Lim Sungju, Rajagopal Shilpa, Jeong Ye Ryn, Nzegwu Dumebi, Wright Michelle L
School of Nursing, The University of Texas at Austin, Austin, TX, United States of America.
College of Natural Sciences, Biology Instructional Office, The University of Texas at Austin, Austin, TX, United States of America.
PeerJ. 2021 May 17;9:e11437. doi: 10.7717/peerj.11437. eCollection 2021.
Vaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of (also known as Group B Streptococcus or GBS), the leading cause of neonatal infectious morbidity and mortality, are notably lacking from the studies of the vaginal microbiome, despite being a known contributor to preterm birth and other complications. Therefore, the purpose of this systematic review was to explore the frequency of GBS reporting in vaginal microbiome literature pertaining to pregnancy and to examine methodological bias that contributes to differences in species and genus-level microbiome reporting. Lack of identification of GBS via sequencing-based approaches due to methodologic or reporting bias may result incomplete understanding of bacterial composition during pregnancy and subsequent birth outcomes.
A systematic review was conducted following the PRISMA guideline. Three databases (PubMed, CINAHL, and Web of Science) were used to identify papers for review based on the search terms "vaginal microbiome", "pregnancy", and "16S rRNA sequencing". Articles were evaluated for methods of DNA extraction and sequencing, 16S region, taxonomy classification database, number of participants or vaginal specimens, and pregnancy trimester.
Forty-five research articles reported employing a metagenomic approach or 16S approach for vaginal microbiome analysis during pregnancy that explicitly reported taxonomic composition and were included in this review. Less than 30% of articles reported the presence of GBS ( = 13). No significant differences in methodology were identified between articles that reported versus did not report GBS. However, there was large variability across research methods used for vaginal microbiome analysis and species-level bacterial community reporting.
Considerable differences in study design and data formatting methods may contribute to underrepresentation of GBS, and other known pathogens, in existing vaginal microbiome literature. Previous studies have identified considerable variation in methodology across vaginal microbiome studies. This study adds to this body of work because in addition to laboratory or statistical methods, how results and data are shared (e.g., only analyzing genus level data or 20 most abundant microbes), may hinder reproducibility and limit our understanding of the influence of less abundant microbes. Sharing detailed methods, analysis code, and raw data may improve reproducibility and ability to more accurately compare microbial communities across studies.
阴道微生物组研究经常报告与生殖健康结果相关的微生物组多样性指标和群落。尽管已知B族链球菌（也称为无乳链球菌或GBS）是新生儿感染性发病和死亡的主要原因，且是早产和其他并发症的一个促成因素，但阴道微生物组研究中却明显缺乏关于它的报告。因此，本系统评价的目的是探讨在与妊娠相关的阴道微生物组文献中GBS报告的频率，并检查导致物种和属水平微生物组报告差异的方法学偏差。由于方法学或报告偏差而未能通过基于测序的方法鉴定出GBS，可能会导致对孕期细菌组成以及随后的分娩结局理解不完整。
按照PRISMA指南进行系统评价。使用三个数据库（PubMed、CINAHL和Web of Science），根据搜索词“阴道微生物组”“妊娠”和“16S rRNA测序”来识别待审查的论文。对文章的DNA提取和测序方法、16S区域、分类学分类数据库、参与者或阴道标本数量以及妊娠 trimester进行评估。
45篇研究文章报告在孕期采用宏基因组学方法或16S方法进行阴道微生物组分析，并明确报告了分类学组成，被纳入本评价。不到30%的文章报告了GBS的存在（n = 13）。报告GBS和未报告GBS的文章在方法学上未发现显著差异。然而，用于阴道微生物组分析和物种水平细菌群落报告的研究方法存在很大差异。
研究设计和数据格式化方法的显著差异可能导致现有阴道微生物组文献中GBS和其他已知病原体的代表性不足。先前的研究已经确定阴道微生物组研究在方法学上存在相当大的差异。本研究补充了这一工作内容，因为除了实验室或统计方法外，结果和数据的共享方式（例如，仅分析属水平数据或20种最丰富的微生物）可能会阻碍可重复性，并限制我们对较不丰富微生物影响的理解。共享详细的方法、分析代码和原始数据可能会提高可重复性，并更准确地比较不同研究中的微生物群落。
