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NCT Number: NCT07307716

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

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.

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Key information

Conditions

Gingivitis Dental Deposits Dental Plaque Gingival Diseases Infections Mouth Diseases Periodontal Diseases Stomatognathic Diseases Tooth Diseases

Age range

18 year and older

Sex eligibility

All sexes

Study type

Interventional

Phase

Not applicable

Primary location

Who can participate

Healthy volunteers accepted: Yes

Only the study team can determine whether someone qualifies for participation.

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.

Treatment and study plan

Mechanical toothbrushing (fluoride toothpaste)

Behavioral

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

Chlorhexidine mouthwash (0.2%)

Drug

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

Oxygen-based cleanser

Other

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

Primary outcomes

  1. 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).

  2. 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).

Secondary outcomes

  1. 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).

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

Study contacts

Contact information is provided by the study sponsor or research team.

Faisal A Althobaiti, BDS

CONTACT

[email protected]

+966594496974

Nancy M Ajwa, MSc

CONTACT

[email protected]

+966554804564

Sponsors and collaborators

Lead sponsor

Riyadh Elm University

Other

Registry information

Official study title

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

Important dates

Study start
2026
Primary completion
2026
Study completion
2026
First posted
Dec 29, 2025
Registry last updated
Jan 8, 2026

OpenTrials presents study information sourced from ClinicalTrials.gov. The official registry record should be consulted for the latest information.

View the official ClinicalTrials.gov record (opens in a new tab)

This listing is for discovery and informational purposes only. It is not medical advice, does not guarantee that a study is recruiting, and does not determine eligibility. Contact the study team and a qualified healthcare professional when considering participation.

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