Clear Aligner Cleaning: Brushing, Chlorhexidine, and BlueM Effects on Oral Microbial Ecology and Periodontal Indices

January 6, 2026 updated by: Faisal Ali Althobaiti, Riyadh Elm University

Investigating the Impact of Cleaning Protocols on Oral Microbial Ecology and Early Dysbiosis Markers on Orthodontic Clear Aligner Patients: A Randomized Cross-over Clinical Study

This randomized crossover study will assess how three aligner-cleaning methods affect early supragingival oral microbial ecology and periodontal health in adults using clear aligners. Each participant will complete three (1-month) periods in a randomized sequence with (1-week) washouts between periods:

  1. Mechanical toothbrushing with fluoride toothpaste (control),
  2. Chlorhexidine (CHX) mouthwash, and
  3. an oxygen-based cleanser (BlueM).

Primary ecological outcomes focus on early dysbiosis indicators Fusobacterium nucleatum and Prevotella intermedia measured on retrieved aligner inner-surface biofilm and on supragingival plaque at the gingival margin. Secondary outcomes include periodontal indices (plaque index, gingival index, bleeding on probing) at index teeth and the host inflammatory marker MMP-8 in matrix-paired extracts (plaque and aligner).

Study visits occur at baseline and at the end of each 1-month period. Supragingival plaque is collected from the upper and lower first molars and central incisors; used aligners are swabbed immediately after removal. Participants are instructed to wear aligners about 22 hours/day, change trays every 10 days, remove aligners for meals and oral hygiene, and drink only water while aligners are in.

Laboratory procedures include blinded culture enumeration under coded labels (performed by a single trained operator, FA), confocal laser scanning microscopy, and RNA isolation with species-specific qRT-PCR; microscopy is conducted unblinded after decoding. The study will determine whether chlorhexidine or an oxygen-based cleanser produces more favorable early ecological changes and periodontal outcomes than mechanical brushing alone in clear aligner therapy.

Study Overview

Status

Not yet recruiting

Conditions

Intervention / Treatment

Study Type

Interventional

Enrollment (Estimated)

21

Phase

  • 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 Contact

Study Contact Backup

Study Locations

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

Ages Eligible for Study

  • Adult
  • Older Adult

Accepts Healthy Volunteers

Yes

Description

Inclusion Criteria:

  • Adults (≥18 years).
  • Undergoing or scheduled for treatment with clear aligners (CA).
  • Presence of upper and lower first molars and central incisors.
  • Periodontal health at baseline (no sites with PD ≥ 4 mm; no clinical attachment loss at index teeth; BI/PI within normal limits).
  • No periodontal therapy within the previous 6 months.
  • Able and willing to comply with study instructions and follow-up visits; signed informed consent.
  • Sufficient remaining CA treatment (clinician-estimated): ≥ 14 weeks to safely cover three 1 month protocol periods plus washouts.

Minimum planned aligners remaining: ≥ 11 aligners (assuming 10 days/aligner) or equivalent continuous CA duration per treating orthodontist.

Exclusion Criteria:

  • Patients requiring orthognathic surgery
  • Uncontrolled systemic diseases (e.g., uncontrolled diabetes mellitus, autoimmune disease).
  • Pregnancy or lactation.
  • Use of systemic antibiotics and/or anti-inflammatory drugs within the last 3 months.
  • Periodontal therapy within the last 6 months.
  • Current tobacco use (smoking/smokeless) or vaping.
  • Limited/express CA plans (e.g., ≤ 11 aligners or expected completion < 14 weeks).

Anticipated early completion of CA or major treatment changes (e.g., switch to fixed appliances) within the next ~4 months.

- Extensive caries, defective restorations, or prostheses affecting index teeth/sites.

