title: Actinomyces spp. gene expression in root caries lesions.
abstract: BACKGROUND
  The studies of the distribution of Actinomyces spp. on carious and non-carious root surfaces have not been able to confirm the association of these bacteria with root caries, although they were extensively implicated as a prime suspect in root caries.
  
  
  OBJECTIVE
  The aim of this study was to observe the gene expression of Actinomyces spp. in the microbiota of root surfaces with and without caries.
  
  
  METHODS
  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 low RNA 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 were mapped to eight Actinomyces genomes. Count data were normalized using DESeq2 to analyse differential gene expression applying the Benjamini-Hochberg correction (false discovery rate [FDR]<0.001).
  
  
  RESULTS
  Actinomyces spp. had similar numbers of reads (Mann-Whitney U-test; p>0.05), except for Actinomyces OT178 (p=0.001) and Actinomyces gerencseriae (p=0.004), which had higher read counts in the SRS. Genes that code for stress proteins (clp, dnaK, and groEL), enzymes of glycolysis pathways (including enolase 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. Genes with the most significant upregulation in RC were those coding for hypothetical proteins and uracil DNA glycosylase (p=2.61E-17). The gene with the most significant upregulation in SRS was a peptide ABC transporter substrate-binding protein (log2FC=-6.00, FDR=2.37E-05).
  
  
  CONCLUSIONS
  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 that allow them to exist in acid environments and to metabolize sugars, saving energy.
authors.affiliation: Faculty of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil; nailedame@hotmail.comn.t.do@leeds.ac.uk.
authors.forename: Naile
authors.initials: N
authors.lastname: Dame-Teixeira
authors.affiliation: Faculty of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
authors.forename: Clarissa Cavalcanti Fatturi
authors.initials: CC
authors.lastname: Parolo
authors.affiliation: Faculty of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
authors.forename: Marisa
authors.initials: M
authors.lastname: Maltz
authors.affiliation: School of Dentistry, University of Leeds, UK.
authors.forename: Aradhna
authors.initials: A
authors.lastname: Tugnait
authors.affiliation: School of Dentistry, University of Leeds, UK.
authors.forename: Deirdre
authors.initials: D
authors.lastname: Devine
authors.affiliation: School of Dentistry, University of Leeds, UK; nailedame@hotmail.comn.t.do@leeds.ac.uk.
authors.forename: Thuy
authors.initials: T
authors.lastname: Do
keywords: Actinomyces spp.; RNA-seq; differential expression; root caries; transcriptome