title: Evidence that the endometrial microbiota has an effect on implantation success or failure.
abstract: BACKGROUND
  Bacterial cells in the human body account for 1-3% of total body weight and are at least equal in number to human cells. Recent research has focused on understanding how the different bacterial communities in the body (eg, gut, respiratory, skin, and vaginal microbiomes) predispose to health and disease. The microbiota of the reproductive tract has been inferred from the vaginal bacterial communities, and the uterus has been classically considered a sterile cavity. However, while the vaginal microbiota has been investigated in depth, there is a paucity of consistent data regarding the existence of an endometrial microbiota and its possible impact in reproductive function.
  
  
  OBJECTIVE
  This study sought to test the existence of an endometrial microbiota that differs from that in the vagina, assess its hormonal regulation, and analyze the impact of the endometrial microbial community on reproductive outcome in infertile patients undergoing in vitro fertilization.
  
  
  METHODS
  To identify the existence of an endometrial microbiota, paired samples of endometrial fluid and vaginal aspirates were obtained simultaneously from 13 fertile women in prereceptive and receptive phases within the same menstrual cycle (total samples analyzed n = 52). To investigate the hormonal regulation of the endometrial microbiota during the acquisition of endometrial receptivity, endometrial fluid was collected at prereceptive and receptive phases within the same cycle from 22 fertile women (n = 44). Finally, the reproductive impact of an altered endometrial microbiota in endometrial fluid was assessed by implantation, ongoing pregnancy, and live birth rates in 35 infertile patients undergoing in vitro fertilization (total samples n = 41) with a receptive endometrium diagnosed using the endometrial receptivity array. Genomic DNA was obtained either from endometrial fluid or vaginal aspirate and sequenced by 454 pyrosequencing of the V3-V5 region of the 16S ribosomal RNA (rRNA) gene; the resulting sequences were taxonomically assigned using QIIME. Data analysis was performed using R packages. The χ2test, Student t test, and analysis of variance were used for statistical analyses.
  
  
  RESULTS
  When bacterial communities from paired endometrial fluid and vaginal aspirate samples within the same subjects were interrogated, different bacterial communities were detected between the uterine cavity and the vagina of some subjects. Based on its composition, the microbiota in the endometrial fluid, comprising up to 191 operational taxonomic units, was defined as a Lactobacillus-dominated microbiota (>90% Lactobacillus spp.) or a non-Lactobacillus-dominated microbiota (<90% Lactobacillus spp. with >10% of other bacteria). Although the endometrial microbiota was not hormonally regulated during the acquisition of endometrial receptivity, the presence of a non-Lactobacillus-dominated microbiota in a receptive endometrium was associated with significant decreases in implantation [60.7% vs 23.1% (P = .02)], pregnancy [70.6% vs 33.3% (P = .03)], ongoing pregnancy [58.8% vs 13.3% (P = .02)], and live birth [58.8% vs 6.7% (P = .002)] rates.
  
  
  CONCLUSIONS
  Our results demonstrate the existence of an endometrial microbiota that is highly stable during the acquisition of endometrial receptivity. However, pathological modification of its profile is associated with poor reproductive outcomes for in vitro fertilization patients. This finding adds a novel microbiological dimension to the reproductive process.
authors.affiliation: Department of Research and Development, Igenomix SL, Valencia, Spain; Department of Obstetrics and Gynecology, School of Medicine, Stanford University, Stanford, CA.
authors.forename: Inmaculada
authors.initials: I
authors.lastname: Moreno
authors.affiliation: Lifesequencing SL, Valencia, Spain.
authors.forename: Francisco M
authors.initials: FM
authors.lastname: Codoñer
authors.affiliation: Fundación Instituto Valenciano de Infertilidad (IVI), Valencia, Spain; Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain; Department of Obstetrics and Gynecology, School of Medicine, Stanford University, Stanford, CA.
authors.forename: Felipe
authors.initials: F
authors.lastname: Vilella
authors.affiliation: Department of Research and Development, Igenomix SL, Valencia, Spain.
authors.forename: Diana
authors.initials: D
authors.lastname: Valbuena
authors.affiliation: Lifesequencing SL, Valencia, Spain.
authors.forename: Juan F
authors.initials: JF
authors.lastname: Martinez-Blanch
authors.affiliation: Department of Bioinformatics, Igenomix SL, Valencia, Spain.
authors.forename: Jorge
authors.initials: J
authors.lastname: Jimenez-Almazán
authors.affiliation: Department of Bioinformatics, Igenomix SL, Valencia, Spain.
authors.forename: Roberto
authors.initials: R
authors.lastname: Alonso
authors.affiliation: IVI Valencia, Valencia, Spain.
authors.forename: Pilar
authors.initials: P
authors.lastname: Alamá
authors.affiliation: IVI Valencia, Valencia, Spain; Department of Pediatrics, Obstetrics, and Gynecology, Universidad de Valencia, Instituto Universitario IVI, Valencia, Spain.
authors.forename: Jose
authors.initials: J
authors.lastname: Remohí
authors.affiliation: Department of Pediatrics, Obstetrics, and Gynecology, Universidad de Valencia, Instituto Universitario IVI, Valencia, Spain; IVI Rome, Rome, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Pellicer
authors.affiliation: Lifesequencing SL, Valencia, Spain; Biopolis SL, Valencia, Spain.
authors.forename: Daniel
authors.initials: D
authors.lastname: Ramon
authors.affiliation: Scientific director, Igenomix SL, Valencia, Spain; Fundación Instituto Valenciano de Infertilidad (IVI), Valencia, Spain; Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain; Department of Pediatrics, Obstetrics, and Gynecology, Universidad de Valencia, Instituto Universitario IVI, Valencia, Spain; Department of Obstetrics and Gynecology, School of Medicine, Stanford University, Stanford, CA. Electronic address: carlos.simon@igenomix.com.
authors.forename: Carlos
authors.initials: C
authors.lastname: Simon
mesh_terms: D015373:Bacterial Typing Techniques; D016022:Case-Control Studies; D010064:Embryo Implantation; D004624:Embryo Transfer; D004717:Endometrium / Q000382:microbiology*; D005260:Female; D005307:Fertilization in Vitro; D006194:Gardnerella vaginalis / Q000235:genetics; D016680:Genome, Bacterial; D006801:Humans; D007246:Infertility / Q000628:therapy*; D007778:Lactobacillus / Q000235:genetics; D050498:Live Birth / Q000453:epidemiology*; D016015:Logistic Models; D007986:Luteinizing Hormone; D008597:Menstrual Cycle; D064307:Microbiota / Q000235:genetics*; D015999:Multivariate Analysis; D010865:Pilot Projects; D016133:Polymerase Chain Reaction; D011247:Pregnancy; D018873:Pregnancy Rate; D018720:Prevotella / Q000235:genetics; D025341:Principal Component Analysis; D011446:Prospective Studies; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013030:Spain / Q000453:epidemiology; D016896:Treatment Outcome; D014621:Vagina / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S; D007986:Luteinizing Hormone
keywords: assisted reproductive techniques; bacterial pathogens; embryo implantation; endometrial microbiota; endometrial receptivity array