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How Your Vaginal Microbiome Shifts Throughout Your Life

Let’s explore how age, hormones, and daily habits influence the vaginal microbiome throughout puberty, pregnancy, and beyond—and learn how to protect this vital ecosystem as the years go on.

8 minutes

31 Citations

The arc of any living thing is one of evolution and transformation. Take the apple: a seed (👋) becomes a seedling, which becomes a tree, which bears buds that turn into blossoms, which contain ovules that are pollinated to eventually become apples, which contain seeds, and on and on. These life cycles happen all over our planet, in millions of distinct and awe-inspiring ways. They also occur within us.

Our microbial worlds are constantly shifting—and nowhere is this more apparent than in the vaginal microbiome (VMB)

The VMB is the community of billions of bacteria, yeasts, and other microorganisms residing within the vaginal canal.1,2 These microbes ensure the stability of your vaginal pH, protect you against infections such as bacterial vaginosis, and can even reduce your risk of certain cancers.3-5 And, just as you grow and change over time, the composition of your VMB naturally shifts—by the year, month, and even the day—in response to hormones and various disruptors. 

These microbial transitions are natural, but sometimes they can bring about unwanted changes or signal medical concerns—which is why body literacy and attention to symptoms are vital. “Typically, these shifts happen and the body is able to get back to homeostasis…It’s when you’re not able to get back to that normal that problems can arise,” explains Michelle Davison, Ph.D., a microbiologist and Senior Scientist at Seed.  

Read on to learn how age, hormones, and daily habits can influence the vaginal microbiome, and how to protect yours through all phases of life. 


The vaginal microbiome begins to form during and after birth, as an individual inherits their first microbes from their biological mother through a process called “seeding.”6 From there, this community of microbes develops into a fairly diverse, steady-state community that exists until the first major disruption: puberty.7 

Puberty is an unruly time for a whole host of reasons (all the feelings!), but for people with vaginas, it is the increase in estrogen and progesterone that causes the biggest fluctuations.8 These two hormones conspire to re-shape the vaginal microbiome; it goes from containing a few different bacterial species to heavily favoring a single species called Lactobacillus.9 

This happens because the progressive increase in estrogen during puberty triggers an increase in glycogen deposits in epithelial cells, which form the inner lining of the vagina.10 Since lactobacilli feed on glycogen, puberty is essentially a feeding frenzy for these bacteria, which begin to outcompete other species and change the composition of the VMB to be Lactobacillus dominant.

Lactobacilli (specifically the particular species, Lactobacillus crispatus) help maintain a protective, homeostatic vaginal microbiome by creating a moderately acidic environment that’s inhospitable to various bacterial foes and pathogens.11

However, many everyday disruptors can throw off the composition of lactobacilli in the VMB—one of which is menstruation.


While the composition of the VMB ebbs and flows from puberty to postmenopause, menstruation is a microcosm of this pattern. The makeup of your VMB can shift day-to-day during menstruation, depending on where you are in your cycle.12 

During the first week of the menstrual cycle, systemic estrogen levels are low. As estrogen begins to rise before ovulation, it precipitates a thickening of the vaginal epithelium and the production of glycogen. This feeds the lactobacilli needed to produce lactic acid and create a protective vaginal microenvironment.13

This means that when estrogen is in low supply during the menstrual cycle, it can disrupt the growth and stability of lactobacilli and make the vagina more prone to infection, sending it into a non-optimal Community State Type (CST).

In addition to these hormonal variations, menstrual blood increases the pH levels of the vagina and is rich in nutrients, including iron, which can serve as a growth factor for some non-optimal bacteria.12 This can lead to a decrease in lactobacilli and leave the VMB vulnerable to pathogens.14 However, this change doesn’t last long: vaginal pH immediately begins to decrease to its normal level once menstruation ends, and studies have shown that vaginal microbiota typically return to baseline within about three days.15

One way you can support your vaginal microbiome during disruptions such as menstruation? Refrain from douching or using synthetic, fragranced cleansers or wipes (this advice applies to every stage of life, actually). Despite what you may have been told, there is nothing “dirty” about menstrual blood, and abrasive cleansing products only further disrupt the VMB.16 As for what you actually need to “clean” the vagina? “Only water has been shown to not disrupt the VMB,” says Dr. Davison. When it comes to caring for the vaginal microbiome, she says, “Less is more.” 

