The Vaginal Microbiome Changes During the Menstrual Cycle
- Mar 17
- 4 min read
Updated: Mar 23
The Vaginal Microbiome Part 2
Many women notice their vaginal symptoms follow a monthly pattern. This is not random. The vaginal microbiome shifts across the menstrual cycle in response to changing hormones and immune activity. In Part 1, I explored how the vaginal microbiome functions as an ecosystem across the lifespan, and why Lactobacillus dominance is central to vaginal health. This is also why Lactobacillus-based probiotics are often used in clinical practice for recurrent thrush, BV, and microbiome disruption. However, the vaginal environment is not regulated by bacteria alone. It is supported by an innate immune system, including antimicrobial factors such as lactoferrin and glycogen, which work alongside beneficial microbes to maintain balance. Microbial populations and immune defences are highly responsive to hormonal changes across the menstrual cycle. In this article, I explore what happens in each phase of the cycle, and why symptoms can appear at predictable times each month like "why do I get thrush when I get my period?".
The Vaginal Microbiome Across the Lifespan
Muhleisen, 2016
How Lactobacillus Dominance Protects the Vagina
A healthy vaginal microbiome is usually dominated by Lactobacillus species. These microbes act as ecological gatekeepers, preventing overgrowth of pathogenic bacteria. They do this several ways:
1. Acidification of the vaginal environment
Lactobacilli ferment a substance called glycogen that is released from vaginal cells into lactic acid, which maintains an acidic vaginal pH of roughly 3.5–4.5. This acidic environment makes it difficult for many pathogens to grow.
2. Direct antimicrobial activity
Many Lactobacillus strains produce antimicrobial compounds that aim to suppress organisms such as Gardnerella, E. coli, and other opportunistic microbes.
3. Competitive exclusion
Beneficial bacteria physically occupy attachment sites on the vaginal surface, making it harder for pathogens to colonise.
4. Immune system modulation
Lactobacilli interact with the vaginal immune system and influence inflammatory signalling, helping maintain a balanced immune response in the genital tract.
Together, these mechanisms explain why our treatment always aims to restore Lactobacillus dominance and stabilise vaginal ecology.
How the Vaginal Microbiome Changes During the Menstrual Cycle
Menstruation
Unless you experience recurring symptoms such as thrush or bacterial vaginosis around your period, you may not realise that the vaginal microbiome naturally fluctuates across the menstrual cycle under the influence of hormones and innate immunity.
During menstruation, both oestrogen and progesterone are at their lowest levels. As the endometrial lining sheds, menstrual blood enters the vaginal environment. This temporarily changes the conditions within the vagina.
Menstrual blood raises vaginal pH and introduces iron. Iron is an important nutrient for many microorganisms, including potentially pathogenic species. As a result, several changes commonly occur during this phase:
Vaginal cells produce less glycogen, the primary fuel source of Lactobacillus species
Lactobacillus numbers temporarily decline in the vagina and cervix
Vaginal pH becomes less acidic, increasing dramatically from 3.5 - 7.4
Microbial diversity increases
Iron becomes available as a potential fuel source for pathogenic microbes
These conditions make the vaginal particularly prone to infection.
When things are working optimally, the body activates protective immune mechanisms during menstruation to protect against infection and pathogen colonisation. One of these is lactoferrin, an antimicrobial protein that plays an important regulatory role by binding iron tightly. By limiting iron availability, lactoferrin helps prevent excessive growth of opportunistic bacteria during menstruation and supports the re-establishment of a healthy microbial balance.
Follicular Phase
As the follicular phase progresses, oestrogen levels rise. Oestrogen stimulates the vaginal epithelium to thicken and increase glycogen production. This glycogen becomes fuel for the Lactobacillus species to regrow and create lactic acid. As lactic acid production increases, vaginal pH becomes more acidic again, creating an environment that discourages pathogen growth.
During this oestrogen-dominant phase, lactoferrin concentrations also increase. Lactoferrin supports vaginal defence through several mechanisms:
It binds iron, limiting microbial access to this nutrient
It has direct antimicrobial activity against bacteria and fungi
It supports the growth of beneficial Lactobacillus microbes
Together, rising oestrogen, increasing Lactobacillus populations, and higher lactoferrin activity help restore the protective microbial environment of the reproductive tract following menstruation.
Ovulatory Phase
Around ovulation, oestrogen reaches its peak. The vaginal epithelium is well supported, glycogen availability and Lactobacillus dominance. The microbiome during this phase is typically at its most stable and protective. Lactobacillus species produce lactic acid and antimicrobial compounds that help maintain a vaginal pH between roughly 3.5 and 4.5. Lactoferrin continues to contribute to mucosal immunity by regulating iron availability and exerting antimicrobial effects.
Luteal Phase
After ovulation, progesterone becomes the dominant hormone. Oestrogen levels decline relative to the follicular phase, and glycogen production in the vaginal epithelium may decrease. During this phase, lactoferrin levels tend to decline, and the vaginal immune environment becomes somewhat less protective compared with the follicular phase. The microbiome may become slightly more variable during this phase, although Lactobacillus species typically remain dominant in healthy individuals. As progesterone falls toward the end of the luteal phase, the menstrual cycle resets and the process begins again.
BUT for some women this increases susceptibility to vaginal dysbiosis or irritation. And this is what we work on in clinic in Bendigo or via telehealth.
Why This Matters
When women experience recurrent vaginal infections, irritation, or microbiome disruption, the underlying issue is often loss of Lactobacillus dominance combined with impaired mucosal defence.
Supporting the microbiome with targeted Lactobacillus probiotics, alongside nutritional and lifestyle strategies that support mucosal immunity, can help restore the ecological balance of the vaginal environment.
My clinical approach aims to:
restore Lactobacillus dominance
re-acidify vaginal pH
support mucosal immunity via lactoferrin and lactic acid
reduce pathogen overgrowth
manage associated risks and diseases such as infertility and endometriosis.
Can we test the vaginal microbiome?
YES! If you experience recurrent thrush, bacterial vaginosis, or unexplained vaginal symptoms, it is now possible to test the vaginal microbiome directly. In clinic we can order specialised testing that analyses the microorganisms present in the vagina, including beneficial Lactobacillus species, opportunistic bacteria, yeasts, and certain viral or sexually transmitted pathogens. The test is performed using a simple vaginal swab at home and helps identify microbial imbalances that may be contributing to symptoms, allowing for a more targeted treatment plan to restore microbial balance and vaginal health.
