Draft Genome Sequences of Two Clinical Isolates of Lactobacillus rhamnosus from Initial Stages of Dental Pulp Infection.

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by  Chen, Zhiliang

Draft Genome Sequences of Two Clinical Isolates of Lactobacillus
rhamnosus from Initial Stages of Dental Pulp Infection
ZhiliangChen,aMarcR.Wilkins,aNeilHunter,b,cMangalaA.Nadkarnib,c
SystemsBiologyInitiative,SchoolofBiotechnologyandBiomolecularSciences,theUniversityofNewSouthWales,NewSouthWales,Australiaa;InstituteofDental
Research,WestmeadCentreforOralHealthandWestmeadMillenniumInstitute,Westmead,Australiab;FacultyofDentistry,theUniversityofSydney,Sydney,Australiac
HerewereportthedraftgenomicsequencesoftwoclinicalisolatesofLactobacillusrhamnosusfrominfecteddentalpulpsrepre-
sentingtheinitialstagesofinfectionofpulptissue.Basedon454FLX(cid:1)pyrosequencing,thetwoclinicalisolatesinfectingvital
pulphadagenomelengthof2.9Mbpwithdistinctgenomicsignatures.
Received28October2012 Accepted12November2012 Published15January2013
CitationChenZ,WilkinsMR,HunterN,NadkarniMA.2013.DraftgenomesequencesoftwoclinicalisolatesofLactobacillusrhamnosusfrominitialstagesofdentalpulp
infection.GenomeAnnounc.1(1):e00073-12.doi:10.1128/genomeA.00073-12.
Copyright©2013Chenetal.Thisisanopen-accessarticledistributedunderthetermsoftheAttribution3.0UnportedCreativeCommonsLicense.
AddresscorrespondencetoMangalaA.Nadkarni,[email protected].
Lactobacillicolonizemultiplenichesinthehumanbody.Lac- 2,910codingsequences(CDSs),7rRNAloci,and56tRNAs,with
tobacilli with probiotic properties are predominantly repre- aG(cid:1)Ccontentof46.6%.Incomparison,thegenomesequenceof
sentedinthehumangastrointestinalmicrofloraandthehealthy LRHMDP3contains2,925CDSs,6rRNAloci,and57tRNAswith
vaginalmicroflora.Manystrainsofvariousspeciesoflactobacilli aG(cid:1)Ccontentof46.6%.
are“generallyregardedassafe(GRAS)”bacteriathatpossesspro- ComparativegenomicanalysisofLRHMDP2andLRHMDP3
bioticbenefitsandarethereforenotconsideredaspathogens(1). withaprobioticL.rhamnosusGG(ATCC53103)showedtheab-
LactobacillusrhamnosusGG(ATCC53103)iswidelyusedandhas senceofexopolysaccharide(eps)andspaCBApilusclustersinboth
been extensively studied in probiotic applications. However, in oftheclinicalisolates.Newgenesconfinedtotheclinicalisolates
additiontothebeneficialeffectsoflactobacilli,strainsofL.rham- includedamodifiedepscluster,atwo-componentsensorhistidine
nosusandLactobacillusparacaseihavebeendetectedaspathogens kinase,aresponseregulator,andABCtransportersforferriciron,
ininfectiveendocarditis(2).Similarly,L.rhamnosuswithadiffer- RNApolymerasesigma54factorRpoN,MutR,NtrC,ArsRand
entpulsed-fieldgelelectrophoresis(PFGE)patternfromthatof zinc-binding Cro/CI family transcriptional regulators. A ThiJ/
L. rhamnosus GG was reported to cause meningitis (3). Diverse PfpIfamilyproteinandphosphotransferasesystem(PTS)system
lactobacillihavebeenconsistentlyimplicatedintheinitiationand mannose, galactitol, mannitol, cellobiose, and beta-glucoside-
progressionofdentalcaries,themostcommondiseaseoftheoral specificIIcomponentswerealsoidentified.
cavity (4, 5). Fluorescence in situ hybridization (FISH) analysis Nucleotide sequence accession numbers. This Whole Ge-
hasprovidedinsightsintothecommunitystructureofpolymicro- nome Shotgun project has been deposited at DDBJ/EMBL/
bialconsortiaininfectedtissuemicrobiomesandthepreciseiden- GenBank under the accession numbers AMQW00000000 for
tificationoflactobacillithatareprominentintheinitialstagesof L.rhamnosusLRHMDP2andAMQX00000000forL.rhamnosus
infectionofdentalpulp(6). LRHMDP3.Theversiondescribedinthispaperisthefirstversion,
Draft genome sequences of two L. rhamnosus strains, LRH- AMQW01000000andAMQX01000000.
