Endometrial microbiome at the time of embryo transfer: next-generation sequencing of the 16S ribosomal subunit

J Assist Reprod Genet. 2016 Jan;33(1):129-36. doi: 10.1007/s10815-015-0614-z. Epub 2015 Nov 7.


Purpose: Characterization of the human microbiome has become more precise with the application of powerful molecular tools utilizing the unique 16S ribosomal subunit's hypervariable regions to greatly increase sensitivity. The microbiome of the lower genital tract can prognosticate obstetrical outcome while the upper reproductive tract remains poorly characterized. Here, the endometrial microbiome at the time of single embryo transfer (SET) is characterized by reproductive outcome.

Methods: Consecutive patients undergoing euploid, SET was included in the analysis. After embryo transfer, performed as per routine, the most distal 5-mm portion of the transfer catheter was sterilely placed in a DNA free PCR tube. Next-generation sequencing of the bacteria specific 16S ribosome gene was performed, allowing genus and species calls for microorganisms.

Results: Taxonomy assignments were made on 35 samples from 33 patients and 2 Escherichia coli controls. Of the 33 patients, 18 had ongoing pregnancies and 15 did not. There were a total of 278 different genus calls present across patient samples. The microbiome at time of transfer for those patients with ongoing pregnancy vs. those without ongoing pregnancy was characterized by top genera by sum fraction. Lactobacillus was the top species call for both outcomes.

Conclusions: The data presented here show the microbiome at the time of embryo transfer can successfully be characterized without altering standard clinical practice. This novel approach, both in specimen collection and analysis, is the first step toward the goal of determining physiologic from pathophysiologic microbiota. Further studies will help delineate if differences in the microbiome at the time of embryo transfer have a reliable impact on pregnancy outcome.

Keywords: 16S ribosomal subunit; Microbiome, embryo transfer; Next-generation sequencing.

MeSH terms

  • Adult
  • Bacteria / classification
  • Bacteria / genetics*
  • Embryo Transfer / methods
  • Endometrium / growth & development
  • Endometrium / microbiology*
  • Female
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Metagenome / genetics
  • Microbiota / genetics*
  • Pregnancy
  • Pregnancy Outcome
  • RNA, Ribosomal, 16S / genetics*


  • RNA, Ribosomal, 16S