Abstract
Research question
Full-length 16S rRNA gene sequencing using nanopore technology is a fast alternative to conventional short-read
16S rRNA gene sequencing with low initial investment costs that has been used for various
microbiome studies but has not yet been investigated as an alternative approach for
endometrial microbiome analysis. Is in-situ 16S rRNA gene long-read sequencing using portable nanopore sequencing technology feasible
and reliable for endometrial microbiome analysis?
Design
A prospective experimental study based on 33 patients seeking infertility treatment
between January and October 2019. A 16S rRNA gene long-read nanopore sequencing protocol for analysing endometrial microbiome
samples was established, including negative controls for contamination evaluation
and positive controls for bias evaluation. Contamination caused by kit and exterior
sources was identified and excluded from the analysis. Endometrial samples from 33
infertile patients were sequenced using the optimized long-read nanopore sequencing
protocol and compared with conventional short-read sequencing carried out by external
laboratories.
Results
Of the 33 endometrial patient samples, 23 successfully amplified (69.7%) and their
microbiome was assessed using nanopore sequencing. Of those 23 samples, 14 (60.9%)
were Lactobacillus-dominated (>80% of reads mapping to Lactobacillus), with 10 samples resulting in more than 90% Lactobacillus reads. Our long-read nanopore sequencing revealed results similar to two conventional
short-read sequencing approaches and to long-read sequencing validation carried out
in external laboratories.
Conclusion
In this pilot study, 16S rRNA gene long-read nanopore sequencing was established to analyse the endometrial microbiome
in situ that could be widely applied owing to its cost efficiency and portable character.
KEYWORDS
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Biography
During her PhD in Hamburg, Anna Oberle studied immunological and therapeutical mechanisms of cancer. During her studies, Anna visited laboratories in Boston and Washington, DC, and published several studies in high-ranking journals. Since 2018, Anna has been developing novel genetic approaches for reproductive health at the ‘Wunschbaby Institut Feichtinger’, Vienna.
Key message
Long-read 16S rRNA gene sequencing using nanopore technology delivers comparable results to short-read 16S rRNA sequencing. We show its potential for in-situ analysis of the endometrial microbiome, which could be widely applied owing to the cost efficiency and portable character of the nanopore sequencing technology.
Article info
Publication history
Published online: March 26, 2021
Accepted:
March 3,
2021
Received in revised form:
March 1,
2021
Received:
November 27,
2020
Declaration: The authors report no financial or commercial conflicts of interest.Identification
Copyright
© 2021 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.
