The Vaginal Microbiome: Investigations Point to a New “Normal”

 In Women's Health


Keegan Sheridan, ND

How the human microbiome coexists with the body is still an unknown in many ways, and yet, even our early understanding of this symbiotic relationship is highly compelling. While research to date has largely focused on microbiota of the gut, this work is rapidly expanding to other areas of the body. For example, new research demonstrates the powerful roles that the vaginal microbiome plays. Thanks to targeted investigations in this area, we are quickly deepening our understanding of what constitutes “normal” vaginal flora, common factors that have the power to disrupt healthy microbial balance, and meaningful tools to positively influence this important microbial community. This article provides an update on research engines driving discoveries of the vaginal microbiome as well as clinical applications to consider.

The Human Microbiome Project

In 2008, the National Institutes of Health (NIH) Common Fund Human Microbiome Project (HMP) was established. Its mission was “generating resources that would enable the comprehensive characterization of the human microbiome and analysis of its role in human health and disease.”1 As part of its initial phase, investigations were divided into 5 sites: oral and nasal cavities, the gastrointestinal and genitourinary tracts, and the skin. The next phase, currently underway, is the Integrative HMP (iHMP). Building upon the first phase, the iHMP strives to integrate “longitudinal datasets from both the microbiome and hosts from three different cohort studies of microbiome-associated conditions.”2

Phases 1 and 2

A leading study group within the iHMP is the Vaginal Microbiome Consortium at Virginia Commonwealth University, which has been funded for 2 stages of investigations.3 In the first stage, the Vaginal Human Microbiome Project, a cross-sectional community study with over 6000 participants, collected vaginal and buccal samples in order to investigate the vaginal microbiome’s role in women’s urogenital health.4 This stage of the study involved collecting and analyzing samples from approximately 250 monozygotic and dizygotic twin pairs. In the second stage, samples from more than 2000 pregnant women and their infants were collected over multiple prenatal visits, at delivery, and early postnatal visits, with the goal of clarifying the roles of the vaginal microbiome “in the etiology or prevention of adverse outcomes of pregnancy, with a specific focus on preterm birth and stillbirth.”4 Insights from this work continue to be published.

More than any other organized effort to date, the HMP serves to evolve our understanding of the human microbiome. In the decade since its establishment, the HMP has offered a wealth of data and insights, some of which are discussed below. To explore this content further, visit the “Publications” tab on the HMP and iHMP websites5,6 or browse an extensive list of tagged articles through a Google Scholar search.7

A New Definition of “Normal”

Our understanding of what constitutes “normal” in the microbial makeup of the vagina and surrounding genitourinary tissues has shifted dramatically in recent years. A major contributor to these shifting perspectives is the development of new investigative tools beyond traditional culturing techniques. Modern “omic” studies (eg, genomics, proteomics, metabolomics) offer greater investigative details regarding these microbial communities and their effects on our health and well-being.

For example, in the not too distant past, the idea that the bladder was a sterile environment was a commonly held belief.8 Today we understand that the bladder and vagina, and areas connecting them, host a diverse ecosystem of more than 200 bacterial species.9 In a 2011 paper, Ravel et al10 suggested that vaginal bacterial communities of most healthy women can be clustered into 5 groups, 4 of which are dominated by distinct species of lactobacilli: Lactobacillus iners, L gasseri, L crispatus, or L jensenii. In the fifth group, however, anaerobic organisms were found to dominate over lactic acid bacteria, challenging the previously held belief that high numbers of lactobacilli and a pH of <4.5 is synonymous with a “healthy” vaginal ecosystem.10 Of the 396 asymptomatic North American women sampled and self-selected into 1 of 4 ethnic groups (white, black, Asian, and Hispanic), researchers found a higher median pH in Hispanic and black women, reflecting a higher prevalence of bacterial communities not dominated by Lactobacillus spp. The findings of this study beg the question of what kinds of bacterial communities are truly “normal” when we consider health of the vagina and surrounding tissues. At least from this study, data suggest that vaginal bacterial communities not dominated by species of Lactobacillus are not only common, but in some women are also both “normal” and “healthy.”

