Women's Health, Vaginal Microbiome

What Is Vaginal Dysbiosis? Understanding Vaginal Microbiome Imbalance

If you experience recurrent bacterial vaginosis, thrush, unusual discharge, odour, irritation or urinary symptoms, you may have come across the term vaginal dysbiosis.

But what does it actually mean?

Vaginal dysbiosis isn't one specific infection, and it doesn't simply mean that you have “bad bacteria”.

It describes a change or disturbance in the vaginal microbial ecosystem.

That can involve changes in:

• which microorganisms are present

• their relative abundance

• Lactobacillus species and abundance

• vaginal pH

• microbial diversity

• interactions between microorganisms

• the vaginal epithelial environment

• microbial stability and resilience

Importantly, not all vaginal dysbiosis looks the same.

Bacterial vaginosis (BV), aerobic vaginitis (AV), Candida-associated disease, menopause-related changes and the microbial patterns associated with recurrent urinary tract infections can involve very different microbial environments. [1–5]

Understanding those differences is important because treating every vaginal microbiome disturbance in the same way doesn't make biological or clinical sense.

What Is the Vaginal Microbiome?

The vaginal microbiome is the community of microorganisms living within the vaginal environment.

These include bacteria and fungi, together with their genes, metabolites and interactions with the vaginal epithelium and local immune system.

One of the landmark studies in vaginal microbiome science was published by Ravel and colleagues in 2011.

Using molecular sequencing in 396 reproductive-aged women, researchers identified several recurring patterns of vaginal bacterial communities, later widely described using Community State Types (CSTs). [1]

Four of the major communities were dominated by different Lactobacillus species:

• Lactobacillus crispatus

• Lactobacillus gasseri

• Lactobacillus iners

• Lactobacillus jensenii

Another group contained relatively fewer Lactobacillus organisms and a more diverse mixture of anaerobic bacteria. [1]

This research helped change the way we think about vaginal health.

Instead of asking only:

“Which bacteria are present?”

we can also ask:

“What type of microbial community is present, how is it functioning, and how stable is it?”

What Does Vaginal Dysbiosis Mean?

The word dysbiosis broadly describes disruption or alteration of a microbial ecosystem.

In the vagina, this may involve:

• loss or reduction of particular protective Lactobacillus species

• expansion of BV-associated anaerobic bacteria

• increased abundance of aerobic organisms

• altered microbial diversity

• changes in vaginal pH

• altered microbial metabolism

• biofilm formation

• changes in epithelial or inflammatory conditions

• reduced resilience following a disturbance

But vaginal dysbiosis should not be treated as one single disease.

For example:

BV-associated dysbiosis may involve increased anaerobic bacterial diversity and polymicrobial biofilm. [6]

Aerobic vaginitis can involve Lactobacillus depletion, aerobic organisms and significant vaginal inflammation. [4]

Candida-associated disease involves fungal overgrowth and host inflammatory responses and can occur despite Lactobacillus dominance. [5]

Menopause-associated microbial change occurs within a fundamentally different hormonal and epithelial environment. [2,3]

These are not interchangeable conditions.

Is a More Diverse Vaginal Microbiome Healthier?

This is one of the most important concepts to understand.

Usually, not in reproductive-aged women.

In gut microbiome research, greater microbial diversity is often associated with health.

The vagina is different.

In many reproductive-aged women, vaginal health is associated with relatively low bacterial diversity, with one or a small number of Lactobacillus species dominating the community. [1]

A highly diverse vaginal microbiome containing numerous anaerobic organisms can instead be associated with bacterial vaginosis and other dysbiotic states. [1,6]

So the common idea that:

“more microbiome diversity is always better”

does not translate neatly from the gut to the vagina.

The biological context matters.

What Are Vaginal Community State Types?

Community State Types are a research framework used to describe recurring patterns within the vaginal microbiome.

The original five major CSTs described by Ravel and colleagues were: [1]

CST I — Lactobacillus crispatus dominant

Predominantly L. crispatus.

