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Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform
Tamaki, Hideyuki1,2; Wright, Chris L.3; Li, Xiangzhen1; Lin, Qiaoyan1,4; Hwang, Chiachi1; Wang, Shiping4; Thimmapuram, Jyothi3; Kamagata, Yoichi2; Liu, Wen-Tso1
2011-09-23
Source PublicationPLOS ONE
ISSN1932-6203
Volume6Issue:9
SubtypeArticle
AbstractBackground: 16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting microbial community profile, little is known about the influence of pyrosequencing methods on the sequencing throughput and the outcome of microbial community analyses. The aim of this study is to compare differences in output, ease, and cost among three different amplicon pyrosequencing methods for the Roche/454 Titanium platform Methodology/Principal Findings: The following three pyrosequencing methods for 16S rRNA genes were selected in this study: Method-1 (standard method) is the recommended method for bi-directional sequencing using the LIB-A kit; Method-2 is a new option designed in this study for unidirectional sequencing with the LIB-A kit; and Method-3 uses the LIB-L kit for unidirectional sequencing. In our comparison among these three methods using 10 different environmental samples, Method-2 and Method-3 produced 1.5-1.6 times more useable reads than the standard method (Method-1), after quality-based trimming, and did not compromise the outcome of microbial community analyses. Specifically, Method-3 is the most cost-effective unidirectional amplicon sequencing method as it provided the most reads and required the least effort in consumables management. Conclusions: Our findings clearly demonstrated that alternative pyrosequencing methods for 16S rRNA genes could drastically affect sequencing output (e. g. number of reads before and after trimming) but have little effect on the outcomes of microbial community analysis. This finding is important for both researchers and sequencing facilities utilizing 16S rRNA gene pyrosequencing for microbial ecological studies.; Background: 16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting microbial community profile, little is known about the influence of pyrosequencing methods on the sequencing throughput and the outcome of microbial community analyses. The aim of this study is to compare differences in output, ease, and cost among three different amplicon pyrosequencing methods for the Roche/454 Titanium platform
WOS HeadingsScience & Technology
WOS KeywordSPECIES RICHNESS ; RARE BIOSPHERE ; GENE ; COMMUNITY ; FRAGMENTS ; TAXONOMY ; PCR
Indexed BySCI
Language英语
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000295267100034
Citation statistics
Document Type期刊论文
Identifierhttp://210.75.249.4/handle/363003/1508
Collection中国科学院西北高原生物研究所
Affiliation1.Univ Illinois, Dept Civil & Environm Engn, Urbana, IL 61801 USA
2.Natl Inst Adv Ind Sci & Technol, Bioprod Res Inst, Tsukuba, Ibaraki, Japan
3.Univ Illinois, WM Keck Ctr Comparat & Funct Genom, Roy J Carver Biotechnol Ctr, Urbana, IL USA
4.Chinese Acad Sci, Key Lab Adaptat & Evolut Plateau Biota, Haibei Alpine Meadow Ecosyst Res Stn, NW Inst Plateau Biol, Xining, Peoples R China
Recommended Citation
GB/T 7714
Tamaki, Hideyuki,Wright, Chris L.,Li, Xiangzhen,et al. Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform[J]. PLOS ONE,2011,6(9).
APA Tamaki, Hideyuki.,Wright, Chris L..,Li, Xiangzhen.,Lin, Qiaoyan.,Hwang, Chiachi.,...&Liu, Wen-Tso.(2011).Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform.PLOS ONE,6(9).
MLA Tamaki, Hideyuki,et al."Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform".PLOS ONE 6.9(2011).
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