Download PDF
Semin Reprod Med 2023; 41(05): 144-150
DOI: 10.1055/s-0043-1777361
Review Article

Uterine Microbiome: Does the Sampling Technique Matter?

Kreete Lüll 
1   Institute of Genomics, Estonian Genome Centre, University of Tartu, Tartu, Estonia
,
Elin Org 
1   Institute of Genomics, Estonian Genome Centre, University of Tartu, Tartu, Estonia
› Author Affiliations Funding This work was funded by an Estonian Research Council grant (no. PUT 1414) and an EMBO Installation grant (no. 3573).
› Further Information
    Permissions and Reprints

Abstract

Studies have proven the significance of microbial communities in various parts of the human body for health. In recent years it has been discovered that the uterine cavity is not sterile, and endometrium has its own microbiome which appears to have an impact on female fertility and gynecological pathologies. Lactobacillus has shown to dominate the microbial profile in the uterus and is considered an indicator of a healthy uterine environment. Yet, many argue that the Lactobacillus dominance is due to vaginal contamination during the sampling process. To date there is no clearly defined healthy endometrial microbial profile, which is largely due to the fact that determining the microbial community from the endometrium is complicated, and there is currently no consensus on sampling methods for the endometrial microbiome. As a result, this restricts ability to replicate discoveries made in other cohorts. Here we aim to give an overview of the sampling methods used and discuss what impedes the endometrial microbiome studies as well as how to reach a consensus on the study design. This knowledge could be incorporated into the future research and the knowledge on endometrial microbiome could be included into the diagnostics and treatment of female reproductive health.

Keywords

endometrial microbiome - uterine microbiome - infertility


Publication History

Article published online:
08 December 2023

© 2023. Thieme. All rights reserved.

Thieme Medical Publishers, Inc.
333 Seventh Avenue, 18th Floor, New York, NY 10001, USA

 

