Evaluation of 16s rDNA-based community profiling for human microbiome research

Doyle V. Ward; Dirk Gevers; Georgia Giannoukos; Ashlee M. Earl; Barbara A. Methé; Erica Sodergren; Michael Feldgarden; Dawn M. Ciulla; Diana Tabbaa; Cesar Arze; Elizabeth Appelbaum; Leigh Aird; Scott Anderson; Tulin Ayvaz; Edward Belter; Monika Bihan; Toby Bloom; Jonathan Crabtree; Laura Courtney; Lynn Carmichael; David Dooling; Rachel L. Erlich; Candace Farmer; Lucinda Fulton; Robert Fulton; Hongyu Gao; John A. Gill; Brian J. Haas; Lisa Hemphill; Otis Hall; Susanna G. Hamilton; Theresa A. Hepburn; Niall J. Lennon; Vandita Joshi; Cristyn Kells; Christie L. Kovar; Divya Kalra; Kelvin Li; Lora Lewis; Shawn Leonard; Donna M. Muzny; Elaine Mardis; Kathie Mihindukulasuriya; Vincent Magrini; Michelle O'Laughlin; Craig Pohl; Xiang Qin; Keenan Ross; Matthew C. Ross; Yu Hui A. Rogers; Navjeet Singh; Yue Shang; Katarzyna Wilczek-Boney; Jennifer R. Wortman; Kim C. Worley; Bonnie P. Youmans; Shibu Yooseph; Yanjiao Zhou; Patrick D. Schloss; Richard Wilson; Richard A. Gibbs; Karen E. Nelson; George Weinstock; Todd Z. DeSantis; Joseph F. Petrosino; Sarah K. Highlander; Bruce W. Birren

doi:10.1371/journal.pone.0039315

Evaluation of 16s rDNA-based community profiling for human microbiome research

Doyle V. Ward, Dirk Gevers, Georgia Giannoukos, Ashlee M. Earl, Barbara A. Methé, Erica Sodergren, Michael Feldgarden, Dawn M. Ciulla, Diana Tabbaa, Cesar Arze, Elizabeth Appelbaum, Leigh Aird, Scott Anderson, Tulin Ayvaz, Edward Belter, Monika Bihan, Toby Bloom, Jonathan Crabtree, Laura Courtney, Lynn CarmichaelDavid Dooling, Rachel L. Erlich, Candace Farmer, Lucinda Fulton, Robert Fulton, Hongyu Gao, John A. Gill, Brian J. Haas, Lisa Hemphill, Otis Hall, Susanna G. Hamilton, Theresa A. Hepburn, Niall J. Lennon, Vandita Joshi, Cristyn Kells, Christie L. Kovar, Divya Kalra, Kelvin Li, Lora Lewis, Shawn Leonard, Donna M. Muzny, Elaine Mardis, Kathie Mihindukulasuriya, Vincent Magrini, Michelle O'Laughlin, Craig Pohl, Xiang Qin, Keenan Ross, Matthew C. Ross, Yu Hui A. Rogers, Navjeet Singh, Yue Shang, Katarzyna Wilczek-Boney, Jennifer R. Wortman, Kim C. Worley, Bonnie P. Youmans, Shibu Yooseph, Yanjiao Zhou, Patrick D. Schloss, Richard Wilson, Richard A. Gibbs, Karen E. Nelson, George Weinstock, Todd Z. DeSantis, Joseph F. Petrosino, Sarah K. Highlander, Bruce W. Birren

Veterinary and Biomedical Sciences

Research output: Contribution to journal › Article › peer-review

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Abstract

The Human Microbiome Project will establish a reference data set for analysis of the microbiome of healthy adults by surveying multiple body sites from 300 people and generating data from over 12,000 samples. To characterize these samples, the participating sequencing centers evaluated and adopted 16S rDNA community profiling protocols for ABI 3730 and 454 FLX Titanium sequencing. In the course of establishing protocols, we examined the performance and error characteristics of each technology, and the relationship of sequence error to the utility of 16S rDNA regions for classification- and OTU-based analysis of community structure. The data production protocols used for this work are those used by the participating centers to produce 16S rDNA sequence for the Human Microbiome Project. Thus, these results can be informative for interpreting the large body of clinical 16S rDNA data produced for this project.

