Improving analysis of the vaginal microbiota of women undergoing assisted reproduction using nanopore sequencing

Theresa Lüth, Simon Graspeuntner*, Kay Neumann, Laura Kirchhoff, Antonia Masuch, Susen Schaake, Mariia Lupatsii, Ronnie Tse, Georg Griesinger, Joanne Trinh, Jan Rupp

*Corresponding author for this work


Purpose: Subclinical alterations of the vaginal microbiome have been described to be associated with female infertility and may serve as predictors for failure of in vitro fertilization treatment. While large prospective studies to delineate the role of microbial composition are warranted, integrating microbiome information into clinical management depends on economical and practical feasibility, specifically on a short duration from sampling to final results. The currently most used method for microbiota analysis is either metagenomics sequencing or amplicon-based microbiota analysis using second-generation methods such as sequencing-by-synthesis approaches (Illumina), which is both expensive and time-consuming. Thus, additional approaches are warranted to accelerate the usability of the microbiome as a marker in clinical praxis. Methods: Herein, we used a set of ten selected vaginal swabs from women undergoing assisted reproduction, comparing and performing critical optimization of nanopore-based microbiota analysis with the results from MiSeq-based data as a quality reference. Results: The analyzed samples carried varying community compositions, as shown by amplicon-based analysis of the V3V4 region of the bacterial 16S rRNA gene by MiSeq sequencing. Using a stepwise procedure to optimize adaptation, we show that a close approximation of the microbial composition can be achieved within a reduced time frame and at a minimum of costs using nanopore sequencing. Conclusions: Our work highlights the potential of a nanopore-based methodical setup to support the feasibility of interventional studies and contribute to the development of microbiome-based clinical decision-making in assisted reproduction.

Original languageEnglish
JournalJournal of Assisted Reproduction and Genetics
Issue number11
Pages (from-to)2659-2667
Number of pages9
Publication statusPublished - 11.2022

Research Areas and Centers

  • Academic Focus: Center for Infection and Inflammation Research (ZIEL)


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