This community is commonly associated with lower vaginal pH and microbial stability.

CST II — Lactobacillus gasseri dominant

Predominantly L. gasseri.

CST III — Lactobacillus iners dominant

Predominantly L. iners.

This is particularly interesting because L. iners can occur in both apparently healthy and dysbiotic vaginal environments. [7]

CST IV — Low Lactobacillus / higher bacterial diversity

This contains relatively fewer Lactobacillus organisms and greater abundance of various anaerobic bacteria.

CST V — Lactobacillus jensenii dominant

Predominantly L. jensenii.

These categories are useful for understanding vaginal ecology.

But an important distinction is:

A Community State Type is not a clinical diagnosis.

For example, CST IV is not automatically synonymous with bacterial vaginosis.

Clinical symptoms, pH, microscopy or Gram stain where available, molecular results and other relevant investigations still need to be interpreted together.

Are All Lactobacillus Species Equally Protective?

Probably not.

This is one of the most fascinating areas of vaginal microbiome research.

Historically, we often spoke about “Lactobacillus” as though all species performed the same function.

They don't.

Four species commonly associated with the vagina include:

• L. crispatus

• L. gasseri

• L. jensenii

• L. iners

But their genomes, metabolic capabilities and ecological behaviour differ.

Lactobacillus crispatus

L. crispatus is frequently associated with a stable, low-pH vaginal environment and has become a major focus of microbiome research.

It produces both D- and L-lactic acid and has several characteristics associated with resistance to colonisation by potentially pathogenic organisms. [8,9]

Lactobacillus iners

L. iners is very different.

It has a relatively small genome, produces L-lactic acid but not D-lactic acid, and can survive across a wider range of vaginal environments. [7]

It is commonly found:

• in healthy vaginal communities

• during transitions between microbial states

• after BV treatment

• alongside BV-associated organisms

This means an L. iners-dominant microbiome isn't necessarily “bad”.

But it also should not automatically be interpreted as equivalent to L. crispatus dominance.

A 2023 review emphasised that L. iners has inconsistent associations with genital-health outcomes and that strain-level differences may be important. [7]

Why Does Lactic Acid Matter?

One important function of vaginal Lactobacillus species is the production of lactic acid.

Lactic acid helps maintain the acidic environment commonly found in reproductive-aged women.

A vaginal pH of approximately 3.5–4.5 is commonly associated with Lactobacillus-dominant communities. [8,10]

But even here, the biology is more sophisticated than simply:

Lactobacillus = acid = healthy.

There are two biologically relevant forms of lactic acid:

D-lactic acid

and

L-lactic acid.

L. crispatus, L. gasseri and L. jensenii can produce D-lactic acid.

L. iners does not. [7–9]

Research has demonstrated significantly higher D-lactic acid concentrations in L. crispatus-dominated vaginal communities compared with communities dominated by L. iners or Gardnerella. [8]

These functional differences may partly explain why different Lactobacillus-dominant communities do not behave identically.

What Is Vaginal Microbiome Resilience?

Another useful concept is resilience.

A healthy microbial ecosystem isn't necessarily one that never changes.

The vaginal microbiome naturally fluctuates.

Changes can occur with:

• menstruation

• sex

• hormonal changes

• antibiotics

• pregnancy

• contraception

• illness

• menopause

The important question may be:

What happens after the disturbance?

One woman's microbiome may temporarily change and then return to its previous Lactobacillus-dominant state.

Another woman's microbiome may transition into a different and more persistent community.

This ability to resist disruption or recover afterwards is sometimes described as microbiome resilience.

Contemporary microbiome research increasingly argues that vaginal health cannot be understood from a single static test alone — temporal stability and functional recovery also matter. [12]

What Can Cause Vaginal Dysbiosis?

There is rarely one universal cause.

