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Some previous studies have identified bacteria in semen as being a potential factor in male infertility. However, only few types of bacteria were taken into consideration while using PCR-based or culturing methods. Here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. Ninety-six semen samples collected were examined for bacterial communities, measuring seven clinical criteria for semen quality (semen volume, sperm concentration, motility, Kruger's strict morphology, antisperm antibody (IgA), Atypical, and leukocytes). Computer-assisted semen analysis (CASA) was also performed. Results showed that the most abundant genera among all samples were  Lactobacillus  (19.9%),  Pseudomonas  (9.85%),  Prevotella  (8.51%) and  Gardnerella  (4.21%). The proportion of  Lactobacillus  and  Gardnerella  was significantly higher in the normal samples, while that of  Prevotella  was significantly higher in the low quality samples. Unsupervised clustering analysis demonstrated that the seminal bacterial communities were clustered into three main groups:  Lactobacillus ,  Pseudomonas , and  Prevotella  predominant group. Remarkably, most normal samples (80.6%) were clustered in  Lactobacillus  predominant group. The analysis results showed seminal bacteria community types were highly associated with semen health.  Lactobacillus  might not only be a potential probiotic for semen quality maintenance, but also might be helpful in countering the negative influence of  Prevotella  and  Pseudomonas . In this study, we investigated whole seminal bacterial communities and provided the most comprehensive analysis of the association between bacterial community and semen quality. The study significantly contributes to the current understanding of the etiology of male fertility.

Bacterial Communities in Semen from Men of Infertile Couples: Metagenomic Sequencing Reveals Relationships of Seminal Microbiota to Semen Quality