Reproductive tract microbiome in assisted reproductive technologies

The human microbiome in the male and female reproductive tracts may affect reproductive competence and provide a more complete understanding of the physiology and pathophysiology of reproduction.

Jason M. Franasiak, M.D., Richard T. Scott Jr., M.D., H.C.L.D.

Volume 104, Issue 6, Pages 1364-1371


The human microbiome has gained much attention recently for its role in health and disease. This interest has come as we have begun to scratch the surface of the complexity of what has been deemed to be our “second genome” through initiatives such as the Human Microbiome Project. Microbes have been hypothesized to be involved in the physiology and pathophysiology of assisted reproduction since before the first success in IVF. Although the data supporting or refuting this hypothesis remain somewhat sparse, thanks to sequencing data from the 16S rRNA subunit, we have begun to characterize the microbiome in the male and female reproductive tracts and understand how this may play a role in reproductive competence. In this review, we discuss what is known about the microbiome of the reproductive tract as it pertains to assisted reproductive technologies.

  • Jason M. Franasiak

    Thank you for the comment Alex. I think the role of antibiotics can be thought of in two ways. One is to prevent infection, like those given peri-operatively at the time of oocyte retrieval. The other is to affect outcomes, like those given to male patients in the week prior to semen sample production to decrease WBC in sample. I think that the microbiome in the reproductive tract is relatively poorly understood as compared to other sites in the body. The use of broad spectrum antibiotics are very large tools for relatively small jobs. I think the use to prevent infection and decrease the bacterial load at the time of procedure can be justified. I think that alteration of the microbiome to improve outcomes beyond prevention of infection will be more in the realm of replacing “good bacteria” rather than killing bad bacteria. The microbiome has far reaching implications as it interacts with and changes the immune milieu at the time of implantation. As we learn more about the normal state of the microbiome, we will be able to more effectively manipulate it – I predict this will lead us away from antibiotic use for the purpose of improving reproductive outcomes.

  • This article nicely highlights the important role that the microbiome will play in the future of ART. Given that prophylactic antibiotics around the time of embryo transfer manipulate the microbiome in uncertain ways (without clearly increasing pregnancy rates)- what do you think is the current role for antibiotic prophylaxis? How about around the time of egg retrieval? Would a well designed prospective trial about antibiotic use be feasible / helpful?

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