The bacterial microbiome and metabolome in caries progression and arrest

Abstract

Aim: This in vivo experimental study investigated bacterial microbiome and metabolome longitudinal changes associated with enamel caries lesion progression and arrest. Methods: We induced natural caries activity in three caries-free volunteers prior to four premolar extractions for orthodontic reasons. The experimental model included placement of a modified orthodontic band on smooth surfaces and a mesh on occlusal surfaces. We applied the cariesinducing protocol for 4-and 6-weeks, and subsequently promoted caries lesion arrest via a 2week toothbrushing period. Lesions were verified clinically and quantitated via micro-CT enamel density measurements. The biofilm microbial composition was determined via 16S rRNA gene Illumina sequencing and NMR spectrometry was used for metabolomics. Results: Biofilm maturation and caries lesion progression were characterized by an increase in Gram-negative anaerobes, including Veillonella and Prevotella. Streptococcus was associated caries lesion progression, while a more equal distribution of Streptococcus, Bifidobacterium, Atopobium, Prevotella, Veillonella, and Saccharibacteria (TM7) characterized arrest. Lactate, acetate, pyruvate, alanine, valine, and sugars were more abundant in mature biofilms compared to newly formed biofilms. Conclusions: These longitudinal bacterial microbiome and metabolome results provide novel mechanistic insights into the role of the biofilm in caries progression and arrest and offer promising candidate biomarkers for validation in future studies.

Ecological Effects of Daily Antiseptic Treatment on Microbial Composition of Saliva-Grown Microcosm Biofilms and Selection of Resistant Phenotypes

“…We found that treatment with CHX significantly reduced alpha-diversity in the biofilms as compared to treatment with CPC or NaCl (with no significant difference between the latter), in accordance with several other studies evaluating the effects of CHX on microbial communities in vitro and in vivo (Fernandez et al, 2017;Tribble et al, 2019;Brookes et al, 2020Brookes et al, , 2021Chatzigiannidou et al, 2020). Furthermore, beta-diversity showed a strong and significant ecological shift following treatment with CHX, resulting in enrichment of Da Costa Rosa et al, 2021). Bescos et al (2020a) investigated the effects of 7-day use of a CHX mouthwash on the salivary microbiota in 36 healthy individuals.…”

“…For instance, the significantly enriched species Streptococcus oralis subsp. oralis and Schaalia odontolytica (formerly classified as Actinomyces odontolyticus ) have been associated with dental caries ( ElSalhy et al, 2016 ; Da Costa Rosa et al, 2021 ). Bescos et al (2020a) investigated the effects of 7-day use of a CHX mouthwash on the salivary microbiota in 36 healthy individuals.…”

Oral Microbiome and Dental Caries Development

“…Additionally, the relative abundance of some caries-associated bacteria was increased in resistant active caries after silver diamine fluoride (SDF) treatment but was decreased in arrested caries [ 105 ]. An in vivo study found that Streptococcus and Veillonella were more evenly distributed with other taxa in arrested caries, while they were predominant in induced active caries [ 107 ]. Further evidence is needed to investigate the microbiome’s role in the shift in caries activity.…”

Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

“…In between a biotic and an abiotic surface stands the enamel, namely the outer human tooth layer, which is composed mainly of 95% carbonated hydroxyapatite ( Robinson et al, 1998 ), and develops through mineralization of a proteinaceous matrix ( Gil-Bona et al, 2020 ). da Costa Rosa et al (2021) induced dental caries lesions over the premolars of healthy individuals. The biofilm grown on appliances of extracted teeth were dried and removed with a phosphate/sodium azide buffer, or those at occlusal surfaces through a microbrush appliance.…”