Your Vaginal Microbiome

By Karen Saunders, BHSc. Illustration by Andrew Rae

We all know now that the gut is colonized by a range of beneficial bacteria that are absolutely essential for healthy gut function and robust immunity. But did you know that the vagina is the same? Yes!

Just like the gut, the vagina has its own unique microbiome ecosystem populated by various bacteria, yeasts and protozoa. 

When this is out of balance we are susceptible to increased vaginal infections like thrush and bacterial vaginosis, sexually transmitted and urinary tract infections. This is a subject I have been borderline obsessing about for four years since discovering it in my naturopathic studies. It has also helped me personally in understanding and treating my own recurrent issues. 

Most women at some stage in their lives will experience the uncomfortable symptoms of itchiness, abnormal discharge, pain during sex or an odor.

Some may experience recurrent infections that follow a cyclical pattern associated with the menstrual cycle, or when they have a new sexual partner, or when they are not eating right. This is due to these factors having a negative impact on the numbers of vaginal bacteria, leaving us vulnerable to infection. It makes perfect sense that our bodies have a built-in system of protection against outside invaders, and the root cause of these infections is usually a disrupted gut or vaginal microbiome. This disrupted microbiome is becoming more widely recognized and is now termed ‘vaginal dysbiosis’.

Signs that you may have vaginal dysbiosis:

  • Recurrent infections such as candida (thrush) and bacterial vaginosis (BV)

  • Sexually transmitted infections (STI’s)

  • Frequent urinary tract infections (UTI’s)

  • Odor - fishy

  • Irregular discharge 

  • Pain during sex

  • Itching, redness, swelling of vaginal mucosa

  • Irregular pap smear results 

  • Gut / digestive issues

The vagina is dominated by various strains of beneficial Lactobacillus bacteria namely Lactobacillus crispatus, Lactobacillus jensenii, Lactobacillus fermentum, Lactobacillus gasseri and Lactobacillus acidophilus1. These are all acid-producing bacteria and flourish in an acidic environment – In fact a healthy vagina is really acidic (between pH 4.0 and 4.5). Good numbers of these bacteria are needed to prevent pathogens (the bad guys) from taking over.

Essentially the good guys out-compete the bad guys for space like a packed car park – so that there is no room for them to take hold. Lactobacillus also produce certain molecules called bacteriocins that can kill unwanted bad guys such as the yeast Candida albicans which cause thrush, and the bacterial vaginosis-inducing Gardnerella bacteria2. Additionally, Lactobacillus strains of bacteria also produce hydrogen peroxide and lactic acid – these are acidic compounds that continue to keep the vagina optimally acidic3.

There are many risk factors that reduce Lactobacillus numbers. They are:

  • Antibiotic use

  • Gut dysbiosis / gastrointestinal issues

  • Diet – particularly sugar and refined carbohydrates

  • Hormonal fluctuations especially around period or post menopause

  • Stress

  • Smoking

  • Semen and spermicide 

  • Poor immune function

  • Frequent douching

  • Soft tissue trauma i.e.: Premature penetration

  • External products used i.e.: Most lubricants, fragranced soaps and washes

  • Sexual practices and new partners

  • Emotional components such as shame and self-worth issues*

Now nearly all women at some point in their lives have experienced one or more of the above symptoms. Lucky for us – nowadays more treatment options available. Conventional medicine will likely treat with antibiotics and antifungals which may work for a time, but often result in a reoccurrence of infection and can cause further damage to your gut/vagina microbiome. Thankfully, as integrated health practitioners we now have more tools to draw on such as probiotics, prebiotics, and herbal and nutritional medicines. 

So if you are one of the many women experiencing some of the above symptoms I strongly suggest adopting the following nutritional, lifestyle and dietary practices that help to love and nourish that precious vaginal microbiome, and kick that infection for good: 

  • Eat prebiotic foods: Prebiotics are the food that bacteria like to eat and need in order to survive. Things like fibre and lactulose. (A Google search will tell you which ones).

  • Take probiotics and eat fermented foods and drinks such as kefir and kimchi to ensure a wide range of probiotic strains. (See specific strains to look for below).

  • Eat a whole food diet, rich in plants and colours.

