{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T23:14:04Z","timestamp":1790723644904,"version":"4.1.0"},"reference-count":32,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2023,3,21]],"date-time":"2023-03-21T00:00:00Z","timestamp":1679356800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UZ Brussel Foundation and Gedeon Richter","award":["GPA17-236-FORWARD"],"award-info":[{"award-number":["GPA17-236-FORWARD"]}]},{"name":"UZ Brussel Foundation and Gedeon Richter","award":["1SD0622N"],"award-info":[{"award-number":["1SD0622N"]}]},{"name":"FWO-SB PhD","award":["GPA17-236-FORWARD"],"award-info":[{"award-number":["GPA17-236-FORWARD"]}]},{"name":"FWO-SB PhD","award":["1SD0622N"],"award-info":[{"award-number":["1SD0622N"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>It is generally accepted that microorganisms can colonize a non-pathological endometrium. However, in a clinical setting, endometrial samples are always collected by passing through the vaginal\u2013cervical route. As such, the vaginal and cervical microbiomes can easily cross-contaminate endometrial samples, resulting in a biased representation of the endometrial microbiome. This makes it difficult to demonstrate that the endometrial microbiome is not merely a reflection of contamination originating from sampling. Therefore, we investigated to what extent the endometrial microbiome corresponds to that of the vagina, applying culturomics on paired vaginal and endometrial samples. Culturomics could give novel insights into the microbiome of the female genital tract, as it overcomes sequencing-related bias. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy were included. An additional vaginal swab was taken from each participant right before hysteroscopy. Both endometrial biopsies and vaginal swabs were analyzed using our previously described WASPLab-assisted culturomics protocol. In total, 101 bacterial and two fungal species were identified among these 10 patients. Fifty-six species were found in endometrial biopsies and 90 were found in vaginal swabs. On average, 28 % of species were found in both the endometrial biopsy and vaginal swab of a given patient. Of the 56 species found in the endometrial biopsies, 13 were not found in the vaginal swabs. Of the 90 species found in vaginal swabs, 47 were not found in the endometrium. Our culturomics-based approach sheds a different light on the current understanding of the endometrial microbiome. The data suggest the potential existence of a unique endometrial microbiome that is not merely a presentation of cross-contamination derived from sampling. However, we cannot exclude cross-contamination completely. In addition, we observe that the microbiome of the vagina is richer in species than that of the endometrium, which contradicts the current sequence-based literature.<\/jats:p>","DOI":"10.3390\/ijms24065947","type":"journal-article","created":{"date-parts":[[2023,3,22]],"date-time":"2023-03-22T07:09:31Z","timestamp":1679468971000},"page":"5947","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Comparing Vaginal and Endometrial Microbiota Using Culturomics: Proof of Concept"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5589-502X","authenticated-orcid":false,"given":"Robin","family":"Vanstokstraeten","sequence":"first","affiliation":[{"name":"Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ellen","family":"Callewaert","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, Entity of In Vitro Toxicology, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3488-8063","authenticated-orcid":false,"given":"Susanne","family":"Blotwijk","sequence":"additional","affiliation":[{"name":"Biostatistics and Medical Informatics Research Group (BISI), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleni","family":"Rombauts","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1269-5546","authenticated-orcid":false,"given":"Florence","family":"Cromb\u00e9","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristof","family":"Emmerechts","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oriane","family":"Soetens","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristof","family":"Vandoorslaer","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah","family":"De Geyter","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2599-9941","authenticated-orcid":false,"given":"Camille","family":"Allonsius","sequence":"additional","affiliation":[{"name":"Department of Bioscience Engineering, University of Antwerp (UA), 2020 Antwerp, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6445-5237","authenticated-orcid":false,"given":"Leonore","family":"Vander Donck","sequence":"additional","affiliation":[{"name":"Department of Bioscience Engineering, University