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Background  Bacterial infections are usually suspected in infertile couples seeking IVF with no clear understanding of the microbial compositions present in the seminal fluids and vaginal niche of the patients. We used next-generation sequencing technology to correlate microbiota compositions with IVF clinical outcomes.    Methods  Thirty-six couples were recruited to provide seminal fluids and vaginal swabs. Bacterial DNA was extracted, and V4 region of the 16S rRNA was amplified and sequenced in a pair-end configuration on the Illumina MiSeq platform rendering 2 × 150 bp sequences. Microbial taxonomy to species level was generated using the Greengenes database. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biologically and statistically significant differences in relative abundance.    Results  Seminal fluid microbiota compositions had lower bacterial concentrations compared with the vagina, but species diversity was significantly higher in seminal fluid samples. Azoospermic subjects had more relative abundance of  Mycoplasma  and  Ureaplasma.  In Normospermic semen,  Lactobacillus  (43.86%) was the most abundant, followed by  Gardnerella  (25.45%), while the corresponding vaginal samples,  Lactobacillus  (61.74%) was the most abundant, followed by  Prevotella  (6.07%) and  Gardnerella  (5.86%).    Conclusions  Semen samples with positive IVF were significantly colonized by  Lactobacillus jensenii  ( P =0.002),  Faecalibacterium  ( P =0.042) and significantly less colonized by  Proteobacteria ,  Prevotella ,  Bacteroides , and lower  Firmicutes / Bacteroidetes  ratio compared with semen samples with negative IVF. Vaginal samples with positive IVF clinical outcome were significantly colonized by  Lactobacillus gasseri , less colonized by  Bacteroides  and  Lactobacillus iners.  This study has opened a window of possibility for  Lactobacillus  replenishments in men and women before IVF treatment.

frontiers in cellular and infection microbiology

Microbiome Compositions From Infertile Couples Seeking In Vitro Fertilization, Using 16S rRNA Gene Sequencing Methods: Any Correlation to Clinical Outcomes?