Characteristics of vaginal microbes and classification of the vaginal microbiome
Authors: Zhu Bin , Spaine Katherine M. , Edupuganti Laahirie , Matveyev Andrey , Serrano Myrna G. , Buck Gregory A. 
Published: August 2023

SummaryBackgroundThe vaginal microbiome (VMB) has been classified into several discrete community state types, some of which have been associated with adverse human health conditions. However, the roles of the many vaginal bacteria in modulating the VMB and health remain unclear.MethodsThe associations among the vaginal taxa and other vaginal taxa, the vaginal pH, and the host gene expression responses were determined by calculating the correlation among the relative abundance of the vaginal taxa, the association between the vaginal pH and the predominant taxon in the VMB, and the correlation between the relative abundance of the vaginal taxa and human gene expression at the transcriptional level, respectively. Using these associations, an alternative more informative method, the biological vagitype (BVT), is proposed to classify community state types of the VMB.FindingsMostLactobacillusspp., with the exception ofLactobacillus iners, show significant correlations with host gene expression profiles and negative associations with dysbiosis-associated vaginal taxa. Many non-Lactobacillusspp. exhibit varied correlations withLactobacillusspp., the vaginal pH, and host gene expression. Compared to other dysbiotic taxa, includingCandidatusLachnocurva vaginae,Gardnerella vaginalishas a stronger positive correlation with vaginal pH and a stronger negative correlation withLactobacillusspp. Most dysbiosis-associated taxa are associated with stress responses of the host at the transcriptional level, but the genusMycoplasmahas a uniquely strong positive correlation with host immune responses. The association between BVTs of the VMBs and host characteristics, e.g., race/ethnicity, microbial infection, smoking, antibiotics, high blood pressure, economic state, diet, and others, was examined. The BVT classification method improved overall performance in associating specific vaginal microbial populations with host characteristics and phenotypes.InterpretationThis study sheds light on the biological characteristics of the vaginal microbiota, including some less abundant or still unculturable taxa. Since the BVT method was established based on these biological characteristics, the classification outcome of the VMB may have more clinical relevance. Because the BVT method performs better in associating specific vaginal community types with diseases, e.g., bacterial vaginosis and gonorrhea, it could be beneficial for the predictive modeling of adverse health.FundingThis work was supported by grants [UH3AI083263, U54HD080784, and R01HD092415] from the National Institutes of Health; and support from the [GAPPS BMGF PPB] grant from the Global Alliance to Prevent Prematurity and Stillbirth. We would also like to thank the Office of Research on Women’s Health at NIH for their generous support.Research in contextEvidence before this studyThe vaginal microbiome (VMB) refers to the community of microorganisms in the female lower reproductive tract. The VMB is often a simple ecosystem dominated by a single species. The most predominant bacteria in the VMB include severalLactobacillusspecies and two non-Lactobacillusspecies, i.e.,CandidatusLachnocurva vaginae andGardnerella vaginalis. Lactobacillusspecies produce lactic acid to lower the vaginal pH and inhibit the growth of disease-associated bacteria. Thus, the predominance of protective Lactobacilli, i.e.,L. crispatus, L. jensenii, andL. gasseri, in the VMB is associated with overall vaginal health. However, the role ofL. inersin promoting a healthy vaginal ecosystem is less clear. Actually, the biological and health relevance of many bacteria in the female lower reproductive tract is largely unknown. Some bacteria have low relative abundances, e.g.,PeptostreptococcusandCoriobacteriaceaespp.; and others are not yet culturable, e.g.,CandidatusLachnocurva vaginae and BVAB TM7. When abundance of a taxon is low, its association with a host characteristic is a challenge. Previous methods to classify the VMB were based simply on their microbial compositions, and the biological characteristics of the vaginal bacteria were largely ignored. Thus, classification of these VMBs into biologically relevant community types, as described herein, should be helpful in determining their relevance to women’s reproductive health.Added value of this studyThis study examines three biological characteristics of bacteria in the VMB, i.e., the associations among different bacterial taxa, the vaginal pH, and the host response. Based on these three characteristics, the influence of these bacteria, particularly low abundant and unculturable bacteria, on vaginal health is evaluated.L. inersseems to be neutral in maintaining overall vaginal health.Gardnerella vaginalisis apparently more easily inhibited byLactobacillusspp. thanCandidatusLachnocurva vaginae because of its stronger positive correlation with vaginal pH and negative correlation withLactobacillus. The genus ofMycoplasmahas a unique positive correlation with local immune responses, implying a role forMycoplasmain promoting inflammation. Compared with previous methods to classify the VMB, a new method, considering the above three biological characteristics of bacteria in the VMB, has been established. The new method performs better in associating specific vaginal communities with host characteristics and phenotypes; e.g., bacterial vaginosis and gonorrhea.Implications of all the available evidenceAccurate biological classification of the VMB is fundamental for assessing its impact on women’s health. Our classification scheme represents a step further toward that correct classification, eventually leading to new strategies for clinical assessment of the potential use of the VMB to diagnose or predict women’s reproductive health.