Vaginal Microbiome

Understand the microbial ecosystem of vaginal and reproductive samples

From women’s health and reproductive outcomes to its correlation with sexually transmitted infections (STIs) and therapeutics, our sequencing workflows support advanced clinical and academic research. We provide 16S rRNA gene sequencing, ITS fungal profiling, shotgun metagenomics, qPCR quantification, and advanced bioinformatics tailored to the unique community dynamics of the vaginal microbiome.

Clinical & Self-Collection: Optimized workflows compatible with both clinician-led and validated at-home self-collection kits
Contamination Control: Strict cross-contamination mitigation strategies to handle varying biomass and diversity levels
Total Quantification: qPCR bacterial quantification to gauge initial sample amplification and absolute abundance
Advanced Bioinformatics: Expert bioinformatic pipelines with a firm understanding of vaginal ecosystem profiles

EXPLORE SERVICES

Understand the microbial ecosystem of oral and saliva samples

1000+

samples processed

Fast

Results in 6 weeks

16S rRNA & ITS2

Gene sequencing

Global CROs | Pharma R&D | Women’s Health Researchers | Clinical Trial Coordinators

Every Vaginal Study, Analyzed with Confidence

From comfortable and compliant sample collection through advanced bioinformatics interpretation, our team delivers optimized workflows designed to accommodate patient sensitivities and study objectives

Healthy Vaginal Microbiome Profiling

Characterize Lactobacillus-dominated communities and establish healthy baseline microbiome profiles.

Bacterial Vaginosis & Dysbiosis Research

Investigate microbial imbalances associated with bacterial vaginosis (BV), candidiasis, and other vaginal infections.

STI & Women’s Health Studies

Explore microbial signatures linked to sexually transmitted infections (STIs) and overall vaginal health

Fertility & Pregnancy Research

Study the relationship between the vaginal microbiome, fertility, implantation, pregnancy outcomes, and preterm birth risk.

Clinical Trials & Product Validation

Evaluate probiotics, microbiome therapeutics, feminine hygiene products, and other interventions using validated microbiome analysis.

Longitudinal & Population Studies

Monitor microbiome changes over time, across menstrual cycles, treatment responses, and diverse patient cohorts using standardized sampling protocols.

Choose the Right Vaginal Microbiome Analysis Approach

Different research questions require different sequencing technologies. We help you select the most appropriate workflow based on sample type, study goals, taxonomic resolution, and functional insights.

16S rRNA Gene Sequencing for Bacterial Profiling

A cost-effective method for profiling bacterial communities, optimized to handle variations in biomass.

Vaginal bacterial diversity and community state type (CST) profiling
Probiotic and feminine hygiene product efficacy studies
Bacterial Vaginosis (BV) and dysbiosis research
Longitudinal monitoring across clinical cohorts

ITS Sequencing for Vaginal Mycobiome Analysis

Characterizes fungal communities that play an important role in vaginal health and opportunistic conditions like candidiasis.

Vaginal fungal diversity and yeast population mapping
Investigating complex bacterial-fungal interactions in the vaginal tract
Chronic vulvovaginal candidiasis (VVC) research
Combined bacterial and fungal community analysis

Shotgun Metagenomic Sequencing

Provides species-level taxonomic resolution together with functional gene analysis for comprehensive health insights.

High-resolution microbial and strain-level profiling (e.g., Lactobacillus species differentiation)
Functional metabolic pathway mapping within the reproductive tract
Antimicrobial resistance (AMR) gene detection and surveillance
Integrated taxonomic and functional vaginal microbiome mapping

Vaginal Microbiome Bioinformatics & Data Analysis

Comprehensive analysis pipelines transform challenging sequencing data into publication-ready biological insights.

Community State Type (CST) classification and diversity analysis
Functional pathway annotation and metabolic mapping
Differential abundance analysis with rigorous quality filtering
Statistical reporting and high-quality visualizations

Protocol

Vaginal samples are extracted using the Macherey-Nagel NucleoMag DNA Microbiome Kit, optimized for high-throughput extraction using the ThermoFisher KingFisher automated robot. A robust bead-beating step is integrated into the protocol to ensure full lysis of robust or cell-wall-heavy microbes.

To maximize yields and protect delicate samples, we optimize starting materials while ensuring absolute sample integrity. All samples are processed under a bio safety cabinet to eliminate environmental contaminants and prevent cross-contamination.

Choosing the Right Collection Method for Your Study

Use validated in-clinic or at-home self-collection kits for reliable vaginal microbiome sampling. Dry swabs provide maximum DNA recovery and should be stored at -80°C and shipped on dry ice, while liquid buffer collection kits (such as Norgen Biotek or DNA Genotek OMNIgene.VAGINAL) remain stable at room temperature and can be shipped without dry ice (unless frozen). Collection involves gently swabbing the vaginal walls as directed, securing the sample in the collection device, and storing it according to the kit instructions. All samples are handled with 100% privacy and discretion using anonymous, non-identifiable packaging and secure data separation.

Send us your vaginal samples

— get results in weeks

Our experts will guide you through sample collection, project design, sequencing strategy, and data interpretation to ensure reliable, publication-quality results.

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Questions About Vaginal Microbiome Sequencing

How should vaginal microbiome samples be collected?

Samples can be collected by a healthcare professional in a clinical setting or by patients at home using validated self-collection kits. For dry swabs, a double-swab method (such as the BD BBL CultureSwab EZ II) rotated against the vaginal walls for 20 seconds is recommended. For room temperature stability, we recommend buffer-based kits.

Why is taxonomic resolution important for vaginal samples?

Vaginal health is deeply tied to specific species, particularly within the Lactobacillus genus (such as L. crispatus vs. L. iners). High-resolution sequencing—like shotgun metagenomics—allows researchers to differentiate between these key strains, which behave differently and heavily impact the local vaginal environment.

Can you support studies evaluating probiotics or consumer health products?

Yes. We regularly partner with pharma R&D, consumer health, and personal care companies to evaluate how topical treatments, oral probiotics, or hygiene products alter the vaginal microbial ecosystem and Community State Types (CSTs).

How long does vaginal microbiome sequencing take?

Most projects are completed within approximately 6 weeks. This timeline depends on total sample volume, the chosen sequencing method, and the depth of the statistical and bioinformatic analysis required.