  • References

  • 1 Ursell LK, Metcalf JL, Parfrey LW, Knight R. Defining the human microbiome. Nutr Rev 2012; 70 (Suppl 1, Suppl 1): S38-S44
    CrossrefPubMedGoogle Scholar
  • 2 Dominguez-Bello MG, Godoy-Vitorino F, Knight R, Blaser MJ. Role of the microbiome in human development. Gut 2019; 68 (06) 1108-1114
    CrossrefPubMedGoogle Scholar
  • 3 Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol 2021; 19 (01) 55-71
    CrossrefPubMedGoogle Scholar
  • 4 Baker JM, Chase DM, Herbst-Kralovetz MM. Uterine microbiota: Residents, tourists, or invaders?. Front Immunol 2018; 9: 208
    CrossrefPubMedGoogle Scholar
  • 5 Koedooder R, Mackens S, Budding A. et al. Identification and evaluation of the microbiome in the female and male reproductive tracts. Hum Reprod Update 2019; 25 (03) 298-325
    CrossrefPubMedGoogle Scholar
  • 6 Benner M, Ferwerda G, Joosten I, van der Molen RG. How uterine microbiota might be responsible for a receptive, fertile endometrium. Hum Reprod Update 2018; 24 (04) 393-415
    CrossrefPubMedGoogle Scholar
  • 7 Molina NM, Sola-Leyva A, Haahr T. et al. Analysing endometrial microbiome: methodological considerations and recommendations for good practice. Hum Reprod 2021; 36 (04) 859-879
    CrossrefPubMedGoogle Scholar
  • 8 Molina NM, Sola-Leyva A, Saez-Lara MJ. et al. New opportunities for endometrial health by modifying uterine microbial composition: present or future?. Biomolecules 2020; 10 (04) 593
    CrossrefPubMedGoogle Scholar
  • 9 Moreno I, Garcia-Grau I, Perez-Villaroya D. et al. Endometrial microbiota composition is associated with reproductive outcome in infertile patients. Microbiome 2022; 10 (01) 1
    CrossrefPubMedGoogle Scholar
  • 10 Moreno I, Simon C. Relevance of assessing the uterine microbiota in infertility. Fertil Steril 2018; 110 (03) 337-343
    CrossrefPubMedGoogle Scholar
  • 11 Moreno I, Codoñer FM, Vilella F. et al. Evidence that the endometrial microbiota has an effect on implantation success or failure. Am J Obstet Gynecol 2016; 215 (06) 684-703
    CrossrefPubMedGoogle Scholar
  • 12 Drbohlav P, Hálková E, Masata J, Rezácová J, Cerný V, Rossová D. [The effect of endometrial infection on embryo implantation in the IVF and ET program]. Ceska Gynekol 1998; 63 (03) 181-185
    PubMedGoogle Scholar
  • 13 Cicinelli E, Matteo M, Tinelli R. et al. Prevalence of chronic endometritis in repeated unexplained implantation failure and the IVF success rate after antibiotic therapy. Hum Reprod 2015; 30 (02) 323-330
    CrossrefPubMedGoogle Scholar
  • 14 Cicinelli E, Matteo M, Tinelli R. et al. Chronic endometritis due to common bacteria is prevalent in women with recurrent miscarriage as confirmed by improved pregnancy outcome after antibiotic treatment. Reprod Sci 2014; 21 (05) 640-647
    CrossrefPubMedGoogle Scholar
  • 15 Romero R, Espinoza J, Mazor M. Can endometrial infection/inflammation explain implantation failure, spontaneous abortion, and preterm birth after in vitro fertilization?. Fertil Steril 2004; 82 (04) 799-804
    CrossrefPubMedGoogle Scholar
  • 16 Naessens A, Foulon W, Cammu H, Goossens A, Lauwers S. Epidemiology and pathogenesis of ureaplasma urealyticum in spontaneous abortion and early preterm labor. Acta Obstet Gynecol Scand 1987; 66 (06) 513-516
    CrossrefPubMedGoogle Scholar
  • 17 Reschini M, Benaglia L, Ceriotti F. et al. Endometrial microbiome: sampling, assessment, and possible impact on embryo implantation. Sci Rep 2022; 12 (01) 8467
    CrossrefPubMedGoogle Scholar
  • 18 Fang RL, Chen LX, Shu WS, Yao SZ, Wang SW, Chen YQ. Barcoded sequencing reveals diverse intrauterine microbiomes in patients suffering with endometrial polyps. Am J Transl Res 2016; 8 (03) 1581-1592
    PubMedGoogle Scholar
  • 19 Walther-António MRS, Chen J, Multinu F. et al. Potential contribution of the uterine microbiome in the development of endometrial cancer. Genome Med 2016; 8 (01) 122
    CrossrefPubMedGoogle Scholar
  • 20 Walsh DM, Hokenstad AN, Chen J. et al. Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome). Sci Rep 2019; 9 (01) 19213
    CrossrefPubMedGoogle Scholar
  • 21 Winters AD, Romero R, Gervasi MT. et al. Does the endometrial cavity have a molecular microbial signature?. Sci Rep 2019; 9 (01) 9905
    CrossrefPubMedGoogle Scholar
  • 22 Moreno I, Cicinelli E, Garcia-Grau I. et al. The diagnosis of chronic endometritis in infertile asymptomatic women: a comparative study of histology, microbial cultures, hysteroscopy, and molecular microbiology. Am J Obstet Gynecol 2018; 218 (06) 602.e1-602.e16
    CrossrefPubMedGoogle Scholar
  • 23 Liu Y, Ko EYL, Wong KKW. et al. Endometrial microbiota in infertile women with and without chronic endometritis as diagnosed using a quantitative and reference range-based method. Fertil Steril 2019; 112 (04) 707-717.e1
    CrossrefPubMedGoogle Scholar
  • 24 Chen C, Song X, Wei W. et al. The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases. Nat Commun 2017; 8 (01) 875
    CrossrefPubMedGoogle Scholar
  • 25 Khan KN, Fujishita A, Masumoto H. et al. Molecular detection of intrauterine microbial colonization in women with endometriosis. Eur J Obstet Gynecol Reprod Biol 2016; 199: 69-75
    CrossrefPubMedGoogle Scholar
  • 26 Hernandes C, Silveira P, Rodrigues Sereia AF. et al. Microbiome profile of deep endometriosis patients: comparison of vaginal fluid, endometrium and lesion. Diagnostics (Basel) 2020; 10 (03) 163
