Actinomyces spp. gene expression in root caries lesions

摘要

Background:ThestudiesofthedistributionofActinomycesspp.oncariousandnon-cariousrootsurfaceshavenotbeenabletoconfirmtheassociationofthesebacteriawithrootcaries,althoughtheywereextensivelyimplicatedasaprimesuspectinrootcaries.Objective:TheaimofthisstudywastoobservethegeneexpressionofActinomycesspp.inthemicrobiotaofrootsurfaceswithandwithoutcaries.Design:Theoralbiofilmsfromexposedsoundrootsurface(SRS;n=10)andactiverootcaries(RC;n=30)sampleswerecollected.ThetotalbacterialRNAwasextracted,andthemRNAwasisolated.SampleswithlowRNAconcentrationwerepooled,yieldingafinalsamplesizeofSRS=10andRC=9.ComplementaryDNA(cDNA)librarieswerepreparedandsequencedonanIllumina?HiSeq2500system.SequencereadsweremappedtoeightActinomycesgenomes.CountdatawerenormalizedusingDESeq2toanalysedifferentialgeneexpressionapplyingtheBenjamini-Hochbergcorrection(falsediscoveryrate[FDR]amp;0.001).Results:Actinomycesspp.hadsimilarnumbersofreads(Mann-WhitneyU-test;pamp;0.05),exceptforActinomycesOT178(p=0.001)andActinomycesgerencseriae(p=0.004),whichhadhigherreadcountsintheSRS.Genesthatcodeforstressproteins(clp,dnaK,andgroEL),enzymesofglycolysispathways(includingenolaseandphosphoenolpyruvatecarboxykinase),adhesion(Type-2fimbrialandcollagen-bindingprotein),andcellgrowth(EF-Tu)werehighly–butnotdifferentially(pamp;0.001)–expressedinbothgroups.GeneswiththemostsignificantupregulationinRCwerethosecodingforhypotheticalproteinsanduracilDNAglycosylase(p=2.61E-17).ThegenewiththemostsignificantupregulationinSRSwasapeptideABCtransportersubstrate-bindingprotein(log2FC=?6.00,FDR=2.37E-05).Conclusion:ThereweresimilarlevelsofActinomycesgeneexpressioninbothsoundandcariousrootbiofilms.Thesebacteriacanbecommensalinrootsurfacesitesbutmaybecariogenicduetosurvivalmechanismsthatallowthemtoexistinacidenvironmentsandtometabolizesugars,savingenergy.Keywords:RNA-seq;Actinomycesspp.;rootcaries;transcriptome;differentialexpression(Published:16September2016)Citation:JournalofOralMicrobiology2016,8:32383-http://dx.doi.org/10.3402/jom.v8.32383