Potential influences include:

• antibiotics

• sexual activity

• new sexual partners

• semen exposure

• menstruation

• hormonal changes

• pregnancy and postpartum changes

• breastfeeding

• perimenopause and menopause

• vaginal douching

• fragranced or irritating vaginal products

• smoking

• antimicrobial exposure

• individual microbial characteristics

• host immune and epithelial factors

Importantly, association does not always mean causation.

Two women exposed to the same trigger may experience very different microbial responses.

Can Antibiotics Cause Vaginal Dysbiosis?

They can alter microbial communities.

Antibiotics are extremely important treatments when appropriately indicated.

But antimicrobial therapy can also affect organisms beyond the intended target.

That does not mean antibiotics should be avoided when they are clinically required.

It means repeated antimicrobial exposure should have an appropriate indication.

In recurrent vaginal conditions, I am particularly interested in:

what condition are we actually treating, what treatment is indicated, and what happens to the vaginal ecosystem afterwards?

Can Sex Change the Vaginal Microbiome?

Yes.

Sex can influence the vaginal environment through several mechanisms.

Semen and vaginal pH

Semen is more alkaline than the normally acidic vaginal environment and can temporarily increase vaginal pH.

Microbial exchange

Sexual partners can exchange microorganisms.

This is particularly important in bacterial vaginosis.

The 2025 Australian StepUp randomised controlled trial found that treating women with BV and their ongoing male partners simultaneously substantially reduced BV recurrence compared with treating the woman alone. [13]

Recurrence within 12 weeks occurred in approximately 35% with partner treatment compared with 63% when only the woman was treated. [13]

This has changed Australian BV management.

Current Australian STI Management Guidelines recommend concurrent treatment of an ongoing or regular partner with a penis when treating vaginal BV. [6]

This does not mean every vaginal dysbiosis is sexually transmitted.

Rather, it demonstrates that sexual microbial exchange can be clinically important in some vaginal conditions.

How Do Hormones Affect the Vaginal Microbiome?

Hormones have an important relationship with vaginal ecology.

Oestrogen influences the vaginal epithelium and its biochemical environment.

During reproductive life, oestrogen supports maturation of vaginal epithelial cells and influences glycogen availability.

Microbial metabolism of glycogen-derived substrates contributes to an environment that can support Lactobacillus species and lactic-acid production. [2,10]

But this is not a simple on/off pathway.

The vaginal microbiome changes across the lifespan and may be influenced by:

• puberty

• menstrual cycling

• pregnancy

• postpartum changes

• breastfeeding

• perimenopause

• menopause

• hormonal therapies

What Happens to the Vaginal Microbiome During Perimenopause and Menopause?

This is particularly important.

As oestrogen declines, changes can occur in:

• vaginal epithelial thickness

• glycogen availability

• Lactobacillus abundance

• vaginal pH

• microbial diversity

• tissue elasticity and lubrication

• urinary and vulvovaginal symptoms [2,3]

Postmenopausal women are therefore biologically different from reproductive-aged women when interpreting vaginal microbiome results.

Lower Lactobacillus abundance in menopause does not automatically mean infection.

The clinical context matters.

Genitourinary Syndrome of Menopause (GSM) can cause:

• vaginal dryness

• burning

• irritation

• dyspareunia

• urinary urgency

• dysuria

• recurrent urinary symptoms

and may coexist with microbial changes.

Research also shows that vaginal oestrogen can alter the postmenopausal vaginal microbiome, often increasing Lactobacillus abundance, although microbial changes do not perfectly predict symptom response. [2,3]

Is Bacterial Vaginosis a Type of Vaginal Dysbiosis?

Yes.

BV is probably the best-characterised example of vaginal dysbiosis.

It typically involves:

reduced Lactobacillus dominance → increased anaerobic bacterial diversity → higher vaginal pH → polymicrobial community formation. [6]

BV-associated organisms may include:

• Gardnerella species

• Fannyhessea vaginae

• Prevotella

• Mobiluncus

• Megasphaera

• other BV-associated bacteria

BV can also involve a polymicrobial biofilm attached to vaginal epithelial cells. [6,14]

But BV is not simply:

“too much Gardnerella.”

