The vagina, like many other body organs (mouth, intestine, colon, skin) has its own unique set of microorganisms which make up the microbiome. These include mostly bacteria - both good and bad - and to a lesser extend fungus, protozoa (microscopic, single celled organisms) and viruses1.

So, what does the perfect, healthy vaginal microbiome look like? As with every living being, there is no uniformity of vaginal microbiomes across the globe and there is some degree of variation based on stage in life and ethnic background. But, in principle, the core of a healthy vaginal microbiome is the same and there are certain microorganisms which are a ‘must have’ in a healthy vagina.

In this article we explore how to increase and maintain the scientifically proven elements of a healthy vaginal microbiome, which, in turn decreases risks of pathogens and bad bugs causing unpleasant symptoms‍.

Healthy vaginal microbiome

Lactobacillus species

The microorganisms that dominate a healthy vagina microbiome and are critical for maintenance of vaginal wellbeing are the Lactobacillus species. Lactobacillus (L.) species produce lactic acid, hydrogen peroxide and other directly antimicrobial agents which have essential role in the fight against microorganisms2 that cause bacterial vaginosis (BV), yeast infections, and itching and burning symptoms in the vagina.

There are around 20 lactobacillus species that have been detected in the vagina. Recent scientific research has shown that healthy vaginal microflora does not contain high numbers of many different lactobacillus species. Rather, 1 or 2 lactobacillus species are dominant (mainly L. crispatus and L. iners but also L. gasseri and L. jensenii), and other species are rare3.

Lactobacillus crispatus

The most important, in fact we like to call it ‘the queen’, of the Lactobacillus species is called Lactobacillus crispatus4. It is the most beneficial healthy bacteria in vaginal microbiome of 65% of women. If you get back a vaginal microbiome test, and see L. crispatus dominance in the results it will usually indicate that there is a balanced and healthy vaginal microbiome. L. crispatus creates very stable colonies which protect vaginal environment from BV causing bacteria. It was found that vaginas colonized with L. crispatus have a five times decreased risk for developing BV5.

Lactobacillus iners

Lactobacillus iners is the second most common bacteria in a healthy vagina. But unlike with L. crispatus, L. iners is associated with both normal and abnormal microflora. The reason why L. iners happily coexists with bad bacteria is still not clear. It has been suggested that either L. iners simply adapts well to the conditions that are associated with BV (like an increase in pH levels) or that it is more resistant than other Lactobacillus species3.

L. iners has been described by scientists as a ‘transitional’ species. Transitional in this sense means that when L. iners has increased in a higher ratio than other “good” bacteria it may indicate that the vaginal microbiome is on the way to becoming disrupted and imbalanced. L. iners is less protective against bad bugs. Women colonized dominantly with L. iners have greater risk for developing BV compared with women colonized predominantly with L. crispatus5.

Lactobacillus gasseri

Lactobacillus gasseri is the ‘second in command’ good bug, entirely connected with the healthy and balanced vaginal microbiome. It is present in healthy vaginal microbiome in more than 40% of women. Although it does not create as stable colonies as L. crispatus, certain L. gasseri strains have the ability to attack bad bugs by releasing antimicrobial substances that interfere with their ability to survive in the vagina and biofilm (a protective layer some bag bugs can create around themselves) formation6.

Vaginal Microbiome of Reproductive-Age Women According to Ethnicity Graph

Vaginal microbiomes normally contain other non-lactobacilli species, but a microbiome with completely different bacterial groups and total absence of lactobacillus species is considered highly unbalanced.

Generally, the rule of the thumb is that the less bacterial diversity the better. However, more diversity within Lactobacillus family is fine, as all their excellent defense mechanisms will have a combined effect in protecting vaginal microbiome.

Lactobacillus jensenii

L. jensenii is another frequently detected good bacteria in a healthy vagina. Its representation in vaginal population varies in different ethnic groups. Currently this lactobacillus species is not on the list of permitted ingredients for use in medical products in Australia.

Unbalanced vaginal microbiome

There are a lot of women with low levels of different Lactobacillus species who do not experience any negative vaginal symptoms. Whether these women are healthy or have asymptomatic BV is still a subject of debate in scientific circles7.

