The Vaginal Microbiome
Lactobacillus dominance, community state types, and clinical implications.
What's covered
By the end of this module you will be able to
- L01Describe the five community state types and their clinical significance.
- L02Explain why L. crispatus is considered protective while L. iners is ambiguous.
- L03Outline the relationship between BV, increased STI risk, and preterm birth.
- L04Discuss the implications of racial variation in CST prevalence for clinical research.
What you should walk away believing
- →A 'healthy' vaginal microbiome is Lactobacillus-dominant — but not all Lactobacillus species are equal.
- →BV is not a simple infection; it's a polymicrobial dysbiosis that recurs because the biofilm persists.
- →CST-IV (diverse, non-Lactobacillus) is more common in Black and Hispanic women — research frameworks must account for this without pathologizing normal variation.
What this means for you
A healthy vagina is normally dominated by Lactobacillus bacteria that produce lactic acid, keeping the environment acidic and protective. When this balance is disrupted — by antibiotics, douching, or other factors — it can lead to bacterial vaginosis, which increases the risk of STIs and pregnancy complications. Not all disruptions cause symptoms, and not all need treatment.
Classify vaginal microbiomes by CST: I (L. crispatus, most protective), II (L. gasseri), III (L. iners, transitional/ambiguous), V (L. jensenii), IV (diverse anaerobes, BV-associated). L. iners (CST-III) can coexist with BV-associated bacteria and may facilitate transition to CST-IV. BV recurrence (~50% at 12 months post-antibiotics) is driven by Gardnerella biofilm persistence — antibiotics suppress but rarely eradicate.
Lactic acid exists in D and L isomers; L. crispatus produces both, while L. iners produces primarily the less-protective L-isomer. D-lactic acid has stronger HIV virucidal activity. Multi-omic studies (metabolomics + metagenomics) are revealing that functional output matters more than taxonomic composition — two women with similar 16S profiles can have different metabolomic landscapes and clinical outcomes.
Douching helps maintain vaginal health.
Douching disrupts the Lactobacillus-dominant community and is associated with increased BV, STI, and PID risk. Every major gynecological society advises against it.
Recurrent BV in a 28-year-old
A 28-year-old woman presents with her fourth episode of bacterial vaginosis in 12 months. Each episode resolved with metronidazole but recurred within 8 weeks. She asks about vaginal probiotic suppositories she saw advertised on Instagram and wants to know about 'vaginal microbiome transplant.'
How would you explain BV recurrence mechanisms, evaluate the evidence for vaginal probiotics, and counsel on the current state of vaginal microbiome transplantation?
What the data says
Engstrand & CTMR — Karolinska Institutet
The Centre for Translational Microbiome Research (CTMR) at Karolinska Institutet, led by Professor Lars Engstrand, has produced some of the most clinically relevant vaginal microbiome research in recent years. Their work combines large population-based cohorts, longitudinal sampling, and strain-level genomics to bridge the gap between microbiome science and clinical decision-making.
Showed that L. crispatus–dominant communities correlate with lower HPV prevalence in vaccinated women — suggesting that microbiome screening could complement vaccination strategies and help identify women at higher risk of persistent HPV infection.
Demonstrated that a panel of host microRNAs can predict vaginal community state type without sequencing — potentially enabling cheap, PCR-based dysbiosis screening in routine gynaecological visits, bringing microbiome assessment closer to standard care.
Recruited 4,043 women from Sweden's national cervical screening program — one of the world's largest vaginal microbiome cohorts. Linked to national health registries, it will define population-level 'normal' variation and reveal how age, hormones, and lifestyle shape vaginal communities over time.
Proved that three strategically timed samples are enough to classify a woman's long-term microbiome pattern. This finding makes clinical microbiome monitoring practical — you don't need continuous sampling, just smart sampling.
Went beyond species to show that microdiversity within L. crispatus populations predicts preterm birth — women with more diverse L. crispatus strains had higher risk. Standard 16S tests miss this signal entirely, arguing for deeper genomic profiling in obstetric risk assessment.