Gardnerella can occur in women without symptomatic BV.

The wider microbial community and clinical context matter.

Is Aerobic Vaginitis the Same as BV?

No.

This distinction is extremely important.

Aerobic vaginitis (AV) is a different vaginal condition and is often confused with BV.

AV may involve:

• reduced Lactobacillus

• increased aerobic or facultative organisms

• vaginal inflammation

• epithelial disturbance

Organisms associated with AV can include:

• Escherichia coli

• Enterococcus

• Staphylococcus aureus

• Group B Streptococcus

Unlike classical BV, which typically produces relatively little vaginal inflammation, inflammation is a central feature of AV. [4]

The distinction matters because diagnosis and management differ.

Is Recurrent Thrush Caused by Vaginal Dysbiosis?

This needs much more nuance than is often suggested online.

Vulvovaginal candidiasis (VVC) is caused by symptomatic Candida-associated disease, most commonly involving Candida albicans.

Candida can exist in the vagina without causing symptoms.

And importantly:

VVC can occur in women whose vaginal bacterial microbiome remains Lactobacillus dominant.

Recent reviews emphasise that the relationship between Candida and Lactobacillus is complex. [5,15]

Some Lactobacillus strains can inhibit Candida adhesion, growth or virulence in laboratory models.

But human studies have also found VVC and recurrent VVC in Lactobacillus-dominant communities. [15]

Candida also tolerates acidic vaginal conditions considerably better than many BV-associated bacteria.

Therefore, I would not describe recurrent thrush simply as:

“you don't have enough good bacteria.”

RVVC can involve Candida species, host immune responses, hormonal influences, antifungal susceptibility and other individual factors.

That distinction is clinically important.

What Is the Relationship Between the Vaginal Microbiome and Recurrent UTIs?

The vagina and urinary tract are neighbouring microbial ecosystems.

Increasing evidence suggests there is microbial overlap between the two.

Studies using paired vaginal and urinary samples have demonstrated shared organisms, and women with recurrent UTIs may be more likely to have vaginal colonisation with uropathogens such as E. coli. [11]

Reduced vaginal Lactobacillus abundance — particularly in postmenopausal women — has also been associated with increased presence of urinary pathogens. [11]

A comprehensive 2026 review concluded that the vaginal and urinary microbiomes appear closely linked, but also emphasised that there remains a lack of studies specifically examining chronic and recurrent UTI populations. [11]

So this is a promising area of research, but we should not overstate it.

The evidence does not currently justify saying:

“vaginal dysbiosis causes all recurrent UTIs.”

Rather:

Vaginal ecology may be one factor influencing susceptibility to urinary infection in some women.

Does Vaginal pH Tell Me If I Have Dysbiosis?

Vaginal pH can provide useful information, but it is not a diagnosis.

During reproductive life, Lactobacillus-dominant communities are commonly associated with vaginal pH around 3.5–4.5. [8,10]

BV commonly raises vaginal pH above 4.5.

But elevated pH can also occur with:

• menstruation

• semen exposure

• menopause

• trichomoniasis

• other vaginal conditions

And importantly, Candida usually does not produce the same elevated-pH pattern as BV.

So pH can provide a useful clue, but it should be interpreted alongside symptoms and appropriate clinical testing.

Can Standard Vaginal Swabs Detect Dysbiosis?

Sometimes they provide enough information for the clinical question.

Standard testing may identify:

• BV

• Candida

• selected aerobic organisms

• sexually transmitted infections

• other pathogens depending on the test

But routine testing does not necessarily characterise the entire vaginal microbial community.

This is where molecular microbiome testing differs.

What Can Vaginal Microbiome Testing Tell Us?

Molecular vaginal microbiome tests can provide a more detailed profile of organisms detected in a sample.

