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Purpose  The present study aimed to analyze the endometrial and vaginal microbiome among a Japanese infertile population by sequencing and the impact of the endometrial and vaginal environment on implantation.    Methods  In total, 102 infertile (79 in vitro fertilization [ IVF ] and 23 non‐ IVF ) patients and seven healthy volunteers were recruited from August to December, 2017. Endometrial fluid and vaginal discharge samples for sequencing were collected by using an intrauterine insemination catheter. The bacterial status of the endometrium and vagina were analyzed.    Results  The  Lactobacillus ‐dominated microbiota (>90%  Lactobacillus  spp.) in the endometrium vs vagina was 38% (30/79) vs 44.3% (44/79) in the  IVF  patients, 73.9% (17/23) vs 73.9% (17/23) in the non‐ IVF  patients, and 85.7% (6/7) vs 85.7% (6/7) in the healthy volunteers. The percentage of endometrial  Lactobacillus  in the healthy volunteers was highly stable within the same menstrual cycle and even in the following cycle. The major taxonomies were  Gardnerella ,  Streptococcus ,  Atopobium ,  Bifidobacterium ,  Sneathia ,  Prevotella , and  Staphylococcus . Fifteen patients achieved pregnancy by a single vitrified‐warmed blastocyst transfer during this study; the median percentage of  Lactobacillus  in the pregnant women was 96.45 ± 33.61%.    Conclusion  A considerable percentage of non‐ Lactobacillus‐ dominated ( NLD ) microbiota was found in the endometrium of Japanese infertile women. Increasing the endometrial level of the  Lactobacilli  to >90% might favor the implantation outcome of  NLD  infertile patients.

Analysis of endometrial microbiota by 16S ribosomal RNA gene sequencing among infertile patients: a single‐center pilot study