Women with healthy vaginal microbiome that is not lactobacilli dominated usually have it replaced with other lactic acid producing bacteria, like Atopobium vaginae, Megasphaera and Leptotrichia species. The healthy vaginal microbiome will be maintained only if lactic acid production continues3.

But it has been shown that women with low representation of Lactobacillus species in their vaginal microbiome are more susceptible to vaginal infections, as their microbiome can more easily be tipped over by pathogens.

An example of this are women of African American descent (who tend to have non-lactobacilli dominated vaginal microbiome) who are twice as likely to suffer from BV than women of European descent (who tend to have lactobacillus dominated vaginal microbome)8. It was found that 60% of women with asymptomatic BV had Candida species (a fungus causing thrush or vaginal yeast infection) present in their vagina, versus only 18% of women with healthy vaginal microbiome9.

As Lactobacillus species have the role of protecting vaginal microenvironment, women who would be candidates of potentially having asymptomatic BV are encouraged to screen and check their vaginal microbiome in order to appropriately manage their reproductive health and avoid further complications of vaginal infections.

Unhealthy vaginal microbiome

Unhealthy vaginal microflora may be result of:

  • overgrowth or increased virulence (or amount) of an organism that is considered a normal element of vaginal flora (e.g. Escherichia coli)
  • colonization by an organism which is not part of the normal vaginal community (e.g. Streptococcus pneumoniae, Haemophilus influenzae, or Listeria monocytogenes)
  • a sexually transmitted infection (STI) (for example trichomoniasis)

As mentioned above, the changes in vaginal microbiome are not necessarily followed by symptoms and the development of a disease. Disease occurs as a result of the interaction, or the ability, of a bad bug to cause harm, the strength of the immune response of the host and dominance or ratio between the good and bad bugs3. Once lactic acid producing bugs (which keep the pH balance in the vagina at a healthy level) are depleted, pathogen species (bad bugs) start freely multiplying and dominating the vaginal space. Once an infection spreads, symptoms such as unpleasant odor, vaginal discomfort, itching, burning and pain sensations start to occur. If this is then left untreated and allowed to progress, serious complications such as pelvic inflammation, infertility, and preterm birth can result.

Gardnerella vaginalis

Gardnerella vaginalis is a bacteria that normally can be detected in a healthy vagina, but in very small quantities. Its overgrowth is the most common reason for the development of BV and something you want to avoid occurring. The environment in which Gardnerella flourishes is when vaginal pH increases above 4.5. The right balance of lactic acid producing bacteria is needed to reduce the vaginal pH back to below 4.5 and suppress the overgrowth of Gardnerella.

Atopobium vaginae

Atopobium vaginae is bacteria that is detected in normal vaginal flora (normally around 8-15% of the vaginas biome), but it is more commonly found in abnormal flora associated with BV (in this instance you’d be looking at levels of Atopobium vaginae of around 50-96%).

Atopobium can create biofilms (a biofilm is a complex structure of microbiome made up of either different bacterial colonies or a single type of cells joining together to form a group aka biofilm) which are related to the resistance of antimicrobial treatment of BV. Bacterial biofilms are a serious health concern due to their abilities to tolerate antibiotics and host defence systems. High loads of Atopobium vaginae in combination with Gardnerella vaginalis have been associated with late miscarriage and premature delivery10.


Candida is a yeast (a type of fungus) that causes yeast infections. Candida albicans species is responsible for 85-90% of vaginal yeast infection (or vaginal thrush) cases, while Candida glabrata and Candida parapsilosis for 5-10% of all cases11.


Trichomonas is a single cell parasite organism that causes trichomoniasis or trich, which is a sexually transmitted infection. Common symptoms include abnormal vaginal discharge, including an increased in volume of discharge with a fishy smell, discharge from opening of penis, vaginal or penile itching and a burning sensation which is experienced during urination or ejection. However, around 70% people do not have any symptoms. It is more common in older people than younger, and more common in women than men. Trichomoniasis can be easily treated with metronidazole and can be avoided by using condoms12.

Mycoplasma & Ureaplasma

Mycomplasma and Ureaplasma species are one of the smallest living organisms that have no cell wall. That is why they often go undiagnosed unless specifically tested and cultured in a lab using special conditions and media.