Depending on the test, this may include:

• Lactobacillus abundance

• individual Lactobacillus species

• Gardnerella

• BV-associated anaerobes

• aerobic organisms

• Candida species

• selected sexually transmitted organisms

• relative or quantitative microbial abundance

This can sometimes provide useful additional information in women with persistent or complex recurrent symptoms.

However, there are important limitations.

Detection does not equal disease.

Finding DNA from an organism does not necessarily mean that organism is causing symptoms.

Relative abundance does not prove causation.

A highly abundant organism is not automatically the cause of the clinical presentation.

CSTs are ecological classifications.

They are not themselves diagnoses.

Commercial microbiome testing does not replace established diagnostic testing.

BV, Candida, STIs, AV and other vaginal conditions still require appropriate clinical interpretation.

For these reasons, I use microbiome testing selectively and in context, rather than treating every organism detected on a report.

What Does “Restoring the Vaginal Microbiome” Actually Mean?

This phrase is used frequently, but it deserves careful definition.

Restoration should not mean:

“kill everything that isn't Lactobacillus.”

The vagina is an ecosystem.

A better clinical question is:

Can we help create an environment associated with longer-term microbial and clinical stability?

For some women — particularly those with recurrent BV — Lactobacillus recovery may be relevant.

The strongest clinical example comes from the LACTIN-V trial.

Women who had completed metronidazole treatment for BV were randomised to receive a specific vaginal Lactobacillus crispatus CTV-05 live biotherapeutic or placebo. [16]

BV recurrence by 12 weeks occurred in approximately:

30% of women receiving L. crispatus

versus

45% receiving placebo. [16]

This provides important proof-of-concept that post-treatment microbial restoration can influence recurrence.

But it does not prove that every probiotic will have the same effect.

Strain, formulation, dose, route and ability to colonise matter.

Do Probiotics Restore Vaginal Dysbiosis?

Sometimes this is presented far too simply.

“Probiotic” is not one intervention.

Different products contain different:

• species

• strains

• doses

• formulations

• routes of administration

A systematic review of Lactobacillus-containing vaginal probiotics found substantial heterogeneity between studies and highlighted the need for better-designed trials. [17]

The LACTIN-V trial provides strong evidence for one specific L. crispatus strain and formulation in recurrent BV. [16]

It should not automatically be extrapolated to every oral or vaginal probiotic sold commercially.

That is why I use the term evidence-informed microbiome strategy, rather than claiming that probiotics universally “restore” the vagina.

Why Can Symptoms Continue When Standard Tests Are Negative?

This is a common and frustrating situation.

A negative routine test doesn't mean symptoms aren't real.

It means the test did not identify the condition it was designed to detect.

Persistent symptoms may require consideration of:

• recurrent or intermittent BV

• Candida, including non-albicans species

• aerobic vaginitis

• STIs

• GSM

• vulval dermatological conditions

• irritant or allergic conditions

• pelvic floor or pain conditions

• other causes of vaginal discharge, burning or urinary symptoms

In selected complex cases, broader microbiome information may add context.

But microbiome testing should not become a substitute for appropriate examination when examination is clinically required.

My Evidence-Informed Approach to Vaginal Dysbiosis

For complex recurrent presentations, I use a clinical framework:

RESET → REBUILD → RESTORE → MAINTAIN → RESCUE

This is my evidence-informed clinical framework for organising complex recurrent cases.

It is not a formally validated vaginal-dysbiosis treatment guideline, and not every patient needs every phase.

RESET — Identify What Is Actually Happening

Before trying to “restore the microbiome”, I want to know what we are treating.

Depending on the presentation, this can involve:

• symptom history

• previous pathology

• vaginal pH

• STI testing

• BV assessment

• Candida testing

• consideration of AV

• hormonal status

• antimicrobial history

• sexual and partner factors

• microbiome testing where clinically useful

If an active condition requires medical treatment, that comes first.

REBUILD — Consider the Post-Treatment Environment

After treating an active condition, I consider what happens next.