Pre-conception and Pregnancy

Menstruation signals the onset of an individual’s fertile years, and, once again, the vaginal microbiome is instrumental throughout the fertility and pregnancy journey

The type of birth control you choose to use during this time can affect the composition of the VMB. “People who use oral birth control, like the pill, tend to have much more stable microbiomes than people who use other forms of birth control, because the consistent hormones in the pill actually level out fluctuations,” says Dr. Davison.17 

Other methods of birth control, such as intrauterine devices (IUDs), have also been shown to modify the VMB. “Copper IUDs are more correlated with infections like bacterial vaginosis,” says Dr. Davison, “whereas hormonal IUDs tend not to have the same effects.”18 (To note: choosing a method of birth control is an intensely personal decision that should factor in many considerations, not just microbial ones.) 

One of the most fascinating (and fruitful) areas of study when it comes to the vaginal microbiome is its implications for fertility. While this is a fairly new field, studies have shown that a Lactobacillus-dominant vaginal microbiome (specifically, Lactobacillus crispatus-dominant) seems to be associated with a healthy pregnancy and positive birth outcomes including a decreased risk of preterm birth.19-21

How, exactly, vaginal L. crispatus modulate implantation is still unclear. It could be that VMBs with an abundance of lactobacilli and low overall diversity help decrease inflammation in the reproductive tract and/or create an acidic environment that supports embryo implantation in the uterine cavity.22,23 Studies have also shown that bacteria from the VMB can impact everything from the composition of cervical mucus to the ability of a fertilized egg to implant in the uterine lining.24,25 

During pregnancy, the vaginal microbiome undergoes an extraordinary transformation largely influenced by estrogen. This hormone, produced by the ovaries and placenta, surges as the pregnancy advances.26 During the early months, increased estrogen and progesterone gradually shift the vaginal microbiome to become more stable.27 Having a protective vaginal microbiome through pregnancy seems to help fend off infections that may pose risks to both the mother and developing fetus (thanks, anatomy!).28


After delivery, the rapid drop in estrogen (by about 100- to 1000-fold) spurs yet another significant shift in the vaginal microbiome. Approximately six weeks after birth, 40% of postpartum people tend to exhibit a Lactobacillus-depleted vaginal microbiome, dominated instead by species associated with bacterial vaginosis.27 This puts them at greater risk of developing vaginal infections—a risk undoubtedly heightened by the sleep-deprived, high-stress lifestyle of a new parent.10

While the postpartum experience is one of intense change—physical, emotional, social—it is also a vital time when it comes to protecting future pregnancies and fertility. “Everything is changing, but these changes can all mean something. Talk to your OB about what you notice, and ask them for ideas if something seems off,” advises Dr. Davison.


Like so many aspects of the female experience, menopause has been “something of a black box,” in the medical field, says Dr. Davison. Thankfully, researchers are finally now learning more about the changes the body goes through during perimenopause and beyond, and how the vaginal microbiome can help you navigate them. 

Menopause is not abnormal: it is part of the process of living.

Michelle Davison, Ph.D.

Here’s what we know so far: As we age, the body slowly begins to produce less estrogen. Since estrogen plays a role in the production of glycogen (again, a key fuel source for protective lactobacilli), menopausal women tend to have fewer of these bacteria.29 As a result, the vaginal environment can become less acidic during perimenopause, making it more vulnerable to pathogens and infection-causing bacteria.30 Menopausal women tend to be at higher risk of bacterial infections like BV and urinary tract infections for this reason.29 

For some people, certain effects of menopause can be mitigated by a topical estrogen product.31 These can increase the glycogen lining in the vagina, giving lactobacilli the energy source they need to establish dominance in the VMB and reduce the risk of discomfort and infections. 

Above all, says Dr. Davison, communication with your medical team (and with your community) is vital during this time. “Information about the physical and emotional symptoms of menopause should be discussed, to empower women not only with the knowledge of what to expect but to assist in making the best choices for their experience. Menopause is not abnormal: it is part of the process of living.” 

Embracing the Cycles of Life

Your vaginal microbiome forms the basis of your sexual, urogenital, and reproductive health—and it’s always in flux. Knowing your own normal—and, by association, knowing when something feels “off”—is the best thing you can do for your vagina throughout your life.

As we age, the changes our bodies undergo are natural, inevitable, and pretty darn incredible. And once we can accept them, the true education can begin. 


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