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dc.contributor.authorBowen De León, Kara
dc.contributor.authorRamsay, Bradley D.
dc.contributor.authorFields, Matthew W.
dc.identifier.citationDe León KB, Ramsay BD, Fields MW, "Quality-score refinement of SSU rRNA gene pyrosequencing differs across gene region for environmental samples," Microbial Ecology, April 2012 64:499–508en_US
dc.description.abstractDue to potential sequencing errors in pyrosequencing data, species richness and diversity indices of microbial systems can be miscalculated. The “traditional†sequence refinement method is not sufficient to account for overestimations (e.g., length, primer errors, ambiguous nucleotides). Recent in silico and single-organism studies have revealed the importance of sequence quality scores in the estimation of ecological indices; however, this is the first study to compare quality-score stringencies across four regions of the SSU rRNA gene sequence (V1V2, V3, V4, and V6) with actual environmental samples compared directly to corresponding clone libraries produced from the same primer sets. The nucleic acid sequences determined via pyrosequencing were subjected to varying quality-score cutoffs that ranged from 25 to 32, and at each quality-score cutoff, either 10 or 15%of the nucleotides were allowed to be below the cutoff. When species richness estimates were compared for the tested samples, the cutoff values of Q2715%, Q3010%, and Q3215% for V1V2, V4, and V6, respectively, estimated similar values as obtained with clone libraries and Sanger sequencing. The most stringent Q tested (Q3210%) was not enough to account for species richness inflation of the V3 region pyrosequence data. Results indicated that quality-score assessment greatly improved estimates of ecological indices for environmental samples (species richness and α-diversity) and that the effect of qualityscore filtering was region-dependent.en_US
dc.titleQuality-score refinement of SSU rRNA gene pyrosequencing differs across gene region for environmental samplesen_US
mus.citation.journaltitleMicrobial Ecologyen_US
mus.identifier.categoryChemical & Material Sciencesen_US
mus.identifier.categoryEngineering & Computer Scienceen_US
mus.identifier.categoryLife Sciences & Earth Sciencesen_US
mus.relation.collegeCollege of Agricultureen_US
mus.relation.collegeCollege of Engineeringen_US
mus.relation.collegeCollege of Letters & Scienceen_US
mus.relation.departmentCenter for Biofilm Engineering.en_US
mus.relation.departmentChemical & Biological Engineering.en_US
mus.relation.departmentChemistry & Biochemistry.en_US
mus.relation.departmentEnvironmental Engineering.en_US
mus.relation.departmentMicrobiology & Immunology.en_US
mus.relation.universityMontana State University - Bozemanen_US
mus.relation.researchgroupCenter for Biofilm Engineering.en_US
mus.contributor.orcidFields, Matthew W.|0000-0001-9053-1849en_US

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