Microbiome in Recurrent Caries Under Direct Restorations With 2bRAD-M Sequencing

Objectives: This study aimed to evaluate the species-resolved microbial and functional profile of the microbial community associated with recurrent caries under direct restorations in adults with a novel species-resolved sequencing technology.
Methods: Thirty-four adults with recurrent caries around direct restorations were recruited for this study. Recurrent carious samples were collected from the carious tissue under the restorations after removing the restorations. Supragingival plaque samples from the sound buccal surface of the same tooth were collected as controls. The microbial profile and functional features of the samples were assessed with Type IIB Restriction-site Associated DNA sequencing for Microbiome.
Results: Thirty-four samples of recurrent carious tissue beneath the restorations were collected, including 21 samples beneath composite restorations and 13 beneath amalgam restorations. Additionally, thirty-four supragingival plaque samples were collected from the corresponding teeth. The composition and structure of the microbial community of the recurrent carious lesions were significantly distinct from those of the supragingival biofilm. However, the microbial community of recurrent carious tissues did not show a significant difference between amalgam and composite restoration groups. Several cariogenic species demonstrated elevated abundance in the collected carious tissues and a strong association with recurrent caries, including Propionibacterium acidifaciens, Lactobacillus gasseri, Olsenella profusa, Parascardovia denticolens, Lactobacillus delbrueckii, Corynebacterium durum, Prevotella multisaccharivorax, and Dialister invisus. Functional traits positively correlated with recurrent caries included carbohydrate metabolism, translation, and membrane transport, along with specific pathways such as the pentose phosphate pathway, aminoacyl-tRNA biosynthesis, alanine, aspartate, and glutamate metabolism, and glycolysis/gluconeogenesis.
Conclusions: Secondary carious lesions exhibit a significantly different microbial profile and functional feature compared to the microbiome of supragingival plaque, with an increased abundance of several cariogenic species. Restorative materials did not significantly impact the microbiome of recurrent caries in this study.