Depending on the individual, this may include reviewing:

• Lactobacillus abundance

• Lactobacillus species

• vaginal pH

• previous antimicrobial exposure

• recurrence patterns

• microbiome results where available

For recurrent BV in particular, the L. crispatus literature suggests that post-treatment microbial recovery may influence recurrence. [16]

But the strategy must be individualised.

RESTORE — Address the Broader Vaginal Environment

This is where an integrative approach becomes particularly useful.

I consider factors such as:

• hormones

• perimenopause or GSM

• vaginal pH

• sexual exposure

• partner factors in recurrent BV

• menstruation-related changes

• unnecessary antimicrobial exposure

• vaginal irritants

• general vulvovaginal health

• microbiome-directed interventions where appropriate

The goal is not to manufacture a theoretically “perfect” microbiome.

It is to support clinical and microbial stability.

MAINTAIN — Support Longer-Term Stability

Recurrent conditions often require thinking beyond the next episode.

Maintenance depends entirely on the diagnosis.

For example:

recurrent BV may require partner management or suppressive strategies. [6,13]

RVVC requires an antifungal management strategy rather than simply treating “dysbiosis”. [5,15]

GSM may require addressing the hypoestrogenic vaginal environment. [2,3]

recurrent UTI requires appropriate urinary assessment while recognising that vaginal ecology may be one contributing factor. [11]

There is no universal “vaginal dysbiosis maintenance protocol”.

RESCUE — Know What to Do When Symptoms Return

Finally, women with recurrent symptoms benefit from knowing what to do when something changes.

Rather than automatically assuming:

“my BV is back”

or

“it's thrush again”

a rescue strategy considers:

• the symptom pattern

• likely trigger

• vaginal pH where useful

• whether testing is needed

• whether symptoms differ from previous episodes

• whether another diagnosis needs consideration

• when face-to-face examination is necessary

This can help reduce repeated empirical treatment of the wrong condition.

The Bigger Picture: Vaginal Dysbiosis Is an Ecosystem Problem

The most important thing I want women to understand is that vaginal dysbiosis isn't simply:

“good bacteria versus bad bacteria.”

The contemporary picture is much more sophisticated.

Vaginal health involves interactions between:

microorganisms + Lactobacillus species + microbial metabolites + vaginal pH + epithelial health + hormones + immunity + sexual exposure + antimicrobial exposure + time.

And increasingly, researchers are interested not only in which organisms are present, but also in how the microbial community functions and how resilient it is when disturbed. [12]

That is why two women with superficially similar symptoms can have completely different underlying microbial patterns.

It is also why repeatedly treating symptoms without understanding what keeps changing may not solve the underlying problem.

For women with recurrent or complex symptoms, my approach is to identify the clinical condition first and then consider whether the broader vaginal microbial environment is contributing to recurrence or instability.

About Kylie Sayce NP

Kylie Sayce is an Australian Endorsed Nurse Practitioner with a clinical focus on recurrent vaginal and urinary conditions, vaginal microbiome health and women's sexual and reproductive health.

The Telehealth Clinic provides Australia-wide consultations for women experiencing recurrent BV, recurrent thrush, recurrent UTIs, aerobic vaginitis, persistent vaginal symptoms and vaginal microbiome disturbances.

For women with recurrent or complex symptoms, consultations allow time to review symptom patterns, previous pathology, antimicrobial treatment, sexual and partner factors, hormonal influences, vaginal pH and, where clinically appropriate, comprehensive vaginal microbiome testing.

My clinical approach is evidence-informed and integrative, combining established medical management with careful consideration of vaginal microbial ecology and emerging microbiome science.

Are You Experiencing Recurrent Vaginal Symptoms?

If symptoms keep returning despite treatment — or standard testing hasn't explained what is happening — a comprehensive review can help determine whether BV, Candida, AV, hormonal change or another condition may be contributing and whether further investigation is appropriate.