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