Actinomyces spp. gene expression in root caries lesions

Abstract

Background: The studies of the distribution of Actinomyces spp. on carious and non-carious root surfaceshave not been able to confirm the association of these bacteria with root caries, although they were extensivelyimplicated as a prime suspect in root caries.Objective: The aim of this study was to observe the gene expression of Actinomyces spp. in the microbiotaof root surfaces with and without caries.Design: The oral biofilms from exposed sound root surface (SRS; n 10) and active root caries (RC; n 30)samples were collected. The total bacterial RNA was extracted, and the mRNA was isolated. Samples with lowRNA concentration were pooled, yielding a final sample size of SRS 10 and RC 9. Complementary DNA(cDNA) libraries were prepared and sequenced on an Illumina† HiSeq 2500 system. Sequence reads weremapped to eight Actinomyces genomes. Count data were normalized using DESeq2 to analyse differential geneexpression applying the Benjamini-Hochberg correction (false discovery rate [FDR] B0.001).Results: Actinomyces spp. had similar numbers of reads (Mann-Whitney U-test; p 0.05), except forActinomyces OT178 (p 0.001) and Actinomyces gerencseriae (p 0.004), which had higher read counts in theSRS. Genes that code for stress proteins (clp, dnaK, and groEL), enzymes of glycolysis pathways (includingenolase and phosphoenolpyruvate carboxykinase), adhesion (Type-2 fimbrial and collagen-binding protein),and cell growth (EF-Tu) were highly but not differentially (p 0.001) expressed in both groups. Geneswith the most significant upregulation in RC were those coding for hypothetical proteins and uracil DNAglycosylase (p 2.61E-17). The gene with the most significant upregulation in SRS was a peptide ABCtransporter substrate-binding protein (log2FC 6.00, FDR 2.37E-05). Conclusion: There were similar levels of Actinomyces gene expression in both sound and carious root biofilms.These bacteria can be commensal in root surface sites but may be cariogenic due to survival mechanisms thatallow them to exist in acid environments and to metabolize sugars, saving energy.