Mycomplasma and Ureaplasma can be present and normally live in a vagina of asymptomatic healthy women and can be transmitted through sex. Mycoplasma hominis, Mycoplasma genitaloum and Ureaplasma urealyticum have been reported to be responsible for causing urogenital infections (problems that affect the urinary and genital tracts), infertility13 and can cause complications during pregnancy14.

How to balance your vaginal microbiome

First, always test yourself so you can know for sure what is going on with your microbiome. You can get a vaginal microbiome home test kit, available both in Australia and overseas (NutriPath, i-screen, Juno, Evvy, invivo etc.).

The resulting vaginal microbiome report will provide you with information on your vaginal pH, which beneficial bacteria you have, bad bacteria you have, along with details on yeast and other microorganisms related to sexually transmitted diseases.

You can also test, medicate, then retest to see what works for your individual microbiome. These tests, while sadly expensive, have taken the guesswork out of vaginal health.

Once your results are in, you can discuss them further with your physician, naturopath or gynecologist.

There are a few things you can do to improve your vaginal health.

Scientific research has indicated certain lifestyle changes we can take to help keep the bad bacteria away or at manageable levels. Unfortunately, the science has shown that a lot of the fun parts of life like: sex, sex toys and naughty food are contributing factors to high or higher levels of bad bacteria. We, at Amelia, want to inform you of the research but would never discourage women to live fun and fulfilling lives, plus we really resent the ‘blame game’ that a women’s health is generally linked to an individual's chosen lifestyle. The reality is, sometimes you do everything right and still experience vaginal symptoms. But here are some tips on lifestyle you may want to consider:

  • A healthy diet – A diet high in fat and low on fresh fruit and vegetables has been linked to increased risk of BV15 - therefore be sure to eat lots of fresh fruit and veg and limit the amount of high fat foods.
  • Hygiene – Over-washing the vulvo-vaginal area was linked to a disrupted vaginal microbiome.
  • Products  Use good quality lubricants and hygiene products. Do not use scented products and sprays.
  • Douching – Douching increases risk of vaginal irritation, dryness, BV, inflammatory pelvic disease, preterm birth, recurrent thrush, ectopic pregnancy and infertility. Douching liquids often have an antimicrobial effect - wiping or washing away the good together with the bad bacteria. Douching once or more per month was associated with the presence of Trichomonas vaginalis (parasite causing trichomoniasis, a very common STD) and Gardnerella vaginalis (bacteria causing BV)16
  • Lactic Acid - Women with healthy vaginal microbiome that is not lactobacilli dominated usually have it replaced with other lactic acid producing bacteria, like Atopobium vaginae, Megasphaera and Leptotrichia species. The healthy vaginal microbiome will be maintained only if lactic acid production continues.
  • The Contraceptive Pill – Changes in estrogen levels affecting glycogen levels in the vagina. Glycogen is produced by vaginal wall cells and is used as the main food source for lactobacilli colonies. Reduced glycogen levels are leading to disturbance in the growth of Lactobacillus species and compromise vaginal microbiome balance.
  • Smoking – It was found that women who smoke have increased susceptibilities to urogenital infections and increased vaginal malodor17 (unpleasant smell or odor).
  • High risk sexual behaviors – Use of condoms during sex was found to limit vaginal microbiome disruption. It was found that the number of sexual partners, and sex with other women, had a direct correlation with BV18. Oral sex and the use of sex toys and aids was also found to be related to a higher risk of vaginal infection19.
  • Antibiotics – The use of antibiotics, regardless of if applied orally or vaginally, influences the vaginal microbiome. The microbiome changes after antibiotic treatment depend on a type of antibiotic, dose, length of a treatment etc. Some lactobacilli species have an innate antibiotic resistance to a wide spectrum of antibiotics. For example, it was shown that STD treatment with azithromycin had little impact on the good bugs within vaginal microbiome, while BV treatment with metronidazole had a significant effect on the diversity or variety of the vaginal microbiome. Treatment with metronidazole influenced a reorganization of the vaginal microbiome more toward  iners dominance which as discussed above is often the beginning phase of a bacterial vaginosis infection20. Sometimes antibiotic treatment can increase lactobacilli. A study found modest growth of L. crispatus colonies and significant surge of L. iners numbers upon BV treatment with metronidazole. One of the possible explanations for this growth of the good bugs is reduced competition for space and food once the bad bugs start to get eliminated. However, a L. iners dominated vaginal microbiome is instable and BV usually reemerges after the cessation of the treatment. Strategies to ensure ongoing presence of good bacteria are highly recommended21.
  • Vaginal probiotics – Vaginal probiotic pessaries contain specific vaginal probiotic strains which can adhere/stick to vaginal wall and colonize the vagina with the beneficial strain of bacteria they contain. Numerous studies confirm the benefits of vaginal probiotics in restoring healthy vaginal microbiome and reducing the recurrent vaginal bacterial and yeast infections22,23,. Clinical studies have found that vaginally applied probiotics are 72% more effective in rebalancing the vaginal microbiome than probiotics taken orally for the same purpose2.Vaginal Pessary Probiotics vs Oral Probiotics - What's the difference in effectiveness?
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See list of references used on this page

