Region-specific similarity cutoff for bacterial species circumscription in 16S rRNA-based studies
Full metadata record
| DC Field | Value | Language |
|---|---|---|
| dc.contributor.author | Kim, Mincheol | - |
| dc.contributor.author | Oh, Hyun-Seok | - |
| dc.date.accessioned | 2017-08-03T12:09:44Z | - |
| dc.date.available | 2017-08-03T12:09:44Z | - |
| dc.date.issued | 2014 | - |
| dc.description.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. | - |
| dc.language | English | - |
| dc.title | Region-specific similarity cutoff for bacterial species circumscription in 16S rRNA-based studies | - |
| dc.type | Poster | - |
| dc.identifier.bibliographicCitation | 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. | - |
| dc.citation.conferenceDate | 2014.08.24-08.29 | - |
| dc.citation.conferenceName | 15th International Symposium on Microbial Ecology. | - |
| dc.citation.conferencePlace | Seoul | - |
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