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Volume 2 (9), 2021, Pages 1027-1049.e7

Complex species and strain ecology of the vaginal microbiome from pregnancy to postpartum and association with preterm birth

Ryan M.Pace1, Derrick M. Chu1,2,3, Amanda L. Prince1, Jun Ma1, Maxim D. Seferovic1, Kjersti M. Aagaard1,2,3,4,5,6

Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, TX, USA.



Lactobacillus was described as a keystone bacterial taxon in the human vagina >100 years ago. Using metagenomics, we and others have characterized lactobacilli and other vaginal taxa across health and disease states, including pregnancy. While shifts in community membership have been resolved at the genus/species level, strain dynamics remain poorly characterized.


We performed a metagenomic analysis of the complex ecology of the vaginal econiche during and after pregnancy in a large US-based longitudinal cohort of women who were initially sampled in the third trimester of pregnancy, and then validated key findings in a second cohort of women initially sampled in the second trimester of pregnancy.


First, we resolved microbial species and strains, interrogated their co-occurrence patterns, and probed the relationship between keystone species and preterm birth (PTB) outcomes. Second, to determine the role of human heredity in shaping vaginal microbial ecology in relation to PTB, we performed a mtDNA-bacterial species association analysis. Finally, we explored the clinical utility of metagenomics in detection and co-occurrence patterns for the pathobiont group B Streptococcus (causative bacterium of invasive neonatal sepsis).


Our highly refined resolutions of the vaginal ecology during and post-pregnancy not only provide insights into structural and functional community dynamics but also highlight the capacity of metagenomics to reveal the finer aspects of the vaginal microbial ecologic framework.

Keywords: 16S rRNA, bacteria, GBS, Lactobacillus, metagenomics, microbiome, preterm birth, strains, streptococcivagina.

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