While the microbial makeup of the vagina is a dominant factor of health, this community does not function in isolation, and likely co-evolved with other elements, such as cytokines and defensins to protect against dysbiosis and infections and to support vaginal health.9 Of these chemical compounds, antimicrobial peptides (AMP) are specific elements worthy of discussion. These multifunctional, amphipathic molecules minimize pathogenic invasion and replication within host cells, and are able to independently modulate the immune system, helping to reduce inflammation and preserve tissue homeostasis.11 In a 2015 paper by Yarbrough et al, AMPs were found to be particularly influential to the lower female reproductive tract (FRT) where they act as a first-line defense against pathogen invasion from sexually transmitted and other opportunistic microbes.11 AMPs were also shown to modulate the vaginal microbiome communities of the lower FRT by preventing the ascension of microbes into the upper FRT.11 Conversely, this paper also demonstrated that the vaginal microbiome was shown to influence expression of AMP. In this respect, AMP and the vaginal microbiome are interdependent, influencing optimum function of one another, or, in the case of dysbiosis, inducing a unique AMP profile with increased susceptibility to pathogens.11

From this research, it becomes clear that previously held beliefs as to what constitutes “normal” and “healthy” vaginal microbiota must evolve. While lactobacilli dominance is still a very common factor of vaginal homeodynamic balance, evidence now suggests it is not a requirement for all women. In addition, we now understand that other critical elements, such as AMPs, work together with and are influenced by the vaginal microbiome to ultimately determine the well-being or the manifestation of disease within these tissues.11 These elements, their interactions, and the potential influence of disrupting factors, like those discussed in the next section, must all be considered when assessing patient health.

Disrupting Factors

Just as the vaginal microbiome is intimately connected to and influenced by chemical messengers in the surrounding region, it is also susceptible to a range of external factors and health states. For example, in a study by Koumans et al, vaginal swabs were collected and tested for the presence of bacterial vaginosis (BV), a common disturbance of vaginal microflora that is associated with an increased risk of acquiring sexually transmitted infections, HIV, and adverse pregnancy outcomes.12 Factors found to be significantly correlated to BV included smoking, higher body mass index, sex with a female sex partner, higher numbers of sexual partners over time, and greater frequency of douching.

Additionally, Freitas et al elucidated that pregnancy was a significant influencer of vaginal microbiota composition.13 In their study of 182 healthy pregnant women, a loss of richness and diversity in vaginal microbiomes due to pregnancy correlated with a shift toward a greater abundance of lactobacilli and a larger total bacterial community. From this investigation, the researchers proposed that the vaginal microbiome potentially plays a significant role in pregnancy outcomes and emphasized that understanding the roles that these communities play during pregnancy, “is a critical step toward being able to exploit the diagnostic potential of the microbiome for the prediction of adverse pregnancy outcomes, as well as to explore alternative therapeutic procedures through microbiological intervention.”13

A Role for Probiotics

A natural next step in the process of understanding the vaginal microbiome is to consider the emerging body of research on probiotics to support and influence microbiota of the vagina.

As mentioned in the previous section, BV is a common disturbance of vaginal microflora that is associated with a range of negative outcomes and which, in many ways, serves as a common form of dysbiosis from which to extrapolate understanding. Research published in recent years suggests the use of probiotics as a compelling tool to treat this disturbance. In a 2014 pilot trial, Lactobacillus fermentum LF15 and L plantarum LP01 (each at 400 million CFU per dose) were delivered via slow-release vaginal tablets over an 8-week trial period. By the end of the trial period, only 4 women of the 24 in the active group still met the clinical criteria for BV (measured as a Nugent score of >7). No significant differences were recorded in the placebo group at any time.14

Another randomized, clinical trial compared the efficacy of adding short-term versus long-term single-strain probiotic supplementation to a standard treatment protocol for concomitant human papilloma virus (HPV) and BV or vaginitis.15 Both groups received a standard treatment of either metronidazole (500 mg twice per day for 7 days) or fluconazole (150 mg orally once per day for 2 consecutive days). Women randomized to the short-term probiotic group additionally received vaginally-implanted Lactobacillus rhamnosus BMX 54 (104 CFU) daily for 3 months, whereas women in the long-term group received the same probiotic daily for 6 months. After a median follow-up of 14 months, women who received the probiotic over 6 months were half as likely to demonstrate HPV-related cytological anomalies and had a total HPV-clearance of 31.2% (as compared to only 11.6% in the short-term group). Results of this study support the long-term use of probiotics to influence and support vaginal microbial health.15


