Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing 英文参考文献.docVIP

ExploringMicrobialDiversityandTaxonomyUsingSSU rRNAHypervariableTagSequencing SusanM.Huse1,LesDethlefsen2,JulieA.Huber1,DavidMarkWelch1,DavidA.Relman2,3,4,MitchellL. Sogin1* 1Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America, 2Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, United States of America, 3Department of Medicine, Stanford UniversitySchoolofMedicine,Stanford,California,UnitedStatesofAmerica,4VeteransAffairsPaloAltoHealthCareSystem,PaloAlto,California,UnitedStatesofAmerica Abstract MassivelyparallelpyrosequencingofhypervariableregionsfromsmallsubunitribosomalRNA(SSUrRNA)genescansample amicrobialcommunitytwoorthreeordersofmagnitudemoredeeplyperdollarandperhourthancapillarysequencingof full-lengthSSUrRNA.Aswithfull-lengthrRNAsurveys,eachsequencereadisatagsurrogateforasinglemicrobe.However, rather than assigning taxonomy by creating gene trees de novo that include all experimental sequences and certain reference taxa, we compare the hypervariable region tags to an extensive database of rRNA sequences and assign taxonomybasedonthebestmatchinaGlobalAlignmentforSequenceTaxonomy(GAST)process.Theresultingtaxonomic censusprovidesinformationonbothcompositionanddiversityofthemicrobialcommunity.Todeterminetheeffectiveness of using only hypervariable region tags for assessing microbial community membership, we compared the taxonomy assignedtotheV3andV6hypervariableregionswiththetaxonomyassignedtofull-lengthSSUrRNAsequencesisolated fromboththehumangutandadeep-seahydrothermalvent.Thehypervariableregiontagsandfull-lengthrRNAsequences provided equivalent taxonomy and measures of relative abundance of microbial communities, even for tags up to 15% divergent from their nearest reference match. The greater sampling depth per dollar afforded by massively parallel pyrosequencing reveals many more members of the ‘‘rare biospher