IADR Abstract Archives
Functional Analysis of the Caries Microbiome
Objectives: In recent years, molecular biological methods, next-generation sequencers, and bioinformatics have rapidly developed. However, the microbiome of carious dentin remains less well understood compared to that of dental plaque. In this study, we aimed to investigate the microbiome profile of coronal caries lesions and compared them with control sites using shotgun metagenomic sequencing to characterize each.
Methods: Carious dentin samples and tongue swabs were collected from five patients (n=5) who provided informed consent at our university hospital. The carious dentin lesion was collected using a sterile excavator. Dentin samples were decalcified using EDTA solution for 72 hours. Following decalcification, zirconia and glass beads were used for homogenization, and microbiome DNA was extracted using a Phenol/Chloroform/Isoamyl alcohol solution. Extracted DNA was purified with AMPure XP. Quality control of raw fastq files was performed using FastQC, and metagenomic analysis was carried out using MetaPhlAn4. Statistical and microbial analyses were carried out using Phyloseq packages in R.
Results: Lactobacillus (19.7%), Propionibacterium (11.1%), and Actinomyces (9.9%) were the most prevalent genera in the coronal caries group, while Rothia (42.5%), Streptococcus (21.4%), and Neisseria (11.7%) were dominant in the swab group. There was no significant difference in alpha diversity between the two groups. LefSe analysis identified Rothia mucilaginosa, Veillonella dispar, and Streptococcus parasanguinis as enriched species in the swab group, whereas Lactobacillus gasseri and Lactobacillus salivarius were enriched in the coronal caries group.
Conclusions: The microbial niches in coronal caries and swab samples differ, as reflected in the differences in the top three prevalent genera between the two groups. This study suggests that certain Lactobacillus species may play a key role in caries progression. This study suggests that Streptococcus is rather less prevalent in the caries group, while certain Lactobacillus species may play an important role in the progression of caries.
Methods: Carious dentin samples and tongue swabs were collected from five patients (n=5) who provided informed consent at our university hospital. The carious dentin lesion was collected using a sterile excavator. Dentin samples were decalcified using EDTA solution for 72 hours. Following decalcification, zirconia and glass beads were used for homogenization, and microbiome DNA was extracted using a Phenol/Chloroform/Isoamyl alcohol solution. Extracted DNA was purified with AMPure XP. Quality control of raw fastq files was performed using FastQC, and metagenomic analysis was carried out using MetaPhlAn4. Statistical and microbial analyses were carried out using Phyloseq packages in R.
Results: Lactobacillus (19.7%), Propionibacterium (11.1%), and Actinomyces (9.9%) were the most prevalent genera in the coronal caries group, while Rothia (42.5%), Streptococcus (21.4%), and Neisseria (11.7%) were dominant in the swab group. There was no significant difference in alpha diversity between the two groups. LefSe analysis identified Rothia mucilaginosa, Veillonella dispar, and Streptococcus parasanguinis as enriched species in the swab group, whereas Lactobacillus gasseri and Lactobacillus salivarius were enriched in the coronal caries group.
Conclusions: The microbial niches in coronal caries and swab samples differ, as reflected in the differences in the top three prevalent genera between the two groups. This study suggests that certain Lactobacillus species may play a key role in caries progression. This study suggests that Streptococcus is rather less prevalent in the caries group, while certain Lactobacillus species may play an important role in the progression of caries.