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Let's talk about the vaginal microbiome

Updated: Oct 22, 2023

How healthy is your vagina? Do you regularly have bouts of vaginal burning or itching? Are you worried about odour or discharge? Do you have endometriosis or period pain?

If you have recurrent vaginal symptoms you will benefit from understanding how to support your vaginal microbiome.

Your vaginal microbiome is the intricate ecosystem of bacteria that live in the mucous layer within your vagina. In our digestive system it is important to have a wide array of bacteria present, however in the vagina it is healthy for Lactobacillus to be dominant.

When there is an increase in the diversity of bacteria in the vagina, it's an unhealthy state and referred to as bacterial vaginosis, or vaginal dysbiosis.

During your reproductive years, the vaginal microbiome is constantly changing due to fluctuations in reproductive hormones throughout a menstrual cycle. The fluctuations in hormones change the pH of the vagina and can be the reason why you might experience recurring vaginal symptoms at the same time of your cycle.

The vaginal microbiome is more stable before puberty, during pregnancy and in menopause. These life stages can be associated with their own vaginal conditions and women who aren't menstruating, due to PCOS or other condition, can also experience vaginal microbiome disruption due to the low levels of estrogen.

When your vaginal microbiome is healthy

A healthy vaginal microbiome:

  • protects against overgrowth by Candida

  • protects against sexually transmitted infections including HPV, HIV, Herpes, Chlamydia, gonorrhoea and trichomonas

  • reduces susceptibility to urinary tract infections

  • reduces your susceptibility to pelvic inflammatory disease, endometriosis and gynaecological cancers

  • is vital for conception, prevention of miscarriage, and prevention of preterm birth.

Vaginal microbiome disruptors

What can cause disruption to your delicate microbiome?

  • being newly sexually active, having a new sexual partner, or multiple sexual partners, frequent sex

  • anything that you put into your vagina can affect the pH levels, including tampons, menstrual cups, sex toys, lubricants and condoms

  • vaginal cleanliness can include poor hygiene such as changing pads infrequently, or over cleaning with antimicrobial soaps, essential oils and douches

  • synthetic fabrics in underwear and period underwear

  • smoking

  • changes in estrogen levels, such as fluctuations in the menstrual cycle; heavy or long periods; perimenopause; menopause; PCOS; absent periods; pregnancy

  • frequent antibiotics or anti-fungal treatments

  • diets high in sugar, or lacking in nutrients to support healthy reproductive hormones

  • stressful, busy lifestyle

Bacterial vaginosis (BV)

When your vaginal microbiome is out of balance it's most commonly known as bacterial vaginosis (BV). Symptoms of BV are watery, gushy vaginal discharge and a fishy odour.

BV affects approximately 30% of women over their lifetime and for some women it can be a source of ongoing frustration for years.

It's good practice to always see your doctor for a swab to make sure you can identify the imbalance within your vagina before deciding on a course of treatment. Frequent mistreatment (such as Canestan creams for yeast overgrowth) due to incorrect self diagnosis can worsen the microbial imbalances.

The standard medical treatment for bacterial vaginosis is oral antibiotic therapy, sometimes accompanied by an antibiotic vaginal cream. These methods can eradicate BV in some women, however many experience temporary remission followed by another flare within 3 months.

There are two main problems with the standard antibiotic treatments. Firstly, antibiotics kill the unwanted bacteria, however without correcting the underlying imbalance, these bacteria are able to regrow. Secondly, many persistent bacteria can grow a biofilm to protect them from antibiotics.

Holistic assessment of your vaginal microbiome

Do you have recurrent BV, Candida, Herpes, HPV, endometriosis, period pain, infertility, or miscarriages? A holistic assessment of your vaginal microbiome can be game changing.

The aim is to:

  • track vaginal discharge changes over time

  • test your microbiome profile using next generation sequencing technology

  • identify the underlying cause(s) of your microbiome disruption

  • restore a healthy balance within your vagina

A naturopathic treatment of vaginal dysbiosis involves uncovering and working with the factors that are most likely causing a disruption to your microbiome. This might mean temporarily modifying the way you have sex, or the hygiene practices that go with sex. It may involve changing your underwear, soap, lubricant, or some aspect of your diet.

If you are experiencing high levels of stress in your life, or imbalances in your menstrual cycle, then starting with these aspects of your health can achieve a breakthrough. I like to prescribe herbal remedies (both orally and intravaginally), targeted probiotics and nutritional changes.

The herbal medicines I prescribe for you may be directly affecting your microbiome (such as antimicrobial herbs), or they may be helping your health in other ways. Herbal formulas can assist with managing stress, reducing sugar cravings, balancing symptoms of high estrogen, or supporting women with low estrogen.

I also love to recommend flower essences to assist with the emotional aspects that often accompany vaginal health, sexual health and fertility.

If you would like to learn more about how to support your unique vaginal microbiome, please get in touch. I would love to work with you to improve any aspect of your hormonal or vaginal health.

Simone :)

attention all women over 40!



Hi! I'm Simone Jeffries. I am a naturopath, nutritionist, herbalist and certified wellness coach. I am also a foodie and an advocate for a whole food diet.

I love to support you with hormonal conditions, histamine intolerance and vaginal imbalances.

I welcome clients to consult with me at my clinic in Manly on Sydney's Northern Beaches, or online from anywhere in Australia.

The information in this blog is from my Bachelor of Health Science degree, experience from working with women in my clinic, and continuing research.

This blog is for information only and not intended to take the place of medical advice. Please seek assistance for any medical concerns.


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