Salivary Microbiota and Antimicrobial Resistance in Relation to Chlorhexidine Use (SMARCH)

April 30, 2026 updated by: Masaryk University

Study Protocol for 16S rRNA Sequencing of Healthy Oral Microbiota

This study evaluated the ecological effects of 0.06% chlorhexidine toothpaste on the salivary microbiota of healthy individuals, focusing on taxonomic composition, functional shifts, and prevalence of predicted antimicrobial resistance genes. Saliva samples were collected from eleven healthy participants at three specific time points: baseline (following a 4-week run-in period using a control toothpaste), intervention (after 12 weeks of using 0.06% chlorhexidine digluconate toothpaste), and washout (after a subsequent 12-week period using the control toothpaste). Sequencing targeted the 16S rRNA V3-V4 region.

Study Overview

Status

Status

Indicates the current recruitment status or the expanded access status.
Completed

Conditions

Conditions

The disease, disorder, syndrome, illness, or injury that is being studied. On ClinicalTrials.gov, conditions may also include other health-related issues, such as lifespan, quality of life, and health risks.

Intervention / Treatment

Intervention / Treatment

A process or action that is the focus of a clinical study. Interventions include drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available. Interventions can also include noninvasive approaches, such as education or modifying diet and exercise.

Study Type

Study Type

Describes the nature of a clinical study. Study types include interventional studies (also called clinical trials), observational studies (including patient registries), and expanded access.
Interventional

Enrollment (Actual)

Enrollment

The number of participants in a clinical study. The "anticipated" enrollment is the target number of participants that the researchers need for the study.
11

Phase

Phase

The stage of a clinical trial studying a drug or biological product, based on definitions developed by the U.S. Food and Drug Administration (FDA). The phase is based on the study's objective, the number of participants, and other characteristics. There are five phases: Early Phase 1 (formerly listed as Phase 0), Phase 1, Phase 2, Phase 3, and Phase 4. Not Applicable is used to describe trials without FDA-defined phases, including trials of devices or behavioral interventions.
  • Not Applicable

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Locations

  • Czechia
      • Brno, Czechia, 62500
        • Department of Public Health, Faculty of Medicine, Masaryk University
      • Brno, Czechia, 62500
        • Skydent s.r.o.

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Eligibility Criteria

The key requirements that people who want to participate in a clinical study must meet or the characteristics they must have. Eligibility criteria consist of both inclusion criteria (which are required for a person to participate in the study) and exclusion criteria (which prevent a person from participating). Types of eligibility criteria include whether a study accepts healthy volunteers, has age or age group requirements, or is limited by sex.

Ages Eligible for Study

  • Adult

Accepts Healthy Volunteers

Yes

Description

Inclusion Criteria:

  • Age: Between 25-44 years.
  • General Health: Good systemic health (absence of chronic inflammatory diseases or conditions affecting oral tissues).
  • Oral Hygiene Routine: Participants must perform toothbrushing twice a day and use interdental cleaning aids once a day.
  • Plaque Index (PI): A score of 0.0-0.2 according to Silness and Löe.
  • Gingival Index (GI): A score of 0.0-0.143 according to Silness and Löe.

Exclusion Criteria:

Systemic and Lifestyle Factors:

  • Presence of any chronic systemic disease (e.g., diabetes mellitus, autoimmune disorders)
  • Regular use of medications that may affect gingival status or saliva production.
  • Use of antibiotics within the last 6 months prior to the study.
  • Current pregnancy or lactation.
  • Current smokers or users of other tobacco/nicotine products.

Oral and Dental Factors:

  • Active dental disease: Presence of untreated tooth decay, gingivitis (GI > 0.143), or any form of periodontitis.
  • Prosthetics and Implants: Presence of dental implants, dentures, or significant tooth loss (excluding extracted third molars).
  • Ongoing fixed or removable orthodontic treatment.

