Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions

Journal of Oral Microbiology

Floyd E. Dewhirst²  Anuj Camanocha¹ 

[1] Harvard School of Dental Medicine;Harvard School of Dental Medicine, The Forsyth Institute

关键词: microbiome;    primers;    cloning;    phylogeny;    16S rRNA;   

DOI  :  

来源: Co-Action Publishing

【 摘 要 】

Backgroundandobjective:Inadditiontothewell-knownphylaFirmicutes,Proteobacteria,Bacteroidetes,Actinobacteria,Spirochaetes,Fusobacteria,Tenericutes,andChylamydiae,theoralmicrobiomesofmammalscontainspeciesfromthelesser-knownphylaorcandidatedivisions,includingSynergistetes,TM7,Chlorobi,Chloroflexi,GN02,SR1,andWPS-2.Theobjectivesofthisstudyweretocreatephyla-selective16SrDNAPCRprimerpairs,createselective16SrDNAclonelibraries,identifynoveloraltaxa,andupdatecanineandhumanoralmicrobiomedatabases.Design:16SrRNAgenesequencesformembersofthelesser-knownphylaweredownloadedfromGenBankandGreengenesdatabasesandalignedwithsequencesinourRNAdatabases.Primerswithpotentialphylumlevelselectivityweredesignedheuristicallywiththegoalofproducingnearlyfull-length16SrDNAamplicons.ThespecificityofprimerpairswasexaminedbymakingclonelibrariesfromPCRampliconsanddeterminingphylaidentitybyBLASTNanalysis.Results:Phylum-selectiveprimerpairswereidentifiedthatallowedconstructionofclonelibrarieswith96–100%specificityforeachofthelesser-knownphyla.Fromtheseclonelibraries,sevenhumanandtwocaninenoveloraltaxawereidentifiedandaddedtotheirrespectivetaxonomicdatabases.Foreachphylum,genomesequencesclosesttohumanoraltaxawereidentifiedandaddedtotheHumanOralMicrobiomeDatabasetofacilitatemetagenomic,transcriptomic,andproteomicstudiesthatinvolvetilingsequencestothemostcloselyrelatedtaxon.Whileexaminingribosomaloperonsinlesser-knownphylafromsingle-cellgenomesandmetagenomes,weidentifiedanovelrRNAoperonorder(23S-5S-16S)inthreeSR1genomesandthesplittingofthe23SrRNAgenebyanI-CeuI-likehomingendonucleaseinaWPS-2genome.Conclusions:Thisstudydevelopedusefulprimerpairsformakingphylum-selective16SrRNAclonelibraries.Phylum-specificlibrarieswereshowntobeusefulforidentifyingpreviouslyunrecognizedtaxainlesser-knownphylaandwouldbeusefulforfutureenvironmentalandhost-associatedstudies.Keywords:microbiome;primers;cloning;phylogeny;16SrRNA(Published:8October2014)Citation:JournalofOralMicrobiology2014,6:25468-http://dx.doi.org/10.3402/jom.v6.25468

【 授权许可】

Unknown