  • Remove sugar and refined carbohydrates such as bread and pasta. Avoid all processed foods and confectionary.

  • Limit alcohol intake to 1 glass red wine per week, or vodka soda.

  • Stress management – stress significantly reduces bacteria levels in vagina.

  • Address any gut issues or food intolerances you may have. This may require some testing – see your practitioner.

  • Boost immune function with zinc, vitamin C, adequate levels of protein (vegans – note!), herbs such as echinaceae, andrographis and mushrooms like reishi and shitake.

  • Get tested: Know your STI status. Most of these are actually sexually transmitted.

  • Sex: practice safe sex if you have multiple partners, ensure you are not penetrated prematurely – use a lubricant if necessary but best is to ensure the vaginal is lubricated and ready naturally before penetration – wait for a full ‘yes’ from your yoni*

  • Explore any emotional issues or trauma you think may be impacting your sexuality*

*These points are not evidence-based but come from clinical experience.

Basic Treatment: In combination with above the following points can help to re-balance your vaginal microbiome:

  1. Probiotics (oral and intra-vaginal application): 1 capsule orally per day, plus optional one capsule 3 times per week inserted deep into the vagina at night – the latter can also be taken prophylactically when vulnerable to infection i.e.: before period or after sex (note: this WILL NOT stop the risk of contracting STI’s though! Still use protection). Look for probiotics that contain CERTAIN SPECIFIC strains of probiotics such as*:

  • Lactobacillus rhamnosus GR-1

  • Lactobacillus fermentum RC-1

  • Lactobacillus acidophilus NAS and LA5 

  • Lactobacillus rhamnosus GG 

*Please note when using probiotics therapeutically, the results are strain specific and you will not get good results from just any probiotic. Get a good practitioner brand, or one off the shelf I do recommend is Blackmore’s Women’s Biobalance.

  1. Prebiotics: Eat prebiotic foods or use the prebiotic lactulose (available at Chemist Warehouse). Note it is not lactose, but be cautious if lactose intolerant. Dose: 5ml/day orally and optional syringe 10ml into vagina at night for 7 nights. (This stuff is a bit goopy).

  2. Antimicrobial herbs and Acids: These may be additionally needed to manage more established infections.  Pomegranate husk, green tea and oregano as shown efficacy against common infections. Substances that lower the pH of the vagina can be beneficial such as hydrogen peroxide and boric acid. Please do not use herbs and acids without the supervision of your practitioner. 

    How long does it take to heal?

    Its impossible to say how long it can take to heal. It depends on many factors unique to each person, and what their aliments are. For example once you have the herpes virus it will never leave your body, but a healthy microbiome will minimise outbreaks. All the other factors mentioned also play a part – woman’ s compliance to treatment, diet, ability to reduce their stress, also – has the underlying emotional issue been addressed? Some women get relief immediately with just probiotics and some need to cycle or stagger pre and probiotics as well as herbs for a number of months. If you are needing more information or breastfeeding / pregnant – please contact a trusted practitioner such as a naturopath or integrated medical practitioner that is familiar with the concept of prescribing strain specific probiotics. If you are suffering in silence with an STI, or recurrent infection – know that there options. Having a healthy vaginal biome is KEY to reproductive and sexual health.

    Karen xo

    Women’s Natural Health Expert



    Disclaimer: Please note this article is not intended to diagnose, treat any disease or health condition and is not a substitute for any professional medical advice. Please keep in mind this is for information purposes only. Please consult your healthcare practitioner before engaging in anything suggested in this blog article. 

    References: 1. The Probiotic Advisor 2018, “Just what is a Leaky Vagina?’, viewed 10 July 2018, <>. 2. Shipitsyna, E, Roos, A, Datcu, R, Hallén, A, Fredlund, H, Jensen, JS, Engstrand, L & Unemo, M 2013, ‘Composition of the Vaginal Microbiota in Women of Reproductive Age - Sensitive and Specific Molecular Diagnosis of Bacterial Vaginosis Is Possible?’, PLoS ONE, vol. 8, no. 4, pp. 1–10. 3. Trickey, R 2011, Women, Hormones and the Menstrual Cycle, 3rd edn, Trickey Enterprises, Fairfield.

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