Strengths and Limitations
Strengths of this review include that both outcomes and methods were
used to analyze the vaginal microbiome composition. We identified
studies from multiple databases and assessed differences across studies
at various decision points to analyze metagenomic data.
The heterogeneity across studies in methods and data reporting limited
the ability to pool and re-analyze the data. This was further
complicated by the fact that some studies reported most microbial taxa
at solely the genus level, whereas other studies only included
species-level data for specific genus like Lactobacillus .
Furthermore, the format and availability of data associated with
manuscripts also varied greatly (e.g., raw data versus including only
taxonomy tables used in the analysis). In cases where the full microbial
datasets were not available, it was difficult to determine whether the
absence of GBS reporting was due to lack of detection, exclusion from
analysis because of low abundance, or some other factor. These
limitations highlight the importance of making study analysis code and
raw data freely available upon publication in order to encourage
reproducibility and comparison.