of Antwerp (UA), 2020 Antwerp, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Blockeel","sequence":"additional","affiliation":[{"name":"Brussels IVF, Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingrid","family":"Wybo","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7756-3691","authenticated-orcid":false,"given":"Denis","family":"Pi\u00e9rard","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6410-9246","authenticated-orcid":false,"given":"Thomas","family":"Demuyser","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"},{"name":"AIMS Lab, Center for Neurosciences, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shari","family":"Mackens","sequence":"additional","affiliation":[{"name":"Brussels IVF, Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,3,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1038\/s41467-017-00901-0","article-title":"The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases","volume":"8","author":"Chen","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2519","DOI":"10.1007\/s10815-021-02247-5","article-title":"The impact of the female genital tract microbiome in women health and reproduction: A review","volume":"38","author":"Labarta","year":"2021","journal-title":"J. Assist. Reprod. Genet."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1067\/mob.2001.115867","article-title":"Defense factors of vaginal lactobacilli","volume":"185","author":"Aroutcheva","year":"2001","journal-title":"Am. J. Obstet. Gynecol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1093\/humrep\/16.9.1809","article-title":"Origins of vaginal acidity: High D\/L lactate ratio is consistent with bacteria being the primary source","volume":"16","author":"Boskey","year":"2001","journal-title":"Hum. Reprod."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"103696","DOI":"10.1016\/j.micpath.2019.103696","article-title":"Crosstalk between Vaginal Microbiome and Female Health: A review","volume":"136","author":"Gupta","year":"2019","journal-title":"Microb. Pathog."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Lebeer, S., Ahannach, S., Wittouck, S., Gehrmann, T., Eilers, T., Oerlemans, E., Condori, S., Dillen, J., Spacova, I., and Vander Donck, L. (2022). Citizen-science map of the vaginal microbiome. Res. Sq.","DOI":"10.21203\/rs.3.rs-1350465\/v1"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Oerlemans, E.F.M., Wuyts, S., Bellen, G., Wittouck, S., De Boeck, I., Ruban, K., Allonsius, C.N., van den Broek, M.F.L., Donders, G.G.G., and Lebeer, S. (2020). The Dwindling Microbiota of Aerobic Vaginitis, an Inflammatory State Enriched in Pathobionts with Limited TLR Stimulation. Diagnostics, 10.","DOI":"10.3390\/diagnostics10110879"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1002\/jcp.25806","article-title":"Subclinical alteration of the cervical-vaginal microbiome in women with idiopathic infertility","volume":"232","author":"Campisciano","year":"2017","journal-title":"J. Cell. Physiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1038\/s41396-018-0337-0","article-title":"Unveiling the role of Gardnerella vaginalis in polymicrobial Bacterial Vaginosis biofilms: The impact of other vaginal pathogens living as neighbors","volume":"13","author":"Castro","year":"2019","journal-title":"ISME J."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Harwich, M.D., Alves, J.M., A Buck, G., Strauss, J.F., Patterson, J.L., Oki, A.T., Girerd, P.H., and Jefferson, K.K. (2010). Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies. BMC Genom., 11.","DOI":"10.1186\/1471-2164-11-375"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Toson, B., Simon, C., and Moreno, I. (2022). The Endometrial Microbiome and Its Impact on Human Conception. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23010485"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"208","DOI":"10.3389\/fimmu.2018.00208","article-title":"Uterine Microbiota: Residents, Tourists, or Invaders?","volume":"2","author":"Baker","year":"2018","journal-title":"Front. Immunol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.fertnstert.2017.05.034","article-title":"Endometrial microbiota-new player in town","volume":"108","author":"Moreno","year":"2017","journal-title":"Fertil. Steril."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1016\/j.ajog.2016.09.075","article-title":"Evidence that the endometrial microbiota has an effect on implantation success or failure","volume":"215","author":"Moreno","year":"2016","journal-title":"Am. J. Obstet. Gynecol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2471","DOI":"10.1007\/s10815-019-01630-7","article-title":"Does dysbiotic endometrium affect blastocyst implantation in IVF patients?","volume":"36","author":"Hashimoto","year":"2019","journal-title":"J. Assist. Reprod. