostic applications.\n \nTable 2   Differentially abundant microbiota-derived metabolites in endometriosis (EM)\nMetabolite name Category Change in EM (abundance) References\n12,13-Epoxyoctadecatrienoic acid Fatty acid derivative Down [87]\n1-Methylhistidine Amino acid derivative Down [76]\n20-Deoxyadenosine Nucleoside Down [43]\n4-Hydroxyindole Tryptophan metabolite (indole pathway) Down [43]\nAcetate Short-chain fatty acid Down [43,45,66]\nAdenine Nucleobase Down [43]\nAdenosine Nucleoside Down [43]\nAlpha-linolenic acid Polyunsaturated fatty acid Down [87]\nButyrate Short-chain fatty acid Down [43,45,51,52,66]\nChenodeoxycholic acid Primary bile acid Up [87]\nCytosine Nucleobase Down [43,76]\nDeoxycholic acid (DCA) Secondary bile acid Down [47,66,78-80]\nFree (deconjugated) estrogen Steroid hormone Up [49,83]\nIndole-3-acetic acid (IAA) Tryptophan metabolite (indole pathway) Down [43,72]\nIndole-3-lactic acid (ILA) Tryptophan metabolite (indole pathway) Down [43]\nIndole-3-propionic acid (IPA) Tryptophan metabolite (indole pathway) Down [43,75]\nKynurenine Tryptophan metabolite (Kynurenine pathway) Up [74]\nL-cysteine Amino acid Up [86]\nLinoleic acid Polyunsaturated fatty acid Down [43]\nLipopolysaccharide (LPS) Bacterial endotoxin Up [48,81–83]\nLithocholic acid (LCA) Secondary bile acid Down [47,66,78,80]\nL-methionine Amino acid Up [86]\nN-formyl-L-methionine Amino acid derivative Up [43]\nPropionate Short-chain fatty acid Down [43,45,66]\nQuinic acid Tryptophan metabolite / Other Up [76]\nUrsodeoxycholic acid Primary bile acid Up [87]\nMicrobiota–metabolite axis in endometriosis 11\nUnproofed\n\nMultiple  studies  have  indicated  that  microbial\nalterations can serve as potential diagnostic targets. F.\nnucleatum  infiltration  is  detectable  in  the\nendometrium  of  64%  of  patients  with  EM[38],\nsuggesting  its  potential  as  a  biomarker  for  the\nauxiliary  diagnosis  of  the  disease[93].  Importantly,  the\ndiagnostic value of this bacterium has been confirmed\nin  colorectal  and  gastric  cancers,  with  area  under  the\ncurve  (AUC)  values  of  0.80[94]  and  0.813[95],\nrespectively,  providing  strong  evidence  for  its\napplication in EM diagnosis. Fecal microbial markers\nalso  demonstrate  diagnostic  potential.  The  ratio  of\nPrevotella  to  Bacteroides  in  the  gut  is  significantly\nhigher in EM patients compared to controls[96]. Known\nas an important biomarker for obesity, its alteration in\nEM  further  supports  its  utility  as  a  non-specific\nindicator  reflecting  the  disease-associated\nmicroenvironment for auxiliary diagnosis[27].\nBeyond  direct  microbial  markers,  microbe-derived\nmetabolites  have  emerged  as  promising  non-invasive\ndiagnostic  tools.  Diagnostic  approaches  based  on\nblood,  urine,  and  stool-derived  metabolites  for  EM\nhave achieved AUC values exceeding 0.8[43]. Multiple\nuntargeted  metabolomics  studies  have  consistently\nidentified distinct metabolic signatures in the blood of\nEM patients[97], involving disturbances in amino acid,\nlipid,  and  energy  metabolism  pathways.  Notably,\ncombined  metabolite  panels  have  shown  excellent\nperformance. Studies have confirmed that a diagnostic\nmodel  incorporating  N-[1H-indol-3-ylacetyl]valine\n(odds ratio [OR]=1.601, a tryptophan metabolite) and\nhippuric  acid  (OR=0.368,  derived  from  gut  microbial\nmetabolism  of  dietary  components)  along  with  other\nfeatures  achieved  an  AUC  greater  than  0.9[98].  These\nmetabolic  alterations  likely  reflect  the  functional\noutput  of  microbial  dysbiosis.  Animal  studies  further\nsuggest the diagnostic potential of related metabolites.\nResearch  has  found  significant  differences  in  fecal\nmetabolites  between  EM  model  mice  and  healthy\ncontrols,  with  quinic  acid,  lactic  acid,  and  N-acetyl\naspartic  acid  showing  high  expression[76].  These\ndifferential  metabolites  hold  promise  as  candidate\ntargets for non-invasive EM diagnosis.\nAlthough  microbe-derived  markers  show  great\npromise  for  non-invasive  EM  diagnosis,  cautious\nadvancement  toward  clinical  application  is  needed.\nCurrent  findings  exhibit  some  heterogeneity,  and\ncertain discoveries are based solely on animal models.