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2 Wu S, Hugerth LW, Schuppe-Koistinen I, Du J. The right bug in the right place: opportunities for bacterial vaginosis treatment. NPJ Biofilms Microbiomes. 2022 May 2;8(1):34. 

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4 Ravel J, et al. Vaginal microbiome of reproductive-age women. Proc NatlAcadSci U S A. 2011 Mar 15;108 Suppl 1(Suppl 1):4680-7.

5 Verstraelen H,Verhelst R, Claeys G, De Backer E, Temmerman M, Vaneechoutte M. Longitudinal analysis of the vaginal microflora in pregnancy suggests that L. crispatus promotes the stability of the normal vaginal microflora and that L.gasseri and/or L. iners are more conducive to the occurrence of abnormal vaginal microflora. BMC Microbiol. 2009 Jun2;9:116. 

6 Atassi F, Pho Viet Ahn DL, Lievin-Le Moal V. Diverse Expression of Antimicrobial Activities Against Bacterial Vaginosis and Urinary Tract Infection Pathogens by Cervicovaginal Microbiota Strains of Lactobacillus gasseri and Lactobacillus crispatus. FrontMicrobiol. 2019 Dec20;10:2900. 

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10 Mendling W, Palmeira-de-Oliveira A, Biber S, Prasauskas V. An update on the role of Atopobium vaginae in bacterial vaginosis: what to consider when choosing a treatment? A mini review. ArchGynecolObstet. 2019 Jul;300(1):1-6. 

11 Moira Bradfield. Dealing with recurrent vaginal fungal infections. Intimate ecology seminar, 02/08/2019.

12, accessed on 18/10/2022

13 Moridi K,Hemmaty M, Azimian A. et al. Epidemiology of genital infections caused by Mycoplasma hominis, M. genitalium and Ureaplasma urealyticum in Iran; a systematic review and meta-analysis study (2000–2019).BMC Public Health, 20, 1020 (2020).

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17 Nelson TM, Borgogna JC, Michalek RD, Roberts DW, Rath JM, Glover ED, Ravel J, Shardell MD, Yeoman CJ, Brotman RM. Cigarette smoking is associated with an altered vaginal tract metabolomic profile. Sci Rep. 2018 Jan 16;8(1):852. 

18 Fethers KA, Fairley CK, Hocking JS, Gurrin LC, Bradshaw CS. Sexual risk factors and bacterial vaginosis: a systematic review and meta-analysis. Clin Infect Dis. 2008 Dec 1;47(11):1426-35.

19 Bradshaw CS, Morton AN, Garland SM, Morris MB, Moss LM, Fairley CK. Higher-risk behavioral practices associated with bacterial vaginosis compared with vaginal candidiasis. ObstetGynecol. 2005 Jul;106(1):105-14.

20 Ahrens P, Andersen LO, Lilje B, Johannesen TB, Dahl EG, Baig S, Jensen JS, Falk L. Changes in the vaginal microbiota following antibiotic treatment for Mycoplasma genitalium, Chlamydia trachomatis and bacterial vaginosis. PLoSOne. 2020 Jul 28;15(7):e0236036. 

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22 Huang H, Song L, Zhao W. Effects of probiotics for the treatment of bacterial vaginosis in adult women: a meta-analysis of randomized clinical trials. ArchGynecolObstet. 2014 Jun;289(6):1225-34.

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