The Vaginal Microbiome Across the Lifespan: Puberty, Fertility and Menopause
- Amy Simpson
- Jan 28
- 5 min read
Updated: 15 hours ago
For over a century, research has shown that the bacteria living in the vagina play a critical role in maintaining vaginal health. When this ecosystem is balanced, it supports normal pH, tissue integrity, fertility, and protection against infections like bacterial vaginosis (BV), thrush, and UTIs. When it becomes disrupted, a state known as dysbiosis, the consequences can extend far beyond discomfort, influencing reproductive health, gynaecological outcomes, and quality of life across all stages of life.
While the vaginal microbiome is important at every age, it becomes especially significant during menopause. As oestrogen levels decline, profound shifts occur within the vaginal environment. These hormonal changes alter glycogen availability (food source for favourable microbial species which relies on oestrogen), tissue thickness, and local immune signalling, creating conditions that favour a loss of protective Lactobacillus species. For many women, this biological shift manifests as vaginal dryness, burning, recurrent infections, pain with intercourse, and symptoms commonly grouped under vulvovaginal atrophy or the newer term, genitourinary syndrome of menopause.
In this article, I show you how the vaginal microbiome changes across the lifespan, especially vaginal dryness after menopause and postpartum. I'll unpack how declining oestrogen reshapes the vaginal ecosystem, how these shifts relate to common symptoms, and introduce naturopathic treatments for vaginal dryness after menopause and how targeted probiotics may help restore and maintain microbial balance and vaginal health across the lifespan.
Childhood and pre-puberty
Prior to puberty, oestrogen production is minimal. As a result, glycogen levels within the vaginal tissue are low, microbial diversity is higher, and vaginal pH is more alkaline. During this stage, the vaginal epithelium is thin and stratified, with minimal mucus coverage, offering less structural and microbial protection. This is fine for most kiddos, but some can develop recurrent childhood UTIs, thrush, and BV and need naturopathic support - usually microbiome testing and targeted probiotic support. For everyone else, the most significant shift in the vaginal microbiome occurs at puberty. As oestrogen levels rise, glycogen content within the vaginal epithelium increases, creating an environment that supports the growth of lactic acid-producing bacteria, particularly Lactobacillus species. This transition establishes a more acidic, resilient vaginal ecosystem that plays a central role in protection against infection and inflammation throughout the reproductive years. We are now learning that the microbiome also plays a critical role in fertility.
The adult vaginal microbiome (pre-menopausal)
The vaginal microbiome is dynamic and changes across a woman’s life. Age, menstrual status, and circulating oestrogen levels all shape the bacterial community of the vagina, alongside lifestyle factors such as smoking, sexual activity, and access to hygiene. In 'normal' circumstances, as a menstruating adult, the vaginal microbiome is usually dominated by beneficial Lactobacillus species and thick, plump labia. While many bacteria naturally live in the vagina and vulva, Lactobacillus plays a key protective role and is strongly associated with vaginal health.
Lactobacillus bacteria produce lactic acid and hydrogen peroxide, creating an acidic environment that helps prevent the overgrowth of other harmful microbes. When this balance is disrupted and Lactobacillus levels fall, dysbiosis can occur, most commonly presenting as bacterial vaginosis (BV). BV has been linked to a range of gynaecological and reproductive health concerns across the lifespan and is very uncomfortable.
Modern microbiome research shows that pre-menopausal vaginal ecosystems tend to fall into a small number of patterns, known as community state types. These patterns vary between individuals, meaning there is no single “normal” vaginal microbiome. However, higher diversity usually correlates with higher symptoms, pain, infections, and discomfort.
Oestrogen plays a central role in maintaining this balance during the fertile years. Higher oestrogen supports glycogen availability, a thicker vaginal lining, and a protective mucus layer. Glycogen fuels Lactobacillus, which in turn maintain an acidic, antimicrobial environment. Together, hormones, tissue health, and beneficial bacteria form a self-reinforcing system that protects vaginal health throughout the reproductive years.
The post menopause vagina, dryness, atrophy, and the microbiome
Menopause triggers significant changes in both the structure of the vaginal tissue and the vaginal microbiome, largely driven by falling oestrogen levels. As oestrogen declines, the vaginal lining becomes thinner, glycogen levels drop, and protective Lactobacillus bacteria decrease. Together, these changes contribute to a cluster of symptoms known as the genitourinary syndrome of menopause (GSM), previously referred to as vulvovaginal atrophy.
GSM can affect the vulva, vagina, and urinary tract. Common symptoms include vaginal dryness, burning, irritation, reduced lubrication, pain with sex, urinary urgency, discomfort with urination, and recurrent urinary tract infections. These symptoms are extremely common, with nearly half of menopausal women reporting bothersome vaginal dryness alone.
While declining oestrogen is the primary driver, research increasingly shows that the vaginal microbiome plays a key role in symptom severity. Women with fewer symptoms tend to have vaginal communities dominated by Lactobacillus species and low bacterial diversity. In contrast, women with more severe dryness, pain, and chronic infection (thrush, UTI, BV) often have reduced Lactobacillus and higher microbial diversity of species that are not associated with good health. This shift away from a Lactobacillus-dominant microbiome is consistently associated with greater vaginal discomfort and poorer vaginal health after menopause.
A note on postpartum
During the postpartum period and while breastfeeding, oestrogen levels remain low, creating a vaginal environment that can closely resemble genitourinary syndrome of menopause (GSM), with a thinner vaginal lining, reduced glycogen, lower Lactobacillus levels, and symptoms such as dryness, discomfort, pain with sex, and increased urinary irritation.
There is help available. You don't need to suffer or wait until you finish breastfeeding to find relief.
How to treat menopause dryness and pain.
Assess the vaginal microbiome using a comprehensive, clinically relevant test where appropriate. See a sample test here.
Consider the oral, gut, and vaginal microbiomes as an interconnected system rather than in isolation.
Use targeted oral and topical probiotics selected for your individual symptoms and life stage.
Support beneficial bacteria with appropriate “fuel” sources to encourage healthy colonisation of the vulva and vagina.
Provide internal and topical herbal support to promote tissue repair, hydration, mucosal integrity and reduction in atrophy.
Review environmental and lifestyle factors that influence vulvovaginal health, including soaps, laundry products, underwear fabrics, tight clothing, moisture exposure, and sweating.
Review sexual and menstrual health practices, including the selection of appropriate lubricants and products that support rather than disrupt the vaginal environment.
Don't accept vagina atrophy and menopause aging as "just apart of aging"
If you’re navigating menopausal vaginal dryness, discomfort, or urinary changes during menopause, you don’t have to push through it or accept it as “just part of ageing.” With the right support, the vaginal microbiome and tissues can be gently restored, improving comfort, intimacy, and quality of life. If you’d like personalised guidance, I invite you to book a one-on-one consultation where we can address the root causes and create a targeted plan that works for your body and life stage.
If this feels like an uncomfortable or taboo topic, please know you’re not alone, and you’re not overreacting. Vaginal pain and dryness can be deeply distressing, especially when it’s so severe that even prescribed treatments feel unbearable, or it is too painful to use the pessary prescribed by the pharmacist or GP. My clinic is a safe, respectful space to talk about these symptoms openly, and there is gentle, effective support available for where you are at (we don't need to use pessaries, if you can't right now). We deserve to navigate this sensitive topic pain-free and with dignity.
