Oral Microbiome

Understand the microbial ecosystem of oral and saliva samples

From oral health and systemic disease links to therapeutic and nutritional innovations, our sequencing workflows support advanced research into dentistry, periodontics, therapeutics, and microbial ecology. We provide 16S rRNA gene sequencing, ITS fungal profiling, shotgun metagenomics, qPCR quantification, and advanced bioinformatics for high-quality oral microbiome studies.

Proven Expertise: Optimized collection & processing workflows for transient, high-abundance samples
Total Quantification: qPCR bacterial quantification to assess initial sample amplification
16S, ITS & Shotgun: Comprehensive high-resolution microbial and functional profiling
Advanced Bioinformatics: Bioinformatic reporting with a firm understanding of advanced analysis

EXPLORE SERVICES

Understand the microbial ecosystem of oral and saliva samples

200+

samples processed

Fast

Results in 6 weeks

16S rRNA & ITS2

Gene sequencing

Global CROs | Pharma R&D | Dental Researchers | Nutrition Innovators

Every Type of Oral Sample, Analyzed with Confidence

From sample collection through bioinformatics interpretation, our team delivers optimized workflows for diverse oral microbiome applications, ensuring transient snapshots are reliably stabilized.

Whole Saliva & Oral Fluid

Ideal for metabolic health, systemic disease biomarker research, and general health tracking. Formulated for liquid saliva collection to capture free-floating microbes and systemic biomarkers.

Buccal & Mucosal Swabs

Optimized for capturing microbes adhering to the inner cheeks, palate, and general oral mucosa. Excellent for studies where liquid spit collection is difficult or tissue-specific mapping is required.

Tongue Microbiome

Designed for the high-density mucosal surface of the tongue. Crucial for breath-related microbial studies, halitosis research, and identifying dorsal tongue coating profiles.

Gum & Plaque Microbiome

Supports localized dental disease investigations. Specifically curated for profiling subgingival and supragingival biofilms involved in periodontitis, gingivitis, and dental caries.

Animal Oral Cavity

Tailored workflows for veterinary research, companion animal health, comparative mammalian microbiomes, and agricultural livestock production tracking.

Nutritional & Clinical Trials

Standardized sampling and stabilization protocols explicitly designed for longitudinal monitoring of oral microbiome shifts following dietary interventions, functional foods, or therapeutic oral care products.

Choose the Right Oral 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 across diverse oral environments.

Oral bacterial diversity profiling
Nutritional and functional food efficacy studies
Periodontal disease and dental caries research
Longitudinal oral microbiome monitoring

ITS Sequencing for Oral Mycobiome Analysis

Characterizes fungal communities that play an important role in oral homeostasis and opportunistic infections.

Oral fungal diversity and thrush studies
Biofilm interaction research (bacterial-fungal synergy)
Immunocompromised cohort oral health studies
Combined bacterial and fungal microbiome profiling

Shotgun Metagenomic Sequencing

Provides species-level taxonomic resolution together with functional gene analysis.

High-resolution microbial and strain-level profiling
Functional metabolic pathway analysis
Antimicrobial resistance (AMR) gene detection
Comprehensive taxonomic and functional oral mapping

Oral Microbiome Bioinformatics & Data Analysis

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

Taxonomic profiling & diversity analysis
Functional pathway annotation
Differential abundance analysis
Statistical reporting and high-quality visualizations

Protocol

Oral 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 particularly resilient microbes, maximizing DNA/RNA recovery.

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

The oral microbiome is highly transient. To capture an accurate snapshot, immediate stabilization is imperative. We support two primary workflows depending on your study design:

Collection Method	Recommended Kits	Storage & Shipping
Dry Swabs (Maximizes DNA recovery)	Becton-Dickinson, BBL CultureSwab EZ II (Double-swab)	Store at -80°C (avoid -20°C). Ship on dry ice (overnight/2-day).
Devices with Liquid Buffer (Ambient stability)	Norgen Biotek & DNA Genotek (OMNIgene.ORAL)	Store and ship at room temperature. No dry ice required.*

*Note: If buffered samples are placed in a freezer, they must be shipped on dry ice to maintain the frozen chain.

100% Private & Discreet: We use blank packaging, never collect direct identifiers (like patient names), and store personal information entirely separate from your sample.

Collection Instructions

Dry Swab Method

Step 1: Peel open the sterile pouch at “peel here” and open the sterile vessel without letting the swab touch any surface.
Step 2: Vigorously rub behind the molar teeth, the roof of the mouth, and the inner cheek with both swabs for 3 minutes, applying sufficient pressure.
Step 3: Carefully return the swab to the tube, ensuring that the swab, stick, and vessel do not contact external surfaces.
Step 4: Place the tube into a biospecimen bag and freeze immediately at -80°C until ready to ship.

Liquid Buffer Method

Step 1: Open the wrapper or clamshell and follow the specific manufacturer collection instructions for saliva or tissue collection.
Step 2: Secure the vial to release the lytic stabilization buffer. Store at ambient temperature until ready to ship.

Resources

Blog: Towards standards for human fecal sample processing in metagenomic studies
Blog: How microbiome science is leading to human nutritional innovations
Norgen Swab Kit (45690): Swab Collection and DNA Preservation System
Norgen Saliva Kit (RU49000): Saliva DNA Collection and Preservation Devices
DNA Genotek OMR-120: OMNIgene.ORAL – Tongue Microbiome
DNA Genotek OMR-110: OMNIgene.ORAL – Gum and Plaque Microbiome
DNA Genotek OM-501 / OM-505: OMNIgene.ORAL – DNA & RNA / Saliva

Send us your oral and saliva 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 Oral Microbiome Sequencing

How should I collect oral microbiome samples?

We recommend utilizing validated collection protocols. For dry swabs, we advise a double-swab method (such as the BD BBL CultureSwab EZ II) rubbed vigorously across oral surfaces for 3 minutes to maximize DNA yield. For saliva, ambient stabilization kits are highly recommended.

Which sequencing method is best for oral studies?

16S rRNA sequencing is excellent for broad bacterial mapping, while ITS targets oral fungi. For high-resolution strain identification and metabolic functional pathway mapping, shotgun metagenomics is preferred.

Can you support nutritional, probiotic, or functional food trials?

Yes. We regularly partner with clinical trial teams, consumer health, and nutrition companies to monitor how foods, rinses, and therapeutics alter oral microbial community structures over time.

How long does oral microbiome sequencing take?

Most projects are completed within approximately 6 weeks, depending on sample volume, selected sequencing technology, and the complexity of the bioinformatic analysis.