Research suggests that the world of the vaginal microbiome is multifaceted and highly influential not only over localized genitourinary health, but also pregnancy and, perhaps, even infant development.16 With recent innovations in investigative tools, the genomic makeup of vaginal microbiota and the nuances of what constitutes “normal” and “healthy” in this community is rapidly evolving. While the presence of lactobacilli is still accepted as an indicator of vaginal health, we now understand that pH and bacterial community dominance varies among healthy women. Additionally, research has demonstrated that probiotic supplementation is an effective first-line and adjunctive tool to positively influence microbial makeup and the manifestation of health in the vaginal microbiome.


  1. NIH Human Microbiome Project. 2018. Institute for Genome Sciences, University of Maryland School of Medicine. Available at: Accessed August 10, 2018.
  2. NIH Integrative Human Microbiome Project. 2018. Institute for Genome Sciences, University of Maryland School of Medicine. Available at: Accessed August 10, 2018.
  3. Vaginal Microbiome Consortium. Available at: Accessed August 10, 2018.
  4. Huang B, Fettweis JM, Brooks JP, et al. The changing landscape of the vaginal microbiome. Clin Lab Med. 2014;34(4):747-761.
  5. NIH Human Microbiome Project, Publications. 2018. Institute for Genome Sciences, University of Maryland School of Medicine. Available at: Accessed August 10, 2018.
  6. NIH Integrative Human Microbiome Project, Publications. 2018. Institute for Genome Sciences, University of Maryland School of Medicine. Available at: Accessed August 10, 2018.
  7. [Google Scholar search for “human microbiome project”]: Accessed Aug 10, 2018
  8. Thomas-White K, Brady M, Wolfe AJ, Mueller ER. The bladder is not sterile: History and current discoveries on the urinary microbiome. Curr Bladder Dysfunct Rep. 2016;11(1):18-24.
  9. Mendling W. Vaginal microbiota. Adv Exp Med Biol. 2016;902:83-93.
  10. Ravel J, Gajer P, Abdo Z, et al. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A. 2011;108 Suppl 1:4680-4687.
  11. Yarbrough VL, Winkle S, Herbst-Kralovetz MM. Antimicrobial peptides in the female reproductive tract: a critical component of the mucosal immune barrier with physiological and clinical implications. Hum Reprod Update. 2015;21(3):353-377.
  12. Koumans EH, Sternberg M, Bruce C, et al. The prevalence of bacterial vaginosis in the United States, 2001-2004; associations with symptoms, sexual behaviors, and reproductive health. Sex Transm Dis. 2007;34(11):864-869.
  13. Freitas AC, Chaban B, Bocking A, et al. The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women. Sci Rep. 2017;7(1):9212.
  14. Vicariotto F, Mogna L, Del Piano M. Effectiveness of the two microoganisms Lactobacillus fermentum LF15 and Lactobacillus plantarum LP01, formulated in slow-release vaginal tablets, in women affected by bacterial vaginosis; a pilot study. J Clin Gastroenterol. 2014;48 Suppl 1:S106-S112.
  15. Palma E, Recine N, Domenici L, et al. Long-term Lactobacillus rhamnosis BMX 54 application to restore a balanced vaginal exosystem: a promising solution against HPV-infection. BMC Infect Dis. 2018;18(1):13.
  16. Barthow C, Wickens K, Stanley T, et al. The Probiotics in Pregnancy Study (PiP Study): rationale and design of a double-blind randomised controlled trial to improve maternal health during pregnancy and prevent infant eczema and allergy. BMC Pregnancy Childbirth. 2016;16(1):133.

Keegan Sheridan, ND, is a naturopathic physician and 2004 graduate of Bastyr University. Since 2006 she has worked in the natural/organic food, beverage, and dietary supplement industries as a technical marketing expert and natural health strategist. Keegan is a scientific consultant for SFI USA, which manufactures the Klaire Labs brand of dietary supplements. She lives in San Diego, CA. For more information, visit:

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