Understanding the Intimate Microbiome: Key Bacteria Every Woman Should Know

When it comes to vaginal health, microbes aren’t just present, they are essential. The vaginal microbiome is a delicate yet dynamic ecosystem made up of bacteria, yeast, and other microorganisms that work in harmony to maintain pH, protect against infection, and support overall reproductive health¹.

But this microbial system is easily influenced by hormones, stress, antibiotics, hygiene, and even the menstrual cycle². Some microbes protect us. Others, when they grow unchecked, can disrupt balance and cause discomfort or infection.

This guide covers five key microbial players including the good, the bad, and the opportunistic along with tips on how to recognise when things go off balance.

 

What are the common microbes found in the vaginal microbiome?

 

Lactobacilli – The Bodyguards Of The Microbiome

Lactobacilli are Gram-positive, rod-shaped bacteria that dominate healthy vaginal microbiomes. They produce lactic acid, maintaining an acidic vaginal pH (3.8–4.5) that prevents the growth of pathogens like E. coli, Gardnerella vaginalis, and Candida species³.

Key species:

• L. crispatus
• L. jensenii
• L. gasseri
• L. iners
  

These commensals rely on oestrogen to colonise the vaginal lining and generate acid. Disruptions from antibiotics, menopause, or hormonal shifts lead to imbalance and vulnerability⁴.

 

 

Gardnerella – The uninvited guest

Gardnerella vaginalis is a Gram-variable bacterium that often exists harmlessly in the vaginal microbiome in low numbers. However, when Lactobacilli decline, whether due to stress, antibiotics, menstrual blood, or hormonal fluctuations. Gardnerella can overgrow and disrupt the pH, tipping the ecosystem toward bacterial vaginosis (BV)⁶.

 

Symptoms of BV include:

• Thin, greyish-white discharge that may be more noticeable after sex
• A strong fishy odour, especially post-intercourse (due to amine release when semen mixes with BV flora)
• Vaginal irritation, burning, or itching, often with no visible redness
• Sometimes no symptoms at all, making it underdiagnosed in some individuals

 

Figure 2: Gardnerella vaginalis (source: Wikipedia⁷)

 

It forms biofilms that make it resistant to treatment and prone to recurrence⁸. Its prevalence is higher around the onset of sexual activity and menstruation due to iron exposure.

 

E. coli – The Invader

Escherichia coli (E. Coli) is a Gram-negative bacterium primarily found in the intestines. While a normal amount in the gut can be harmless, it becomes problematic when it enters the urinary or vaginal tract, commonly causing UTIs⁹.

 

E. coli often make their way to the intimate area from the anus, transferring via the perineum. As women have no external genitalia, and a much shorter urinary tract than men, bacteria can easily transfer and enter the urovaginal system, especially when lactobacilli are low and the vaginal environment is less acidic¹⁰. Once introduced, they disrupt the microbiome and may lead to infections causing painful urination, smelly pee, urgency, and pelvic discomfort - getting rid of the infection often involves the use of antibiotics.

 

Candida – The Opportunistic Overgrower

Candida albicans is a yeast that normally lives harmlessly in the body. But antibiotics, high oestrogen, or diabetes can cause it to overgrow, leading to vulvovaginal candidiasis (yeast infection)¹¹.

Symptoms:

• White, thick discharge
• Intense itching
• Redness or swelling
  
  

Managing sugar intake and restoring microbiome balance with probiotics may help prevent recurrence¹².

 

How Do You Know If Your Microbiome Is Suffering Due To Imbalance?

Your vaginal microbiome is like a tiny, intelligent ecosystem. When it’s in balance, you often feel nothing at all. But when something disrupts it (like antibiotics, hormonal shifts, stress, or harsh products), your body sends signals that it’s out of sync.