MDP2andLRHMDP3,havebeengenerated.BothL.rhamnosus
clinicalisolatesweresourcedfrominfecteddentalpulpsfromcar- ACKNOWLEDGMENTS
iousteethcategorizedasrepresentingtheinitialstagesofinfection ThisstudywassupportedpartiallybyNIDCRgrantR01DE015272-07
ofpulptissue.GenomicDNAwassequencedbyawhole-genome andbytheWestmeadCentreforOralHealth,theAustralianGovernment
shotgunstrategyusingRoche454GS(FLX(cid:1))pyrosequencingat SuperScienceScheme,theNewSouthWalesStateGovernmentScience
theRamaciottiCentreforGeneFunctionAnalysis,Universityof LeveragingFund(SLF),andtheUniversityofNewSouthWales.
NewSouthWales.Atotalof77,329readsfromLRHMDP2and
REFERENCES
75,985readsfromLRHMDP3weregeneratedtoreachadepthof
~17-foldgenomecoverage,andassembledbyaNewblerassem- 1. LebeerS,VanderleydenJ,DeKeersmaeckerSC.2008.Genesandmole-
culesoflactobacillisupportingprobioticaction.Microbiol.Mol.Biol.Rev.
bler2.6into51and47contigslongerthan200bp,respectively.
72(4):728–764.
Gene definition and annotation of these two strains were per- 2. HartyDW,OakeyHJ,PatrikakisM,HumeEB,KnoxKW.1994.Patho-
formedbymergingtheresultfromtheRAST(RapidAnnotation genicpotentialoflactobacilli.Int.J.FoodMicrobiol.24(1-2):179–189.
usingSubsystemTechnology)server(7)andtRNAscan-SE(8). 3. RobinF,PaillardC,MarchandinH,DemeocqF,BonnetR,Hennequin
C.2010.Lactobacillusrhamnosusmeningitisfollowingrecurrentepisodes
Thesequencesofthetwostrains,L.rhamnosusLRHMDP2and
of bacteremia in a child undergoing allogeneic hematopoietic stem cell
L.rhamnosusLRHMDP3,include2,911,290bpand2,911,934bp,
transplantation.J.Clin.Microbiol.48(11):4317–4319.
respectively.ThegenomicsequenceofLRHMDP2iscomprisedof 4. ByunR,NadkarniMA,ChhourKL,MartinFE,JacquesNA,HunterN.
January/February2013 Volume1 Issue1 e00073-12 GenomeAnnouncements genomea.asm.org 1
Chenetal.
2004.Quantitativeanalysisofdiverselactobacillusspeciespresentinad- 7. AzizRK,BartelsD,BestAA,DeJonghM,DiszT,EdwardsRA,Formsma
vanceddentalcaries.J.Clin.Microbiol.42(7):3128–3136. K,GerdesS,GlassEM,KubalM,MeyerF,OlsenGJ,OlsonR,Osterman
5. ChhourKL,NadkarniMA,ByunR,MartinFE,JacquesNA,HunterN. AL,OverbeekRA,McNeilLK,PaarmannD,PaczianT,ParrelloB,Pusch
2005.Molecularanalysisofmicrobialdiversityinadvancedcaries.J.Clin. GD,ReichC,StevensR,VassievaO,VonsteinV,WilkeA,ZagnitkoO.
Microbiol.43(2):843–849. 2008.TheRASTserver:rapidannotationsusingsubsystemstechnology.
6. Nadkarni MA, Simonian MR, Harty DW, Zoellner H, Jacques NA, BMCGenomics9:75.
Hunter N. 2010. Lactobacilli are prominent in the initial stages of 8. LoweTM,EddySR.1997.tRNAscan-SE:aprogramforimproveddetec-
polymicrobial infection of dental pulp. J. Clin. Microbiol. 48(5): tionoftransferRNAgenesingenomicsequence.NucleicAcidsRes.25(5):
1732–1740. 955–964.
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