Unfolding the Semen Microbiota: Implications for Male Infertility

In recent years, the growing interest in microbiota, supported by increasing evidence from next-generation sequencing (NGS)-based studies, has led to the hypothesis that multifactorial conditions such as male infertility may have their bases in its imbalance. Despite rapid advances in the field over the past decade, findings remain fragmented and sometimes inconsistent. Furthermore, analyses frequently exclude non-bacterial components, such as viruses (e.g., human papillomavirus and herpes simplex virus), protozoa (e.g., Trichomonas vaginalis) and fungi (e.g., Candida spp.), with a few studies focusing on the influence of individual components. This review provides an integrative and critical synthesis of current knowledge on the composition and functional relevance of the male reproductive tract microbiota, including both bacterial and non-bacterial components. Particular attention is given to the methodological strengths and limitations of NGS approaches, the main bacterial taxa identified in seminal samples, and the emerging roles of viruses, protozoa, and fungi. The review also explores proposed mechanisms linking microbial dysbiosis to impaired spermatozoa function, the potential anatomical origins of seminal microorganisms, and evidence for microbiota exchange between sexual partners. By integrating recent data and addressing underexplored components beyond bacteria, this work provides a coherent framework to support future research on the role of the seminal microbiome in male infertility.