\nTherefore,  large-scale,  multi-center  independent\ncohort  studies  are  still  required  to  systematically\nvalidate  the  diagnostic  performance  of  existing\nmarkers. \nTherapeutic strategies\nModulating the \"microbiota–metabolite\" axis opens\nup  a  new  frontier  for  potentially  safer  and  less  toxic\nadjunctive  therapies  for  EM.  The  following  sections\nprovide  an  overview  of  these  therapies  and  their\npotential use in treating EM. \nProbiotic interventions\nFuture  therapeutic  strategies  for  EM  will  move\nbeyond  generic  probiotic  supplementation  toward\nprecision nutrition tailored to the individual microbial\nand  metabolic  profiles.  For  instance,  in  patients  with\nlow  fecal  butyrate  levels,  the  targeted  administration\nof  butyrate-producing  strains  (Clostridium\nbutyricum)[99]  or  prebiotics  rich  in\nfructooligosaccharides  and  inulin  may  be  more\neffective  than  conventional  Lactobacillus-based\nproducts.  Supplementation  with  Bifidobacterium\nbifidum  for  4  weeks  modulated  the  gut  microbiota  in\nhealthy  adults,  reducing  the  abundance  of\nPrevotellaceae and Prevotella while increasing that of\nRuminococcaceae  and  Lachnospiraceae,  along  with\nelevating  butyrate  concentrations[100].  Animal  models\nhave provided proof-of-concept evidence that specific\nprobiotics  can  reduce  lesion  size  and  alleviate  pain-\nrelated behaviors in EM mice[101]. \nMetabolite-based interventions\nTargeting  the  gut  microbiota–metabolite  axis\nrepresents  a  novel  therapeutic  approach  for  EM,  with\nthe  direct  supplementation  of  key  metabolites\ndemonstrating  significant  potential.  First,  butyrate\n(sodium  butyrate)  has  been  shown  to  effectively\ninhibit lesion growth in animal models by suppressing\nendometrial  cell  survival  through  multiple  pathways,\nincluding activation of GPCRs, inhibition of HDACs,\nand  upregulation  of  the  GTPase-activating  protein\nRAP1GAP[63].  Second,  bile  acid  metabolites  have\nregulatory  value;  chenodeoxycholic  acid  and  its\nderivatives  may  alleviate  EM  pathology  by\nmodulating  the  activity  of  the  associated  metabolic\nenzymes[102].  Furthermore,  the  microbial  Trp\nmetabolite 4-HI is found at reduced levels in patients\nwith  EM,  and  its  supplementation  inhibits  disease\nprogression, underscoring its potential as a therapeutic\ncandidate[43].  In  summary,  interventions  targeting\nbutyrate, bile acids, and Trp metabolites offer diverse\nand promising avenues for the metabolic management\nof EM. \nDietary modifications\nEncouraging  patients  with  EM  to  adopt  a  high-\n12 et al. J Biomed Res, 2026, 40(0)\nUnproofed\n\nfiber, omega-3 fatty acid-rich Mediterranean diet[103] is\na  safe,  cost-effective,  and  multi-beneficial  strategy.\nHigh-fiber  diets  are  fermented  by  the  gut  microbiota\ninto  SCFAs,  which  exert  direct  anti-inflammatory\neffects, whereas omega-3 fatty acids are potent natural\nanti-inflammatory  agents[104].  Observational  studies\nhave  identified  associations  between  dietary  patterns\nand  EM  risk[105],  although  large-scale  randomized\ncontrolled  trials  are  required  to  provide  high-level\nevidence.  Moreover,  cruciferous  vegetables  supply\nindole-3-carbinol,  which  is  converted  in  the  acidic\ngastric  environment  into  various  bioactive\ncompounds —including  diindolylmethane[106]—that\nmodulate  estrogen  metabolism  and  exhibit  anti-\ninflammatory  effects,  potentially  restricting  the\nprogression of EM. \nFecal microbiota transplantation\nAs the most radical method of microbial ecosystem\nreconstruction, fecal microbiota transplantation (FMT)\nhas  strong  theoretical  potential  for  patients  with\nrefractory  EM  who  fail  conventional  treatments  and\nexhibit  severe  dysbiosis[107].  For  example,  the\ntransplantation  of  Lachnospiraceae,  which  produces\nSCFAs[50],  Lactobacillus  species  capable  of\nsynthesizing AhR ligands[67], and Clostridium difficile,\nwhich  is  involved  in  the  conversion  of  SBAs[47].