What is a “normal and healthy” microbiome seems to differ among individuals and ethnic groups.  One of the goals with the Human Microbiome Project (HMP) was to characterize the healthy microbiome of different human body sites. The idea being that microbiome science needed to have a baseline of “normal and healthy” to compare to “dysbiotic and ill”. The ~200 individuals sampled for the HMP provided a surprising insight – there is no one healthy microbiome for a given site. Just as there are healthy people of a range of heights from 4’8” to 7’8”, so are there a range of healthy microbiome communities. However, the one body site thought to have a distinct microbiome across all women was the vaginal microbiome.

Surprizingly, the vaginal microbiome had a range of healthy microbiome community types. Historically, a healthy vaginal microbiome was thought to have only a few bacterial species and mostly be Lactobacillus. Lactobacillus produces lactic acid that reduces the pH of the vagina and restricts pathogen growth. A “dysbiotic and ill” vagina was characterized as having bacterial vaginosis (BV), an overgrowth of anaerobic pathogens (Prevotella, Peptostreptococcus, Gardnerella vaginalis, Mobiluncus, and Mycoplasma hominis which replace the “normally protective lactobacilli” (Soper 2015) and may even be an issue for surgery (Bieber 2015). Women with an abundance of Lactobacillus do not have bacterial vaginosis. However, this does not necessarily mean that women without Lactobacillus have BV!

Bacterial vaginosis does not have a single causative agent, one specific bacterial, viral, or fungal species that is associated with this disease. Instead, three of the four symptoms are present: 1) a white discharge, 2) a fishy odor of the discharge, 3) the presence of specific vaginal cells covered with bacteria, and/or 4) a vaginal pH over 4.5 (Bieber 2015; Ma, et al. 2012; Soper 2015). A correlation between a pH over 4.5 and a lack of the lactic acid producing bacterial genus Lactobacillus sp. has also been seen. Thus, women lacking Lactobacillus were thought to be at greater risk or have bacterial vaginosis. Oral or topical antibiotics and sometimes probiotics are used to treat BV, but these treatments have a high failure rate.

Previous gaps in the data = incorrect conclusion

The problem is that previous studies focused of Caucasian women, usually in the U.S. or Europe. Ethnicity had not really been considered. Additionally, conclusions were reached based on culturing. Growing bacteria in the lab. However, the majority of bacteria cannot be currently cultured. New DNA-based techniques now let us examine those bacteria that cannot be grown in a laboratory.

In Vaginal Microbiome of Reproductive-Aged Women (Ravel, et al. 2011) the vaginal microbiome of ~ 400 North American reproductive-aged women from 4 ethnic groups (white, black, Hispanic, and Asian), who did not have symptoms of bacterial vaginosis was characterized. The presence of bacterial vaginosis was determined by vaginal pH levels and gram stain smears of vaginal samples. Sexual behavior and hygiene practices were recorded. None of the women had taken antibiotics in the past 30 days, had sexual activity in the 48 h before the study, or used any douches, sprays, spermicides, or other vaginal medicines in the 48 h before the study.

Different ways to be healthy

Vaginal microbiome samples clustered into 5 groups characterized by different bacteria.
Figure 1. Vaginal microbiome samples (columns) clustered into 5 groups characterized by different bacterial taxa (rows).

Surprisingly, there was no single healthy  vaginal microbiome across all subjects. Instead, pH and microbiome composition varied across ethnic groups (see Figure 1). Five clusters with different microbiome compositions were found across ethnic groups. White and Asian women predominately had vaginal microbiomes dominated by Lactobacillus, whereas Hispanic and black women had microbial communities dominated by anaerobic bacteria and higher median pH (> 4.5) (see Figure 3). This suggests that the normal and healthy vaginal microbiome of Hispanic and black women is NOT dominated by Lactobacillus. Host genetic or other factors may influence which bacteria can colonize and survive in women of different ethnic backgrounds. How and why ethnicity corresponds to different microbiome communities has yet to be determined. These data do suggest that a woman’s ethnicity should be taken into account when determining the “health” of her vaginal microbiome.

In women with microbiome clusters where Lactobacillus did not dominate, lactic acid was still produced by the bacterial species that were present. This suggests that lactic acid production, which reduces vaginal pH and provides a protective function against pathogen colonization, is not restricted to Lactobacillus. Perhaps other bacteria can do the job that Lactobacillus does.

