The Gut and Oral Microbiomes in Dental Caries

Abstract

Background

Dental caries remains one of the most prevalent chronic diseases worldwide, yet its etiology is primarily understood within the context of the oral microbiome. While interactions between the oral and gut microbiomes have been described in inflammatory diseases, their relationship in dental caries remains poorly defined.

Objective

This study aimed to evaluate the association between the oral and gut microbiomes in individuals with dental caries compared to those without.

Methods

Supragingival plaque, saliva, and stool samples were collected from 24 systemically healthy adults (12 with caries, 12 controls). Microbial communities were characterized using 16S rRNA gene sequencing (V3–V4 region). Alpha and beta diversity metrics were used to assess microbial richness and community structure, and differential abundance analysis was performed to identify taxa-level differences.

Results

No significant differences in alpha or beta diversity were observed between caries and control groups across oral or gut samples. In contrast, strong separation was observed between oral and stool microbiomes regardless of disease status, indicating that anatomical niche is the primary driver of microbial community structure. Differential abundance analysis identified increased relative abundance of cariogenic taxa in oral samples from individuals with caries. In stool samples, taxa-level differences were observed, including increased relative abundance of Streptococcus spp. and Actinomyces spp., although global gut microbial structure remained unchanged.

Conclusion

Dental caries appears to be associated with taxa-level compositional shifts within the oral and gut microbiomes, while overall microbial community structure remains stable and is primarily determined by anatomical niche. These findings support a model in which caries is driven by localized ecological changes rather than systemic microbial disruption. However, in light of differences that emerged between health and disease in the stool core microbiome, coupled with increases to relative abundance of commonly implicated caries pathogens found in caries patient’s stool, our study reveals evidence of systemic microbial interactions that warrant further investigation in larger studies.

Public Abstract

Dental caries (tooth decay) is one of the most common chronic diseases worldwide and is primarily caused by bacteria in the mouth that produce acid and damage tooth structure. While the oral microbiome has been well studied in caries, less is known about whether the gut microbiome is also involved.

This study examined both oral and gut microbial communities in adults with and without dental caries. Saliva, supragingival plaque, and stool samples were collected and analyzed using DNA sequencing to identify and compare bacterial populations. A total of 24 participants were enrolled, including 12 caries-free individuals (control group) and 12 individuals diagnosed with dental caries.

The results showed that overall microbial community structure was similar between individuals with and without caries. However, specific bacteria associated with caries were more abundant in both oral and gut samples from affected individuals. Importantly, oral and gut microbiome global structure remained distinct from one another regardless of disease status.

These findings suggest that dental caries is primarily a localized disease driven by changes in the oral environment rather than widespread changes in the body’s microbial communities. This reinforces the importance of focusing on local prevention strategies such as diet and oral hygiene to manage disease risk. However, the observed differences in gut bacteria between individuals with and without caries suggest there may be a broader connection between oral and gut health in caries disease, that warrants further investigation in larger studies.

Limitations

This study has several limitations that should be acknowledged. First, its cross-sectional design precludes conclusions regarding causality, limiting interpretation to associations rather than mechanistic pathways. The severity and extent of caries within this cohort should also be considered when interpreting the findings. Although all participants in the caries group had at least two clinically confirmed ICDAS ≥3 lesions, with a median of four cavitated lesions per individual, lesion-level classification was not uniformly available due to limitations of chart review. It is possible that the disease burden in this cohort was not sufficient to drive detectable changes in global microbial community structure, particularly in the gut microbiome.

Determining the Association Between the Gut and Oral Microbiomes in Patients with Dental Caries. A thesis submitted in partial fulfillment of the requirements for the Master of Science degree in Oral Science in the Graduate College of The University of Iowa, May 2026. Thesis Committee: Sukirth Ganesan, Thesis Supervisor; Clark Stanford, Thesis Supervisor; Sandra Guzman; Franciele Floriani; Jeff Banas; Shareef Dabdoub.

Official record: Iowa Research Online, University of Iowa. The full text is under embargo there until June 29, 2028.