Clear aligners protect oral microbiome better than fixed braces

By Dr. Liji Thomas, MDReviewed by Benedette Cuffari, M.Sc.Feb 4 2026

A six-month randomized study reveals how orthodontic appliance choice shapes oral bacteria, periodontal health, and oxidative stress, showing that choosing fixed braces or clear aligners may influence long-term oral health outcomes. 

Study: Comparison of the effects of clear aligners and fixed appliances on the oral microbiota and reactive oxygen species: a prospective study. Image Credit: Reshetnikov_art / Shutterstock.com

A recent study published in Frontiers in Cellular and Infectious Microbiology compares the effects of clear aligners and fixed appliances on oral microbiota and oxidative stress in the oral cavity.

Fixed dental appliances vs. clear aligners

Fixed dental appliances are designed to provide precise control of tooth movement by using brackets bonded directly to the enamel surface, which are connected to bands and archwires. Despite their widespread use as orthodontic devices, the design of fixed dental appliances creates protected plaque pockets that are difficult to clean, thereby increasing the risk of dental caries and gingivitis.

Fixed dental appliances may promote colonization by cariogenic and periodontal-associated bacteria, as suggested by prior studies, and can contribute to shifts in the oral microbiome associated with inflammation. This appliance-induced oral dysbiosis contributes to excessive reactive oxygen species (ROS) production by pathogenic bacteria, which further exacerbates inflammation.

Compared with traditional braces, clear aligners are thermoplastic appliances created through computer-aided design (CAD) and computer-aided manufacturing (CAM) that have been shown to improve patient comfort and esthetics during treatment. Furthermore, clear aligners are associated with a lower risk of inflammation and oral dysbiosis.

Clear aligners must be worn for at least 22 hours a day; however, they are removable, allowing thorough teeth cleaning. Nevertheless, the constant wearing of clear aligners may interfere with the free flow of saliva and promote plaque accumulation.

Prospective randomized comparison of aligners and fixed appliances

The current study included 24 patients who were randomly fitted with either clear aligners or fixed appliances.

At baseline, saliva, supragingival plaque, and gingival crevicular fluid (GCF) samples were collected to assess the oral microbiome, the microbial profile associated with dental caries, and periodontal and gum inflammation, respectively. Periodontal health was assessed using plaque index (PI), gingival index (GI), probing depth (PD), and bleeding on probing (BOP).

ROS generation was based on 8-hydroxy-2’-deoxyguanosine (8-OHdG) levels measured in GCF and saliva. All tests were repeated at three and six months.

Spearman correlation was used to assess monotonic associations between these measures.

Study findings

Clinical indices

As compared to baseline, all markers of periodontal disease including PI, GI, PD, and bleeding on probing (BOP) were higher at one or both time points in the fixed appliance group. Compared with the clear aligners group, a significant increase in BOP and PI was observed at three and six months.

Despite higher GI at six months, the clear aligners group showed no significant changes in probing depth and lower plaque accumulation than the fixed appliance group, suggesting a lower risk of plaque accumulation and gingivitis with clear aligners. 

Microbial profile

The fixed appliance group exhibited greater alpha diversity in saliva with no significant differences in the distribution of these species, whereas richness and evenness indices increased throughout treatment in the supragingival plaque samples of these patients. Comparatively, those in the clear aligner group exhibited reduced alpha diversity that eventually recovered, with progressive rises in its distribution.

Dominant saliva taxa shared between both fixed-appliance and clear-aligner patients included Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria. At the first sampling time point, Veillonella, Corynebacterium, and Prevotella were significantly enriched in fixed-appliance patients, whereas Rothia levels were higher in clear-aligner patients. Throughout the study period, Veillonella, Prevotella, and Lactobacillus levels were higher in the fixed appliance group.

Prevotella is directly implicated in the development of periodontitis through its roles in biofilm formation and pro-inflammatory signaling. Veillonella is similarly enriched in periodontitis, which may reflect periodontal damage caused by its pro-inflammatory metabolic products. Lactobacillus and Corynebacterium are both associated with dental caries.

Conversely, health-associated genera such as Lautropia were more abundant in gingival crevicular fluid samples from clear aligner patients. These differences could be due to a combination of surface factors promoting pathogenic colonization of the devices and device-specific effects on the microbiome.

ROS levels

ROS levels in saliva and GCF were comparable between groups over time, except at six months, when GCF 8-OHdG levels, an indirect indicator of oxidative stress, were higher in the fixed appliance group. This difference represented a between-group effect at six months rather than a significant change over time within either group. Potential mechanisms underlying this difference include the degradation of metallic device components, neutrophil activation, ROS release induced by plaque and gingivitis, and oral cavity dysbiosis.  

Pathway analysis

In the fixed appliance group, carbohydrate metabolic pathways were significantly enriched, particularly those involved in glycan biosynthesis and metabolism, glycosaminoglycan degradation, and glycosyltransferases. Comparatively, clear aligners exhibited greater enrichment in lipid metabolism pathways, including those affecting peroxisome proliferator-activated receptor (PPAR), adipocytokines, and fatty acids. These functional pathways were computationally predicted based on microbial composition and were not directly measured.

Fixed appliances were associated with a higher relative abundance of periodontal and cariogenic pathogens, indicating a potential increased risk of periodontitis and caries.