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: Prevention
  • Allocation: Randomized
  • Interventional Model: Crossover Assignment
  • Masking: Single

Arms and Interventions

Participant Group / Arm
Intervention / Treatment
Experimental: Sequence ABC: Brushing then CHX Mouthwash then BlueM
Participant completes three 1-month periods in order (A to B to C), each separated by a 1-week washout. A = Mechanical toothbrushing with fluoride toothpaste (control); B = Chlorhexidine (CHX) mouthwash; C = Oxygen-based cleanser (BlueM). Trays are changed every 10 days; aligners are worn 22 h/day; water-only while aligners are in.
Behavioral: Mechanical toothbrushing (fluoride toothpaste)
Control oral-hygiene period using mechanical toothbrushing with a fluoride-containing toothpaste, per standardized study instructions, for the assigned 1-month period. No chlorhexidine or oxygen-based cleanser is used during this period; aligners are removed for oral-hygiene procedures per protocol.
Other Names:
  • Colgate Total
Drug: Chlorhexidine mouthwash (0.2%)
Chlorhexidine mouthwash used per standardized study instructions for the assigned 1-month period. No oxygen-based cleanser is used during this period; aligners are removed for mouthrinse use and oral-hygiene procedures per protocol. A 1-week washout without cleaning products separates periods.
Other Names:
  • CHX
Other: Oxygen-based cleanser
Oxygen-based cleanser (BlueM) used per standardized study instructions for the assigned 1-month period. No chlorhexidine is used during this period; aligners are removed for product use and oral-hygiene procedures per protocol. A 1-week washout without cleaning products separates periods.
Other Names:
  • BlueM
Experimental: Sequence BCA: CHX Mouthwash then BlueM then Brushing
Participant completes three 1-month periods in order (B to C to A), each separated by a 1-week washout. A = Mechanical toothbrushing with fluoride toothpaste (control); B = CHX mouthwash; C = Oxygen-based cleanser (BlueM). Trays are changed every 10 days; aligners are worn 22 h/day; water-only while aligners are in.
Behavioral: Mechanical toothbrushing (fluoride toothpaste)
Control oral-hygiene period using mechanical toothbrushing with a fluoride-containing toothpaste, per standardized study instructions, for the assigned 1-month period. No chlorhexidine or oxygen-based cleanser is used during this period; aligners are removed for oral-hygiene procedures per protocol.
Other Names:
  • Colgate Total
Drug: Chlorhexidine mouthwash (0.2%)
Chlorhexidine mouthwash used per standardized study instructions for the assigned 1-month period. No oxygen-based cleanser is used during this period; aligners are removed for mouthrinse use and oral-hygiene procedures per protocol. A 1-week washout without cleaning products separates periods.
Other Names:
  • CHX
Other: Oxygen-based cleanser
Oxygen-based cleanser (BlueM) used per standardized study instructions for the assigned 1-month period. No chlorhexidine is used during this period; aligners are removed for product use and oral-hygiene procedures per protocol. A 1-week washout without cleaning products separates periods.
Other Names:
  • BlueM
Experimental: Sequence CAB: BlueM then Brushing then CHX Mouthwash
Participant completes three 1-month periods in order (C to A to B), each separated by a 1-week washout. A = Mechanical toothbrushing with fluoride toothpaste (control); B = CHX mouthwash; C = Oxygen-based cleanser (BlueM). Trays are changed every 10 days; aligners are worn 22 h/day; water-only while aligners are in.
Behavioral: Mechanical toothbrushing (fluoride toothpaste)
Control oral-hygiene period using mechanical toothbrushing with a fluoride-containing toothpaste, per standardized study instructions, for the assigned 1-month period. No chlorhexidine or oxygen-based cleanser is used during this period; aligners are removed for oral-hygiene procedures per protocol.
Other Names:
  • Colgate Total
Drug: Chlorhexidine mouthwash (0.2%)
Chlorhexidine mouthwash used per standardized study instructions for the assigned 1-month period. No oxygen-based cleanser is used during this period; aligners are removed for mouthrinse use and oral-hygiene procedures per protocol. A 1-week washout without cleaning products separates periods.
Other Names:
  • CHX
Other: Oxygen-based cleanser
Oxygen-based cleanser (BlueM) used per standardized study instructions for the assigned 1-month period. No chlorhexidine is used during this period; aligners are removed for product use and oral-hygiene procedures per protocol. A 1-week washout without cleaning products separates periods.
Other Names:
  • BlueM