\nHowever,  the  application  of  FMT  in  EM  remains\nentirely  theoretical,  and  no  clinical  studies  have\nevaluated its safety or efficacy. First, despite rigorous\ndonor  screening,  potential  risks  include  the\ntransmission  of  pathogens  (multidrug-resistant\norganisms) and adverse events, ranging from transient\nabdominal  discomfort  and  diarrhea  to  rare  severe\ninfections[108,109].  Second,  ethical  considerations,\nincluding  informed  consent  procedures,  privacy\nprotection,  and  sample  ownership,  raise  concerns,\nwith  most  survey  respondents  expressing\nskepticism[110].  Third,  FMT  products  vary  widely  in\ntheir preparation methods, donor selection criteria, and\nadministration  routes,  and  currently  lack  regulatory\napproval  for  non-Clostridioides  difficile  infection\nindications[108]. Consequently, FMT for EM must first\nbe  evaluated  in  well-designed  early-phase  clinical\ntrials  (Phase  I/II)  to  thoroughly  assess  its  safety  and\npreliminary  efficacy  before  any  clinical  application\nand should not be attempted empirically. \nConclusions\nEM  has  long  been  viewed  as  a  localized\ngynecological  condition;  however,  growing  evidence\npositions  it  within  a  broader  systemic  framework\ncentered  on  the  \"microbiota–metabolite\"  axis.  This\nreview  integrates  current  findings  to  reveal  a\nconsistent  pathological  pattern  in  EM:  depletion  of\nbeneficial  microbes  (butyrate  producers  such  as\nRuminococcus  and  Eubacterium),  overgrowth  of  pro-\ninflammatory  taxa,  reduced  SCFA  levels,  a  shift  in\nTrp metabolism toward the immunosuppressive KYN\npathway,  increased  β-glucuronidase  activity  driving\nestrogen  reactivation,  and  elevated  LPS  release\npromoting  inflammation.  These  alterations  disrupt\nimmune  homeostasis,  enhance  estrogenic  stimulation,\nand foster a chronic inflammatory milieu that supports\nthe persistence and progression of ectopic lesions.\nHowever,  despite  these  advances,  several  key\nchallenges remain. Few findings from existing animal\nmodels have been translated into clinical applications\nin  humans.  The  limitations  of  the  animal  models\ndiscussed  in  this  study  include  exogenous  estrogen\nfailing to mimic the natural human cycle, interspecies\nimmune differences hindering mechanistic translation,\nsurgical  transplantation  deviating  from  the  natural\ncourse  of  retrograde  menstruation,  and  disparities  in\nbaseline  microbial  abundances  between  animals  and\nhumans,  limiting  the  extrapolation  of  metabolic\nfindings. Other key challenges remain, particularly in\nestablishing  causality  and  overcoming  the\nheterogeneity  of  studies.  Therefore,  future  efforts\nshould  focus  on  developing  standardized  protocols;\nintegrating  multi-omics  data;  conducting  multi-\nregional,  multi-cohort  longitudinal  studies;  advancing\nlesion-based  stratification  studies  that  correlate\nmicrobial and metabolic profiles with EM phenotypes\nto  lay  the  groundwork  for  personalized  diagnostics\nand treatments; and designing metabolite intervention\ntrials  to  validate  the  feasibility  of  using  microbiota-\nderived metabolites as therapeutic targets.\nWell-designed  clinical  trials  testing  microbiota-\ntargeted interventions are essential for translating this\nparadigm  into  effective  diagnostic  and  therapeutic\nstrategies. In redefining EM through the lens of host-\nmicrobe  metabolic  crosstalk,  we  gaindeeper\nmechanistic insight and transformative opportunity for\nearly disease detection and the precision management\nof patients with EM. \nFunding\nThis  project  was  supported  by  Nanjing  Medical\nScience  and  Technique  Development  Foundation\n(Grant  No.  YKK24153  to  S.X.),  and  Research\nInnovation Program for Graduates of Jiangsu Province\n(SJCX24_0755 to N.Y.) \nMicrobiota–metabolite axis in endometriosis 13\nUnproofed\n\nAuthor contributions\nMoyuan  Li:  Conceptualization,  Writing–original\ndraft,  Visualization.  Aiyuan  Yue:  Formal  analysis.\nLingfeng  Gu:  Investigation.  Feiyang  Li:\nVisualization.  Nuo  Ye:  Investigation,  Funding\nacquisition.  Sujuan  Xu:  Funding  acquisition.  Zhen\nGong:  Supervision,  Project  administration.  Dake  Li:\nConceptualization.  Pengfei  Xu:  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