Abstract
Background: Current analysis methods of the vaginal microbiome
often fail to identify and/or report known pathogens such as S.
agalatiae (GBS), resulting in an incomplete clinical understanding of
bacterial composition during pregnancy.
Objective: To determine the frequency of GBS reporting in
vaginal microbiome literature pertaining to pregnancy and examine
methodological bias that contributes to differences in species and
genus-level microbiome reporting.
Search strategy: PubMed, CINAHL, and Web of Science databases
were used to identify papers for review based on the search terms
“vaginal microbiome”, “pregnancy”, and “16S rRNA sequencing”.
Selection criteria: Forty-five research articles reported
employing a metagenomic approach for vaginal microbiome analysis during
pregnancy that explicitly reported taxonomic composition and were
included in this review.
Data collection and analysis: Articles were evaluated for
methods of DNA extraction and sequencing, 16S region, taxonomy
classification database, number of participants or vaginal specimens,
and pregnancy trimester.
Main results: Less than 30% of articles reported the presence
of GBS. No significant differences in methodology were identified
between articles that reported versus did not report GBS. However, large
variability across the types of research methods used for vaginal
microbiome analysis and species-level bacterial community reporting were
observed.
Conclusion: Considerable differences in study design and data
formatting methods may contribute to underrepresentation of GBS, and
other known pathogens, in existing vaginal microbiome literature.
Providing detailed methods, analysis code and raw data may improve
reproducibility and ability to compare microbial communities across
studies.
Keywords vaginal microbiome, pregnancy, 16S ribosomal RNA,
whole genome sequencing, Group B Streptococcus
Tweetable abstract: Heterogeneity in methods and taxonomy
reporting may underestimate known pathogens in the vaginal microbiome.