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Fusobacterium nucleatum CFU in supragingival plaque at the gingival margin (index teeth)
Time Frame: Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3); 1-week washouts between periods.
Anaerobic culture enumeration (CFU) of Fusobacterium nucleatum from supragingival plaque collected along the gingival margin of upper/lower first molars and central incisors using the standardized swab/microbrush protocol. Species confirmation per SOP. Culture processing blinded under coded labels (P1-P3) by FA. Metric: CFU per specimen (report also as log10 CFU if analyzed).
Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3); 1-week washouts between periods.
Fusobacterium nucleatum CFU on retrieved aligner inner-surface biofilm
Time Frame: Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3); 1-week washouts between periods.
Anaerobic culture enumeration (CFU) of Fusobacterium nucleatum from a standardized inner-surface swab of the used aligner (zones corresponding to gingival margins of index teeth). Species confirmation per laboratory SOP. Culture processing blinded under coded labels (P1-P3) by a single trained operator (FA). Metric: CFU per specimen (report also as log10 CFU if analyzed).
Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3); 1-week washouts between periods.

Secondary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Prevotella intermedia CFU on retrieved aligner inner-surface biofilm
Time Frame: Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3); 1-week washouts between periods.
Anaerobic culture enumeration (CFU) of Prevotella intermedia from a standardized inner-surface swab of the used aligner (zones corresponding to the gingival margins of the index teeth).
Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3); 1-week washouts between periods.
Prevotella intermedia CFU in supragingival plaque at the gingival margin (index teeth)
Time Frame: Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3); 1-week washouts between periods.
Anaerobic culture enumeration (CFU) of Prevotella intermedia from supragingival plaque collected along the gingival margin of upper/lower first molars and central incisors using the study's standardized swab/microbrush protocol.
Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3); 1-week washouts between periods.
MMP-8 concentration/activity in matrix-paired plaque and aligner extracts
Time Frame: Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3); 1-week washouts between periods.
MMP-8 measured from paired extracts obtained from supragingival plaque and retrieved aligner inner-surface biofilm collected from the same participant at each time point.
Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3); 1-week washouts between periods.
Plaque Index (PI) at index teeth
Time Frame: Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3).
Plaque Index recorded at the upper and lower first molars and central incisors; six sites per tooth.
Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3).
Gingival Index (GI) at index teeth
Time Frame: Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3).
Gingival Index recorded at the upper and lower first molars and central incisors; six sites per tooth.
Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3).
Bleeding on Probing (BoP) at index teeth
Time Frame: Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3).
BoP recorded at the upper and lower first molars and central incisors; six sites per tooth.
Baseline and end of each 1-month period (end of Period 1, Period 2, Period 3).

Collaborators and Investigators

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

Sponsor

Riyadh Elm University

Investigators

  • Principal Investigator: Dr. Faisal A Althobaiti, BDS, Riyadh Elm University
  • Study Director: Dr. Nancy M Ajwa, MSc, Riyadh Elm University

Publications and helpful links

The person responsible for entering information about the study voluntarily provides these publications. These may be about anything related to the study.

General Publications

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 (Estimated)

February 1, 2026

Primary Completion (Estimated)

October 1, 2026

Study Completion (Estimated)

October 1, 2026

Study Registration Dates

First Submitted

December 15, 2025

First Submitted That Met QC Criteria

December 15, 2025

First Posted (Estimated)

December 29, 2025

Study Record Updates

Last Update Posted (Actual)

January 8, 2026

Last Update Submitted That Met QC Criteria

January 6, 2026

Last Verified

January 1, 2026

More Information

Terms related to this study

Keywords

Additional Relevant MeSH Terms

Other Study ID Numbers

  • REU-ORTHO-ECOALIGN-XO-01

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

UNDECIDED

IPD Plan Description

Individual participant data (IPD) sharing will follow Riyadh Elm University IRB and SFDA requirements. A de-identified dataset (microbiological counts/abundances, MMP-8 values, periodontal indices, randomization order, and minimal demographics) may be shared after primary publication, subject to IRB approval and a data-use agreement

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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