 Here's what to watch for:

• Unusual discharge - Discharge that is grey, yellow, greenish, or clumpy like cottage cheese can signal an imbalance. While some discharge is normal, sudden changes in colour, consistency, or amount are a red flag.
• Strong or foul odour - A fishy smell, particularly after sex, may indicate bacterial vaginosis, while a yeasty or bread-like scent can be a sign of Candida overgrowth.
• Itching, burning, or redness - These symptoms often suggest irritation, yeast infections, or a rise in pathogenic bacteria. Persistent discomfort can indicate an ongoing inflammatory response or pH imbalance.
• Dryness or general discomfort - Often overlooked, vaginal dryness can be linked to declining oestrogen levels (especially during perimenopause or menopause).
• Recurring UTIs or yeast infections - If you’re getting UTIs or yeast infections multiple times a year, it may be a sign your microbiome is chronically disrupted, particularly if antibiotics or hormonal contraception are involved.
• Pain or discomfort during sex (dyspareunia) - This could stem from inflammation, dryness, or tissue sensitivity caused by microbial shifts. It may also be linked to atrophic vaginitis if oestrogen is low¹³.

 

Note : Talk to your healthcare provider if these symptoms persist. Taking a swab and checking the composition of your microbiome can offer further insights.

How Can You Look After Your Microbiome? The Key Is Balance

Your vaginal microbiome is not just a passive system, it’s a living, responsive ecosystem that protects you every single day. Understanding the key players, both good and bad can help you make more informed choices about your health and your body. From the protective power of Lactobacilli, to the disruptive nature of Gardnerella and E. coli, and the revolutionary potential of Bdellovibrio bacteriovorus, it’s clear that microbiome care is entering an exciting new chapter.

Whether you're dealing with recurring infections or simply want to feel more in tune with your body, remember: you deserve comfort, clarity, and science that works for you—not against you. Don’t hesitate to speak up, seek support, and explore solutions that restore balance without compromise.

 

References

1. Ma, B., Forney, L. J., & Ravel, J. (2012). Vaginal microbiome: Rethinking health and disease. Annual Review of Microbiology, 66, 371–389. https://doi.org/10.1146/annurev-micro-092611-150157
2. Brotman, R. M. (2011). Vaginal microbiome and sexually transmitted infections: An epidemiologic perspective. Journal of Clinical Investigation, 121(12), 4610–4617. https://doi.org/10.1172/JCI57172
3. Martin, D. H. (2012). The microbiota of the vagina and its influence on women’s health and disease. The American Journal of the Medical Sciences, 343(1), 2–9. https://www.amjmedsci.org/article/S0002-9629(15)31063-6/abstract
4. P.Happi: What is the impact of menopause on oestrogen? https://p-happi.com/blogs/phappi-blog/what-is-the-impact-of-menopause-on-estrogen
5. International Probiotics Association. (n.d.). Lactobacillus acidophilus. https://internationalprobiotics.org/home/lactobacillus-acidophilus/\
6. Schwebke, J.R., & Desmond, R. A. (2007). A longitudinal study of bacterial vaginosis. American Journal of Obstetrics and Gynecology, 196(2), 214.e1–214.e7. https://doi.org/10.1016/j.ajog.2006.11.002
7. Wikipedia. https://en.wikipedia.org/wiki/Gardnerella_vaginalis
8. , A., et al. (2005). Adherent biofilms in bacterial vaginosis. Obstetrics & Gynecology, 106(5), 1013–1023. https://doi.org/10.1097/01.AOG.0000183594.45524.d2
9. Foxman, B. (2010). The epidemiology of urinary tract infection. Nature Reviews Urology, 7(12), 653–660. https://doi.org/10.1038/nrurol.2010.190
10. Brannon, J. R., & Hadjifrangiskou, M. (2016). The arsenal of pathogens: Virulence factors of uropathogenic E. coli. Current Opinion in Microbiology, 29, 66–73. https://doi.org/10.1016/j.mib.2015.11.005
11. Sobel, J. D. (2007). Vulvovaginal candidosis. The Lancet, 369(9577), 1961–1971. https://doi.org/10.1016/S0140-6736(07)60917-9
12. Mendling, W. (2016). Vaginal microbiota. In W. R. Mayers (Ed.), Advances in Experimental Medicine and Biology, 902, 83–93. https://doi.org/10.1007/978-3-319-31248-4_8
13. Nasioudis, D., Forney, L. J., Schneider, G. M., & Bongiovanni, A. M. (2017). The role of probiotics in gynecological health. Frontiers in Cellular and Infection Microbiology, 7, 145. https://doi.org/10.3389/fcimb.2017.00145