First Nordic longitudinal study tracking the microbiome through IVF treatment. Found that pre-transfer microbiome composition influences implantation success, supporting the emerging case for microbiome screening before assisted reproduction.
Taken together, the CTMR body of work supports three clinical directions: (1) vaginal microbiome screening as a complement to HPV testing and fertility workup; (2) strain-level profiling rather than species-level reporting for obstetric risk; and (3) longitudinal monitoring with minimal sampling burden. These studies are shifting the vaginal microbiome from a research curiosity to a clinically actionable biomarker.
Test yourself
Spaced review
Key terms & abbreviations
- Community state typeCST
- Classification of vaginal microbiome composition based on dominant Lactobacillus species or diverse anaerobic community.
- Bacterial vaginosisBV
- Polymicrobial dysbiosis characterized by depletion of Lactobacillus and overgrowth of anaerobes including Gardnerella.
Optional deeper dive
- Vaginal microbiome of reproductive-age women — Ravel J et al., PNAS 2011↗
- Vaginal microbiota composition and HPV prevalence in young Swedish women — Norenhag J et al., Int J Cancer 2020↗
- •Studied 345 young Swedish women to map vaginal microbiome types alongside HPV status.
- •Women with L. crispatus–dominant communities had lower rates of HPV infection.
- •Gardnerella and L. iners were linked to higher HPV detection — suggesting the microbiome influences viral persistence.
- •High HPV vaccination coverage in the cohort allowed clearer separation of microbiome effects from vaccine effects.
- A MicroRNA gene panel predicts the vaginal microbiota composition — Cheng L et al., mSphere 2021↗
- •Identified a set of tiny RNA molecules (microRNAs) in vaginal fluid that predict which bacterial community a woman has.
- •This could lead to a simple, cheap lab test for vaginal dysbiosis — no DNA sequencing needed.
- •The host's own cells produce these RNAs, meaning your body 'knows' its microbiome and responds to it.
- •Opens the door to PCR-based screening that could be done in routine gynaecological visits.
- The VaMiGyn study — a population-based Swedish cohort of 4,043 women — Norenhag J et al., npj Womens Health 2025↗
- •One of the world's largest vaginal microbiome studies, recruiting over 4,000 women from Sweden's national cervical screening program.
- •Covers a wide age range, capturing effects of hormonal contraception, menopause, and lifestyle on vaginal bacteria.
- •Linked to Sweden's national health registers, enabling long-term follow-up of gynaecological outcomes.
- •Provides a population-level reference for what 'normal' vaginal microbiome variation looks like.
- Longitudinal sampling reveals intra-individual stability and inter-individual variation — Fransson E et al., Microbiome 2024↗
- •Tracked the same women's vaginal microbiomes repeatedly over months to see how stable they are.
- •Found that most women maintain a consistent bacterial community over time — your microbiome 'type' is fairly stable.
- •L. crispatus communities were the most stable; L. iners communities were more likely to fluctuate.
- •Just three well-timed samples were enough to classify a woman's long-term microbiome pattern.
- Microdiversity of the vaginal microbiome is associated with preterm birth — Norenhag J et al., Nat Commun 2023↗
- •Even among women who all had L. crispatus, subtle strain-level differences predicted preterm birth risk.
- •It's not just which species you have — it's which exact strain, down to fine genetic differences.
- •This means standard microbiome tests (which report species) may miss clinically important variation.
- •Suggests future screening could use strain-level profiling to identify high-risk pregnancies early.
- Longitudinal analysis of vaginal microbiota during IVF and early pregnancy — Norenhag J et al., Microbiol Spectr 2024↗
- •First Nordic study to track vaginal bacteria through IVF treatment and into early pregnancy.
- •Found that the microbiome before embryo transfer may influence whether implantation succeeds.
- •Hormonal stimulation during IVF changed vaginal communities in some women — a previously under-recognized effect.
- •Supports the idea that microbiome screening before IVF could help improve success rates.