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

  • Primary Purpose: Health Services Research
  • Allocation: N/A
  • Interventional Model: Single Group Assignment
  • Masking: None (Open Label)

Arms and Interventions

Participant Group / Arm

Participant Group / Arm

A group or subgroup of participants in a clinical trial that receives a specific intervention/treatment, or no intervention, according to the trial's protocol.
Intervention / Treatment

Intervention / Treatment

A process or action that is the focus of a clinical study. Interventions include drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available. Interventions can also include noninvasive approaches, such as education or modifying diet and exercise.
Experimental: Experimental: Chlorhexidine group
A single group of 11 healthy volunteers. The study consists of three consecutive phases: baseline (4 weeks), intervention with 0.06% chlorhexidine toothpaste (12 weeks), and washout (12 weeks).
Drug: 0.06% Chlorhexidine Digluconate Toothpaste
Participants used the toothpaste twice daily for 12 weeks.

What is the study measuring?

Primary Outcome Measures

Primary Outcome Measures

In a clinical study's protocol, the planned outcome measure that is the most important for evaluating the effect of an intervention/treatment. Most clinical studies have one primary outcome measure, but some have more than one.
Outcome Measure
Measure Description
Time Frame
Change in Salivary Microbial Alpha Diversity (Shannon and Simpson Indices)
Time Frame: Baseline (week 0), after intervention (week 12), and after washout (week 24).
Evaluation of microbial richness and evenness within individual saliva samples. Alpha diversity is quantified using the Shannon and Simpson indices based on 16S rRNA gene sequencing data. Differences between study phases (baseline, intervention, washout) are assessed using the Kruskal-Wallis test or Mann-Whitney U test, as appropriate, with a significance threshold of p < 0.05.
Baseline (week 0), after intervention (week 12), and after washout (week 24).
Change in Salivary Microbial Beta Diversity (Community Structure)
Time Frame: Baseline (week 0), after intervention (week 12), and after washout (week 24).
Evaluation of differences in microbial community composition between study phases. Calculated using Bray-Curtis dissimilarity on Centered Log-Ratio (CLR) normalized data and assessed via PERMANOVA to detect significant shifts (p < 0.05).
Baseline (week 0), after intervention (week 12), and after washout (week 24).

Secondary Outcome Measures

Secondary Outcome Measures

In a clinical study's protocol, a planned outcome measure that is not as important as the primary outcome measure for evaluating the effect of an intervention but is still of interest. Most clinical studies have more than one secondary outcome measure.
Outcome Measure
Measure Description
Time Frame
Differential Abundance of Salivary Bacterial Taxa
Time Frame: Baseline (week 0), after intervention (week 12), and after washout (week 24).
Evaluation of shifts in the relative abundance of bacterial taxa (at phylum, family, genus, and species levels) using 16S rRNA sequencing (V3-V4 region). Statistical analysis is performed using DESeq2 and edgeR to identify significant differences between study phases, with multiple testing corrections applied using the Benjamini-Hochberg (FDR) method (FDR < 0.05).
Baseline (week 0), after intervention (week 12), and after washout (week 24).
Changes in Predicted Antimicrobial Resistance Genes (ARGs)
Time Frame: Baseline (week 0), after intervention (week 12), and after washout (week 24).
Functional prediction of the salivary microbiota conducted using PICRUSt2. Assessment of metabolic potential and antimicrobial resistance pathways with significance assessed using adjusted p-values (p-adj < 0.05).
Baseline (week 0), after intervention (week 12), and after washout (week 24).
Gingival Index (GI) for Clinical Stability Assessment
Time Frame: Screening (Week -4) and after washout (Week 24).
Assessment of gingival health using the Silness and Löe Gingival Index (scale 0-3). This measure is used to verify that participants maintain optimal oral health throughout the study. Eligibility is strictly limited to participants with a maximum GI of 0.143 at screening to ensure a healthy baseline and to monitor that no gingival inflammation occurs during the study period.
Screening (Week -4) and after washout (Week 24).
Plaque Index (PI) for Clinical Stability Assessment
Time Frame: Screening (Week -4) and after washout (Week 24).
Assessment of dental plaque accumulation using the Silness and Löe Plaque Index (scale 0-3). This measure is used to ensure consistent oral hygiene. Eligibility is strictly limited to participants with a maximum PI of 0.2 at screening. The index is monitored to confirm that participants adhere to the required oral hygiene protocol throughout the study.
Screening (Week -4) and after washout (Week 24).

