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Region-specific similarity cutoff for bacterial species circumscription in 16S rRNA-based studies

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Title
Region-specific similarity cutoff for bacterial species circumscription in 16S rRNA-based studies
Authors
Kim, Mincheol
Oh, Hyun-Seok
Issue Date
2014
Citation
Kim, Mincheol, Oh, Hyun-Seok. 2014. Region-specific similarity cutoff for bacterial species circumscription in 16S rRNA-based studies. 15th International Symposium on Microbial Ecology.. Seoul. 2014.08.24-08.29.
Abstract
16SribosomalRNAisthemostwidelyusedmolecularmarkerinmicrobialcommunitystudies.Generally,16SrRNAgenesequencesareclusteredintooperationaltaxonomicunits(OTUs)basedonsequencesimilarityandtheOTUdefinedat97%similaritycutoffiscommonlyusedasa‘proxy’forbacterialspecies.Theproblemisthatthecutofforiginallysetforthefulllength16SrRNAhasalsobeenusedinsubregionsof16SrRNAwithoutpropervalidation.Here,wetestedfirstthesuitabilityofusingsequencesimilarityitselfinthreesubregionsof16SrRNAandthendeterminedtheoptimalsimilaritycutoffforspeciesdemarcationineachregiononthebasisofgenomicevidence.Theeffectofalignmentanddistancecalculationmethodsonsimilaritycutoffvalueswasadditionallyinvestigated.F-measureanalysisrevealedthatV1-V3regionshowedthehighesttaxonomicaccuracy,asimilarextenttothatoffulllength,andloweredinothertworegions,V3-V5andV6-V9regions.Optimalsimilaritycutoffcorrespondingtobacterialspeciesboundarydifferedbyregions.SimilardegreeofcutoffwasobtainedforV3-V5(99.0%)andV6-V9regions(99.1%),whereasamuchlowerlevelofcutoffwasestimatedforV1-V3region(98.0%).Alignmentmethodshavelittleinfluenceontheoptimalcutoffvalues,whilethecutoffvaluesdifferedmorebydistancecalculationmethods.Takentogether,ourresultsshowthatregion-optimizedsimilaritycutoffshouldbeusedwhenclusteringsubregionsof16SrRNAintoOTUsandamongthreesubregionsV1-V3isthemostappropriatetargetforsimilarity-basedOTUclustering.
Conference Name
15th International Symposium on Microbial Ecology.
Conference Place
Seoul
Conference Date
2014.08.24-08.29
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