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Salter, S.J., Cox, M.J., Turek, E.M., Calus, S.T., Cookson, W.O., Moffatt, M.F., Turner, P., Parkhill, J., Loman, N.J., and Walker, A.W. (2014). Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol., 12.","DOI":"10.1186\/s12915-014-0087-z"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Brooks, J.P., Edwards, D.J., Harwich, M.D., Rivera, M.C., Fettweis, J.M., Serrano, M.G., Reris, R.A., Sheth, N.U., Huang, B., and Girerd, P. (2015). The truth about metagenomics: Quantifying and counteracting bias in 16S rRNA studies. BMC Microbiol., 15.","DOI":"10.1186\/s12866-015-0351-6"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/s41586-022-05546-8","article-title":"Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies","volume":"613","author":"Kennedy","year":"2023","journal-title":"Nature"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"8467","DOI":"10.1038\/s41598-022-12095-7","article-title":"Endometrial microbiome: Sampling, assessment, and possible impact on embryo implantation","volume":"12","author":"Lagier","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1111\/1469-0691.12023","article-title":"Microbial culturomics: Paradigm shift in the human gut microbiome study","volume":"18","author":"Lagier","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Vanstokstraeten, R., Mackens, S., Callewaert, E., Blotwijk, S., Emmerechts, K., Cromb\u00e9, F., Soetens, O., Wybo, I., Vandoorslaer, K., and Mostert, L. (2022). Culturomics to Investigate the Endometrial Microbiome: Proof-of-Concept. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms232012212"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41579-018-0041-0","article-title":"Culturing the human microbiota and culturomics","volume":"16","author":"Lagier","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"197","DOI":"10.34297\/AJBSR.2019.04.000797","article-title":"Influence of Endometrial Microbiota on Reproductive Outcomes in IVF Programs","volume":"4","author":"Smolnikova","year":"2019","journal-title":"Am. J. Biomed. Sci. Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"S21","DOI":"10.1093\/infdis\/jiw192","article-title":"More Easily Cultivated Than Identified: Classical Isolation with Molecular Identification of Vaginal Bacteria","volume":"214","author":"Srinivasan","year":"2016","journal-title":"J. Infect. Dis."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1038\/s41579-021-00536-5","article-title":"The human virome: Assembly, composition and host interactions","volume":"19","author":"Liang","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Lykke, M.R., Becher, N., Haahr, T., Boedtkjer, E., Jensen, J.S., and Uldbjerg, N. (2021). Vaginal, Cervical and Uterine pH in Women with Normal and Abnormal Vaginal Microbiota. Pathogens, 10.","DOI":"10.3390\/pathogens10020090"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2103","DOI":"10.1093\/humrep\/deg392","article-title":"Mycoplasma genitalium attaches to human spermatozoa","volume":"18","author":"Svenstrup","year":"2003","journal-title":"Hum. Reprod."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1136\/bmj.282.6271.1189","article-title":"Bacteriological colonisation of uterine cavity: Role of tailed intrauterine contraceptive device","volume":"282","author":"Sparks","year":"1981","journal-title":"Br. Med. J."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"148","DOI":"10.3389\/fcimb.2019.00148","article-title":"The Healthy Human Blood Microbiome: Fact or Fiction?","volume":"9","author":"Castillo","year":"2019","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"4680","DOI":"10.1073\/pnas.1002611107","article-title":"Vaginal microbiome of reproductive-age women","volume":"108","author":"Ravel","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.mimet.2017.11.009","article-title":"Extensive evaluation of fastidious anaerobic bacteria recovery from the Copan eSwab\u00ae transport system","volume":"144","author":"Demuyser","year":"2018","journal-title":"J. Microbiol. Methods"},{"key":"ref_32","unstructured":"(2018). MM18. Interprative Criteria for Identification of bacteria and Fungi by targeted DNA Sequencing. Inst. Clin. Lab. Stand., 25\u2013117."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/6\/5947\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T18:59:59Z","timestamp":1760122799000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/6\/5947"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,21]]},"references-count":32,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2023,3]]}},"alternative-id":["ijms24065947"],"URL":"https:\/\/doi.org\/10.3390\/ijms24065947","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,21]]}}}