Detailed findings

  • Though the vagina is considered a “low diversity” microbiome, a total of 282 types (taxa) of bacteria were found across all the vaginal microbiomes of the women surveyed. In contrast, the digestive system has thousands of different bacterial taxa.
  • The microbiomes clustered into 5 groups. Groups were defined as either being dominated by a characteristic Lactobacillus or having a diversity of anaerobic bacteria.
  • Group II and V had ~ 2 dozen bacterial taxa with the other groups having over 100 taxa. However, there may be additional “rare” taxa present in abundance that could not be captured at the current sequencing depth.
  • Different groups had different median pH, which might be related to the microbiome composition, though all communities had bacterial genera (Lactobacillus, Megasphaera, Streptococcus, and Atopobium) that are known to produce lactic acid, suggesting some functional redundancy of microbiome members.
  • Communities with high pH (4.4 to 5.0) were dominated by Lactobacillus species other than L. crispatus.
  • Group IV was dominated by a diversity of strictly anaerobic bacteria, but also included L. iners and L. cripsatus, though the lactobacilli did not dominate the microbiome.
  • Prevotella sp. were also found in 68.5% of the samples and could be linked to bacterial vaginosis. Prevotella is known to produce ammonia and amino acids that promote the growth of Gardnerella vaginalis and Peptostreptococcus anaerobius, other bacteria commonly found in BV.
  • High Nugent scores (indicating BV) were most frequently associated with group IV microbiome community compositions that were not dominated by Lactobacillus, though some individuals of all group types had high Nugent scores.
  • Lowest pH values associated with groups dominated by L. iners and L. crispatus.

    Proportions of women of different ethnicity with different microbiome community types. Community type IV is most prevalent in black and Hispanic women and lacks Lactobacillus. All other community types have some species of Lactobacillus, though different species dominate each community type. The number of women sampled from each ethnic group is in parentheses.


Why does microbiome community type matter for women’s health?

First, it’s important to establish a personal healthy baseline. We need to realize that healthy Hispanic and black women are more likely to have a vaginal pH and microbiome that lacks Lactobacillus and is similar to that of a white or Asian woman with bacterial vaginosis. Hispanic and black women may be more likely to be incorrectly diagnosed as having BV, which might explain the high failure rate of current treatments. These women can potentially be characterized as having an “unhealthy” vaginal microbiome, when they are perfectly healthy.

Second, as with any body site good healthcare practices are important to maintain a healthy microbiome. Such care would include regular doctor visits, but also good diet and exercise. Third, understanding what disrupts a microbiome. This would include avoiding oral or topical antibiotics and antibacterial or antiseptic washes or douches unless recommended by your medical practitioner.

Human microbiome studies, such as this one are increasingly important to a future of personalized medicine and health. With the decreasing costs of microbiome community analyses, a broader diversity of people can be examined, and we have the potential to see an increase in the “democratization” of healthcare practices tailored to individual needs. Additionally, comparing data from a diversity of people may lead to a broader understanding of human-microbiome interactions.

Citizen Science: What’s your healthy baseline?

To understand what your personal healthy baseline and to add your data to the growing collection being analyzed, there are two programs providing sequencing of vaginal samples for citizen science projects. The American Microbiome Institute is conducting a program called Your Private Biome which studies the health of the vaginal microbiome. For additional information a podcast with the lead author on this study and the American Microbiome Institute (AMI) can be heard here. The private company uBiome also provides sequencing of genital and other body sites. If you are interested in uBiome’s services, use the code “ESTES20” when you are making your purchase. You will receive 20% off the costs of the kit. This is a commissioned link, so your purchases will support this blog.

Stay tuned for future posts to summarize additional research that has been done on the vaginal microbiome and how it fluctuates monthly with changing hormone levels and changes throughout a woman’s life.

What do you think?

Do you have questions about this work? Feel free to email me at mostlymicrobes at gmail dot com.

Share the Microbial Love

Thank you for reading my blog.

Please share this post if you enjoyed it.

If you received something of value from this post or the blog, please consider supporting the blog either directly, through a “tip” at the PayPal link below or indirectly through my affiliate links.



Bieber EJ, J.S. Sanfiilippo, I.R. Horowitz, M.I. Shafi. 2015. Clinical Gynecology. In: Cambridge University Press.

Ma B, Forney LJ, Ravel J 2012. Vaginal microbiome: rethinking health and disease. Annu Rev Microbiol 66: 371-389. doi: 10.1146/annurev-micro-092611-150157

Ravel J, et al. 2011. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A 108 Suppl 1: 4680-4687. doi: 10.1073/pnas.1002611107

1002611107 [pii]

Soper DE. 2015. Bacterial Vaginosis. In:  Porter RS, editor. Merck Manual, Professional Version. Kenilworth, NJ: Merck Manuals.


2 thoughts on “The Vaginal Microbiome: “Healthy” Differs with Ethnicity

Comments are closed.