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Sponsor

The organization or person who initiates the study and who has authority and control over the study.
Masaryk University

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (Actual)

Study Start

The actual date on which the first participant was enrolled in a clinical study. The "anticipated" study start date is the date that the researchers think will be the study start date.
April 11, 2022

Primary Completion (Actual)

Primary Completion

The date on which the last participant in a clinical study was examined or received an intervention to collect final data for the primary outcome measure. Whether the clinical study ended according to the protocol or was terminated does not affect this date. For clinical studies with more than one primary outcome measure with different completion dates, this term refers to the date on which data collection is completed for all the primary outcome measures. The "anticipated" primary completion date is the date that the researchers think will be the primary completion date for the study.
November 29, 2022

Study Completion (Actual)

Study Completion

The date on which the last participant in a clinical study was examined or received an intervention/treatment to collect final data for the primary outcome measures, secondary outcome measures, and adverse events (that is, the last participant's last visit). The "anticipated" study completion date is the date that the researchers think will be the study completion date.
November 29, 2022

Study Registration Dates

First Submitted

First Submitted

The date on which the study sponsor or investigator first submitted a study record to ClinicalTrials.gov. There is typically a delay of a few days between the first submitted date and the record's availability on ClinicalTrials.gov (the first posted date).
April 30, 2026

First Submitted That Met QC Criteria

First Submitted That Met QC Criteria

The date on which the study sponsor or investigator first submits a study record that is consistent with National Library of Medicine (NLM) quality control (QC) review criteria. The sponsor or investigator may need to revise and submit a study record one or more times before NLM's QC review criteria are met. It is the responsibility of the sponsor or investigator to ensure that the study record is consistent with the NLM QC review criteria.
April 30, 2026

First Posted (Actual)

First Posted

The date on which the study record was first available on ClinicalTrials.gov after National Library of Medicine (NLM) quality control (QC) review has concluded. There is typically a delay of a few days between the date the study sponsor or investigator submitted the study record and the first posted date.
May 6, 2026

Study Record Updates

Last Update Posted (Actual)

Last Update Posted

The most recent date on which changes to a study record were made available on ClinicalTrials.gov. There may be a delay between when the changes were submitted to ClinicalTrials.gov by the study's sponsor or investigator (the last update submitted date) and the last update posted date.
May 6, 2026

Last Update Submitted That Met QC Criteria

Last Update Submitted That Met QC Criteria

The most recent date on which the study sponsor or investigator submitted changes to a study record that are consistent with National Library of Medicine (NLM) quality control (QC) review criteria. It is the responsibility of the sponsor or investigator to ensure that the study record is consistent with the NLM QC review criteria.
April 30, 2026

Last Verified

Last Verified

The most recent date on which the study sponsor or investigator confirmed the information about a clinical study on ClinicalTrials.gov as accurate and current. If a study with a recruitment status of recruiting; not yet recruiting; or active, not recruiting has not been confirmed within the past 2 years, the study's recruitment status is shown as unknown.
April 1, 2026

More Information

Terms related to this study

Keywords

Other Study ID Numbers

Other Study ID Numbers

Identifiers or ID numbers other than the NCT number that are assigned to a clinical study by the study's sponsor, funders, or others. These numbers may include unique identifiers from other trial registries and National Institutes of Health grant numbers.
  • 68/2020
  • MUNI/A/1807/2025 (Other Grant/Funding Number: Masaryk University)

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

NO

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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