The structure and diversity of strain-level variation in vaginal bacteria

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: Gardnerella vaginalis , Lactobacillus crispatus , Lactobacillus iners , Lactobacillus jensenii , Lactobacillus gasseri and Atopobium 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.

Student-Driven Course-Based Undergraduate Research Experience (CUREs) Projects in Identifying Vaginal Microorganism Species Communities to Promote Scientific Literacy Skills

“…Lactobacillus species including L. crispatus, L. gasseri, L. jensenii , and L. iners , dominated the primary vaginal microbiota have been associated with reproductive disease ( 15 ). 16S rRNA sequencing is a method widely applied for microbiology detection in the laboratory, while general bacterial culture is commonly implemented in clinical use ( 31 , 37 ).…”

“…Lactobacillus was the primary flora before menopause. Loss of Lactobacillus dominance promotes the colonization by anaerobic bacterial species with an increase in microbial diversity ( 15 ). The decrease in lactobacilli postmenopause leads to opportunistic pathogens, such as Gardnerella, Prevotella, Streptococcus, Escherichia/Shigella becoming the dominant bacteria.…”

“…For females, the vaginal microorganism environment includes a diverse set of species, constitute a biological barrier to pathogenic microorganisms ( 13 ), and protect Gynecologic Cancers ( 14 ).Beneficial bacteria, such as Lactobacillus , account for more than 80% of all vaginal bacteria and constitute the first line of defense against invasive microorganisms. The absence of Lactobacillus has been associated with disturbances in the vaginal microbiota, resulting in an inflammatory vaginal disease in ~40% of healthy women and allowing infection through overgrowth of harmful anaerobes, such as Gardnerella vaginalis and vulvovaginal candidiasis ( 15 , 16 ).…”

Persistence and In Vivo Evolution of Vaginal Bacterial Strains over a Multiyear Time Period

“…1A ), indicating that the L. crispatus at the initial time point was supplanted by another at the second sampling. It could be that these L. crispatus populations went extinct and were subsequently reestablished or that the population experienced a shift in the dominant strain, as prior studies have indicated these populations are often comprised of multiple strains ( 14 , 19 ). Participant 4 had a L. iners - dominated VMB at the initial time point, which shifted to a community that contained a majority of L. crispatus and a minority of L. iners at the second time point.…”

Impact of Infectious Disease on Humans and Our Origins

“…Interestingly, based on studies of non-human primates (Yildirim et al 2014) and other empirical arguments, Lewis postulates that the "Gardnerella" microbiome type might be the "ancestral state" (cf. Gilbert et al 2021;Tortelli et al 2021). E.g., the lactobacilli dominance is not found in other primates, while women with bacterial vaginosis show similar microbiome compositions to healthy baboons and macaques, but the pH-values still tend to be lower in women with bacterial vaginosis compared to non-human primates (Miller et al 2016).…”