    CrossrefPubMedGoogle Scholar
  • 27 Altmäe S, Rienzi L. Endometrial microbiome: new hope, or hype?. Reprod Biomed Online 2021; 42 (06) 1051-1052
    CrossrefPubMedGoogle Scholar
  • 28 Bwanga PK, Tremblay-Lemoine P-C, Timmermans M. et al. The endometrial microbiota: challenges and prospects. Preprint at Preprints.org; DOI: 10.20944/preprints202307.0891.v1. (Online July 13, 2023;
    CrossrefPubMedGoogle Scholar
  • 29 Carosso A, Revelli A, Gennarelli G. et al. Controlled ovarian stimulation and progesterone supplementation affect vaginal and endometrial microbiota in IVF cycles: a pilot study. J Assist Reprod Genet 2020; 37 (09) 2315-2326
    CrossrefPubMedGoogle Scholar
  • 30 Tao LC. Direct intrauterine sampling: the IUMC Endometrial Sampler. Diagn Cytopathol 1997; 17 (02) 153-159
    CrossrefPubMedGoogle Scholar
  • 31 Verstraelen H, Vilchez-Vargas R, Desimpel F. et al. Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the V1-2 region of the 16S rRNA gene. PeerJ 2016; 4: e1602
    CrossrefPubMedGoogle Scholar
  • 32 Canha-Gouveia A, Pérez-Prieto I, Rodríguez CM. et al. The female upper reproductive tract harbors endogenous microbial profiles. Front Endocrinol (Lausanne) 2023; 14: 1096050
    CrossrefPubMedGoogle Scholar
  • 33 Liu Y, Wong KKW, Ko EYL. et al. Systematic comparison of bacterial colonization of endometrial tissue and fluid samples in recurrent miscarriage patients: implications for future endometrial microbiome studies. Clin Chem 2018; 64 (12) 1743-1752
    CrossrefPubMedGoogle Scholar
  • 34 Lüll K, Saare M, Peters M. et al. Differences in microbial profile of endometrial fluid and tissue samples in women with in vitro fertilization failure are driven by Lactobacillus abundance. Acta Obstet Gynecol Scand 2022; 101 (02) 212-220
    CrossrefPubMedGoogle Scholar
  • 35 Vomstein K, Reider S, Böttcher B. et al. Uterine microbiota plasticity during the menstrual cycle: differences between healthy controls and patients with recurrent miscarriage or implantation failure. J Reprod Immunol 2022; 151 (06) 103634
    CrossrefPubMedGoogle Scholar
  • 36 Sola-Leyva A, Andrés-León E, Molina NM. et al. Mapping the entire functionally active endometrial microbiota. Hum Reprod 2021; 36 (04) 1021-1031
    CrossrefPubMedGoogle Scholar
  • 37 Gajer P, Brotman RM, Bai G. et al. Temporal dynamics of the human vaginal microbiota. Sci Transl Med 2012; 4 (132) 132ra52
    CrossrefPubMedGoogle Scholar
  • 38 Toson B, Simon C, Moreno I. The endometrial microbiome and its impact on human conception. Int J Mol Sci 2022; 23 (01) 485
    CrossrefPubMedGoogle Scholar
  • 39 Pelzer ES, Willner D, Buttini M, Huygens F. A role for the endometrial microbiome in dysfunctional menstrual bleeding. Antonie van Leeuwenhoek 2018; 111 (06) 933-943
    CrossrefPubMedGoogle Scholar
  • 40 Kunz G, Beil D, Deiniger H, Einspanier A, Mall G, Leyendecker G. The uterine peristaltic pump. Normal and impeded sperm transport within the female genital tract. Adv Exp Med Biol 1997; 424: 267-277
    PubMedGoogle Scholar
  • 41 Salter SJ, Cox MJ, Turek EM. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014; 12: 87
    CrossrefPubMedGoogle Scholar
  • 42 Stinson LF, Keelan JA, Payne MS. Identification and removal of contaminating microbial DNA from PCR reagents: impact on low-biomass microbiome analyses. Lett Appl Microbiol 2019; 68 (01) 2-8
    CrossrefPubMedGoogle Scholar
  • 43 Weyrich LS, Farrer AG, Eisenhofer R. et al. Laboratory contamination over time during low-biomass sample analysis. Mol Ecol Resour 2019; 19 (04) 982-996
    CrossrefPubMedGoogle Scholar
  • 44 Laurence M, Hatzis C, Brash DE. Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes. PLoS One 2014; 9 (05) e97876
    CrossrefPubMedGoogle Scholar
  • 45 Kyono K, Hashimoto T, Nagai Y, Sakuraba Y. Analysis of endometrial microbiota by 16S ribosomal RNA gene sequencing among infertile patients: a single-center pilot study. Reprod Med Biol 2018; 17 (03) 297-306
    CrossrefPubMedGoogle Scholar
  • 46 Kitaya K, Nagai Y, Arai W, Sakuraba Y, Ishikawa T. Characterization of microbiota in endometrial fluid and vaginal secretions in infertile women with repeated implantation failure. Mediators Inflamm 2019; 2019: 4893437
    CrossrefPubMedGoogle Scholar
  • 47 Grahn N, Olofsson M, Ellnebo-Svedlund K, Monstein HJ, Jonasson J. Identification of mixed bacterial DNA contamination in broad-range PCR amplification of 16S rDNA V1 and V3 variable regions by pyrosequencing of cloned amplicons. FEMS Microbiol Lett 2003; 219 (01) 87-91
    CrossrefPubMedGoogle Scholar
  • 48 Glassing A, Dowd SE, Galandiuk S, Davis B, Chiodini RJ. Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples. Gut Pathog 2016; 8: 24
    CrossrefPubMedGoogle Scholar
  • 49 Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 2018; 6 (01) 226
    CrossrefPubMedGoogle Scholar
  • 50 McKnight DT, Huerlimann R, Bower DS, Schwarzkopf L, Alford RA, Zenger KR. microDecon: a highly accurate read-subtraction tool for the post-sequencing removal of contamination in metabarcoding studies. Environ DNA 2019; 1 (01) 14-25
    CrossrefPubMedGoogle Scholar
  • 51 Stämmler F, Gläsner J, Hiergeist A. et al. Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. Microbiome 2016; 4 (01) 28
    CrossrefPubMedGoogle Scholar