Soil Bacterial Diversity Screening Using Single 16S rRNA Gene V Regions Coupled with Multi-Million Read Generating Sequencing Technologies 英文参考文献.docVIP

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Soil Bacterial Diversity Screening Using Single 16S rRNA Gene V Regions Coupled with Multi-Million Read Generating Sequencing Technologies 英文参考文献.doc

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Soil Bacterial Diversity Screening Using Single 16S rRNA Gene V Regions Coupled with Multi-Million Read Generating Sequencing Technologies 英文参考文献

SoilBacterialDiversityScreeningUsingSingle16SrRNA GeneVRegionsCoupledwithMulti-MillionRead GeneratingSequencingTechnologies SotiriosVasileiadis1,EdoardoPuglisi2,MariaArena1,FabrizioCappa2,PierS.Cocconcelli2, MarcoTrevisan1* 1Universita` CattolicadelSacroCuore,FacultyofAgriculturalSciences,InstituteofAgriculturalandEnvironmentalChemistry,Piacenza,Italy,2InstituteofMicrobiology, Piacenza,Italy Abstract The novel multi-million read generating sequencing technologies arevery promising for resolving the immense soil 16S rRNA gene bacterial diversity. Yet they have a limited maximum sequence length screening ability, restricting studies in screeningDNAstretchesofsingle16SrRNAgenehypervariable(V)regions.Theaimofthepresentstudywastoassessthe effects of properties of four consecutive V regions (V3-6) on commonly applied analytical methodologies in bacterial ecologystudies.Usinganinsilicoapproach,theperformanceofeachVregionwascomparedwiththecomplete16SrRNA genestretch.WeassessedrelatedpropertiesofthesoilderivedbacterialsequencecollectionoftheRibosomalDatabase Project(RDP)databaseandconcomitantlyperformedsimulationsbasedonpublisheddatasets.Resultsindicatethatoverall themostprominentVregionforsoilbacterialdiversitystudieswasV3,eventhoughitwasoutperformedinsomeofthe tests.Despiteitshighperformanceduringmosttests,V4waslessconservedalongflankingsites,thusreducingitsabilityfor bacterialdiversity coverage. V5 performed well in thenon-redundant RDPdatabasebased analysis. HoweverV5 did not resemblethefull-length16SrRNAgenesequenceresultsaswellasV3andV4didwhenthenaturalsequencefrequencyand occurrence approximation was considered in the virtual experiment. Although, the highly conserved flanking sequence regionsofV6providetheabilitytoamplifypartial16SrRNAgenesequencesfromverydiverseowners,itwasdemonstrated thatV6wastheleastinformativecomparedtotherestexaminedVregions.Ourresultsindicatethatenvironmentspecific databaseexplorationandtheoreticalassessmentoftheexperimentalapproacharestrong