Abstract
The vaginal microbiome plays an important role in human health and species of vaginal bacteria have been associated with reproductive disease. Strain level variation is also thought to be important, but the diversity, structure and evolutionary history of vaginal strains is not as well characterized. We developed and validated an approach to measure strain variation from metagenomic data based on SNPs within the core-genomes for six species of vaginal bacteria: G. vaginalis, L. crispatus, L. iners, L. jensenii, L. gasseri, and A. vaginae. Despite inhabiting the same environment, strain diversity and structure varies across species. All species except L. iners are characterized by multiple distinct groups of strains. Even so, strain diversity is lower in the Lactobacillus species, consistent with a more recent colonization of the human vaginal microbiome. Both strain diversity and the frequency of multi-strain samples is related to species-level diversity of the microbiome in which they occur, suggesting similar ecological factors influencing diversity within the vaginal niche. We conclude that the structure of strain level variation provides both the motivation and means of testing whether strain level differences contribute to the function and health consequences of the vaginal microbiome.
Data Summary All vaginal metagenomic sequence data generated for this project can be found on the Sequence Read Archive under BioProject PRJNA639592.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Repositories: Sequence Read Archive BioProject PRJNA639592
Conflict of interest: The authors report no conflict of interest.
Funding information: This study was supported the Eunice Kennedy Shriver National Institute of Child Health & Human Development of the NIH: F30HD094435, a pilot research grant from the Center for Women’s Infectious Disease Research at Washington University School of Medicine and the March of Dimes Prematurity Research Center at Washington University. The sponsors had no role in the study design, the collection, analysis or interpretation of data, or the decision to submit the article for publication. The content of this study is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Ethical approval: Vaginal specimens were collected under appropriate IRB approval with informed consent and all human subject data was deidentified. Human metagenomic data were removed prior to analysis as described in the methods.
