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Review
. 2020 Jan;127(2):139-146.
doi: 10.1111/1471-0528.15978. Epub 2019 Nov 1.

Understanding and interpreting community sequencing measurements of the vaginal microbiome

H L Berman  1 , M R McLaren  1 , B J Callahan  1   2
Affiliations
Review

Understanding and interpreting community sequencing measurements of the vaginal microbiome

H L Berman et al. BJOG. 2020 Jan.

Abstract

Community-wide high-throughput sequencing has transformed the study of the vaginal microbiome, and clinical applications are on the horizon. Here we outline the three main community sequencing methods: (1) amplicon sequencing, (2) shotgun metagenomic sequencing, and (3) metatranscriptomic sequencing. We discuss the advantages and limitations of community sequencing generally, and the unique strengths and weaknesses of each method. We briefly review the contributions of community sequencing to vaginal microbiome research and practice. We develop suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome. TWEETABLE ABSTRACT: We review the advantages and limitations of amplicon sequencing, metagenomics, and metatranscriptomics methods for the study of the vaginal microbiome.

Keywords: 16S rRNA gene; amplicon sequencing; metagenomics; metatranscriptomics; vaginal microbiome.

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Conflict of interest statement

Disclosure of interests

None declared. Completed disclosure of interests forms are available to view online as supporting information.

Figures

Figure 1.
Figure 1.
Preparing vaginal microbiome samples for community sequencing. The vaginal microbiome is often sampled via vaginal swab, and such samples will contain both microbes and vaginal epithelial cells. DNA for amplicon and metagenomic sequencing, or RNA for metatranscriptomic sequencing, is extracted from the sample. Typically, a significant fraction of the RNA and an even higher fraction of the DNA extracted from vaginal swab samples are from the human host. Amplicon sequencing sidesteps the problem of human DNA contamination, as the PCR step of amplicon sequencing amplifies gene regions present only in microbes.
See this image and copyright information in PMC

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