Let’s talk about something that doesn’t get nearly enough airtime but affects everything from your libido to your risk of infection to your quality of life—your vaginal microbiome.
If you’re like most women, you’ve probably heard of the gut microbiome. Maybe you’re even taking probiotics or eating fermented foods to support it. But your vagina has a microbiome, too—and just like the gut, when it’s out of balance, your whole body can feel the ripple effects.
So what exactly is the vaginal microbiome? What throws it out of whack (spoiler: it’s not just antibiotics), and what can you do to protect and restore it—especially during the hormone rollercoaster of perimenopause and menopause?
Let’s dive in.
What Is the Vaginal Microbiome?
The vaginal microbiome is the community of microorganisms—mostly bacteria—that live in your vaginal canal. A healthy vaginal microbiome is dominated by Lactobacillus species. These friendly bacteria produce lactic acid, which helps keep the vaginal environment acidic (ideally between pH 3.5 and 4.5). That low pH makes it hard for harmful bacteria, yeast, and pathogens to thrive.
Think of your vaginal microbiome as a bouncer at an exclusive nightclub: if the wrong guests show up, it boots them out. But when the bouncer takes a break (thanks to hormones, medications, or poor lifestyle habits), chaos can erupt.
The Good, The Bad, and The Uninvited
Let’s break it down:
Organisms you want in there:
- Lactobacillus crispatus
- Lactobacillus jensenii
- Lactobacillus gasseri
- Lactobacillus iners (although this one is a bit of a wild card)
These guys help maintain pH, prevent overgrowth of bad actors, and keep your tissues resilient.
Organisms you don’t want taking over:
- Gardnerella vaginalis (linked to bacterial vaginosis)
- Candida albicans (yeast overgrowth)
- Mobiluncus, Atopobium, Prevotella, and other anaerobes
- E. coli and other gut microbes (usually migrate where they shouldn’t)
What Throws Off the Vaginal Microbiome?
Short answer? A lot.
- Hormonal shifts – Especially during perimenopause and menopause, when estrogen levels drop. Estrogen helps maintain vaginal thickness and encourages glycogen production, which feeds good bacteria. Lactobacillus begins to drop when estrogen falls allowing overgrowth of the “bullies on the playground”.
- Antibiotics – These wipe out both good and bad bacteria.
- Douching, scented products, or harsh soaps – Disrupt the balance and raise vaginal pH.
- Sexual activity – Especially unprotected sex with partners whose semen can alter vaginal pH.
- Synthetic underwear or poor airflow – Creates a warm, moist environment bacteria love.
- Diet and blood sugar imbalances – A high-sugar diet can feed yeast and contribute to inflammation.
- Stress – Impacts cortisol, immune function, and mucosal immunity.
What Does an Imbalance Look (or Feel) Like?
Many women are told their symptoms are “just normal aging” or “all in their head,” but let’s clear that up right now.
Common symptoms of imbalance before and after menopause include:
- Itching, burning, or irritation
- Vaginal dryness or pain with sex
- Recurring yeast or bacterial infections
- Unusual discharge (grayish, yellowish, fishy-smelling, or thick and white)
- Increased urinary tract infections
- Urgency, frequency, or discomfort with urination
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The Downstream Effects: It’s Not Just About Discomfort
Vaginal dysbiosis is more than an annoying case of BV or a yeast infection. When the microbiome is out of balance—especially chronically—it can impact your overall health and disease risk in some surprising ways.
Increased Risk of Urinary Tract Infections (UTIs)
A healthy vaginal microbiome acts as a protective barrier against uropathogens like E. coli. When Lactobacillus levels decline, there’s less defense at the vaginal opening, allowing bacteria to travel up the urethra more easily. This is particularly common in postmenopausal women.
Greater Susceptibility to STIs
An imbalanced microbiome—especially one dominated by Gardnerella or Atopobium —is linked to higher risk of acquiring chlamydia, gonorrhea, herpes simplex virus, and even HIV.
Persistent HPV and Cervical Dysplasia
Women with bacterial vaginosis or non-Lactobacillus-dominant microbiomes are less likely to clear HPV, which increases cervical cancer risk.
Inflammation and Systemic Health
A disrupted vaginal microbiome may also fuel systemic inflammation, increasing your risk of chronic conditions like metabolic dysfunction or cardiovascular disease.
Fertility and Pregnancy Complications
Dysbiosis has been linked to infertility, early miscarriage, preterm birth, and low birth weight.
How to Restore (and Maintain) a Healthy Vaginal Microbiome
Your body wants to be in balance. With a little care and smart support, you can help it get there.
Consider Vaginal Microbiome Testing
If you’re dealing with persistent infections, chronic irritation, or are just curious about what’s going on “down there,” vaginal microbiome testing can offer valuable insights. Companies like Tiny Health offer at-home tests that analyze the balance of bacteria, yeast, and pH, giving you a detailed view of your unique microbiome. I regularly use this kind of testing in my practice to create personalized protocols for restoring balance. If you’re interested in testing and tailored support, this is absolutely something I can help you with.
Lifestyle Shifts
- Skip scented soaps and douches
- Use breathable, cotton underwear
- Avoid unnecessary antibiotics
- Balance blood sugar with real, whole foods
- Manage stress with movement, meditation, or breathwork
- Use condoms if not in a monogamous relationship
- Consider vaginal estrogen (postmenopause)
Supplements That Can Help
- Targeted probiotics – Look for L. rhamnosus GR-1 and L. reuteri RC-14
- Boric acid suppositories – Helpful short-term for yeast or BV
- Vitamin D – Supports vaginal tissue and immune balance
- Omega-3s – Reduce inflammation
- Vaginal moisturizers – Especially those with hyaluronic acid
Final Thoughts
Your vaginal microbiome isn’t just about comfort or avoiding infection—it’s a window into your overall health. And in midlife, when hormones shift and inflammation creeps up, supporting this tiny ecosystem can make a big impact on how you feel and function.
Let’s stop ignoring this overlooked ecosystem. Instead, let’s give it the support it needs to do what it’s designed to do: protect, restore, and help you thrive.
References
- Stapleton AE. The Vaginal Microbiome, Urinary Tract Infection and Antibiotic Resistance. Front Cell Infect Microbiol. 2022;12:879595. doi:10.3389/fcimb.2022.879595
- Gosmann C, Anahtar MN, Handley SA, et al. Lactobacillus-deficient cervicovaginal bacterial communities are associated with increased HIV acquisition in young South African women. Lancet Infect Dis. 2017;17(12):1240-1249. doi:10.1016/S1473-3099(17)30461-8
- Mitra A, MacIntyre DA, Marchesi JR, et al. The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia: what do we know and where are we going next? BJOG. 2020;127(2):221-230. doi:10.1111/1471-0528.15951
- Wang J, Jia H. Metagenome-wide association studies: fine-mining the microbiome. Nat Rev Microbiol. 2016;14(8):508-522. doi:10.1038/nrmicro.2016.83
- Ma B, Forney LJ, Ravel J. Vaginal microbiome: rethinking health and disease. Annu Rev Microbiol. 2012;66:371-389. doi:10.1146/annurev-micro-092611-150157
Dr. Anna Garrett is a menopause expert and Doctor of Pharmacy. She helps women who are struggling with symptoms of perimenopause and menopause find natural hormone balancing solutions so they can rock their mojo through midlife and beyond. Dr. Anna is the author of Perimenopause: The Savvy Sister’s Guide to Hormone Harmony. Order your copy at www.perimenopausebook.com.
Dr. Anna is available for 1-1 consultation. Find out more at www.drannagarrett.com/lets-talk