Original language	English (US)
Article number	e39315
Journal	PloS one
Volume	7
Issue number	6
DOIs	https://doi.org/10.1371/journal.pone.0039315
State	Published - Jun 13 2012

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Ward, D. V., Gevers, D., Giannoukos, G., Earl, A. M., Methé, B. A., Sodergren, E., Feldgarden, M., Ciulla, D. M., Tabbaa, D., Arze, C., Appelbaum, E., Aird, L., Anderson, S., Ayvaz, T., Belter, E., Bihan, M., Bloom, T., Crabtree, J., Courtney, L., ... Birren, B. W. (2012). Evaluation of 16s rDNA-based community profiling for human microbiome research. PloS one, 7(6), Article e39315. https://doi.org/10.1371/journal.pone.0039315

Ward, DV, Gevers, D, Giannoukos, G, Earl, AM, Methé, BA, Sodergren, E, Feldgarden, M, Ciulla, DM, Tabbaa, D, Arze, C, Appelbaum, E, Aird, L, Anderson, S, Ayvaz, T, Belter, E, Bihan, M, Bloom, T, Crabtree, J, Courtney, L, Carmichael, L, Dooling, D, Erlich, RL, Farmer, C, Fulton, L, Fulton, R, Gao, H, Gill, JA, Haas, BJ, Hemphill, L, Hall, O, Hamilton, SG, Hepburn, TA, Lennon, NJ, Joshi, V, Kells, C, Kovar, CL, Kalra, D, Li, K, Lewis, L, Leonard, S, Muzny, DM, Mardis, E, Mihindukulasuriya, K, Magrini, V, O'Laughlin, M, Pohl, C, Qin, X, Ross, K, Ross, MC, Rogers, YHA, Singh, N, Shang, Y, Wilczek-Boney, K, Wortman, JR, Worley, KC, Youmans, BP, Yooseph, S, Zhou, Y, Schloss, PD, Wilson, R, Gibbs, RA, Nelson, KE, Weinstock, G, DeSantis, TZ, Petrosino, JF, Highlander, SK & Birren, BW 2012, 'Evaluation of 16s rDNA-based community profiling for human microbiome research', PloS one, vol. 7, no. 6, e39315. https://doi.org/10.1371/journal.pone.0039315

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abstract = "The Human Microbiome Project will establish a reference data set for analysis of the microbiome of healthy adults by surveying multiple body sites from 300 people and generating data from over 12,000 samples. To characterize these samples, the participating sequencing centers evaluated and adopted 16S rDNA community profiling protocols for ABI 3730 and 454 FLX Titanium sequencing. In the course of establishing protocols, we examined the performance and error characteristics of each technology, and the relationship of sequence error to the utility of 16S rDNA regions for classification- and OTU-based analysis of community structure. The data production protocols used for this work are those used by the participating centers to produce 16S rDNA sequence for the Human Microbiome Project. Thus, these results can be informative for interpreting the large body of clinical 16S rDNA data produced for this project.",

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AU - Methé, Barbara A.

AU - Sodergren, Erica

AU - Feldgarden, Michael

AU - Ciulla, Dawn M.

AU - Tabbaa, Diana

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AU - Appelbaum, Elizabeth

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AU - Carmichael, Lynn

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AU - Erlich, Rachel L.

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AU - Fulton, Lucinda

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AU - Gao, Hongyu

AU - Gill, John A.

AU - Haas, Brian J.

AU - Hemphill, Lisa

AU - Hall, Otis

AU - Hamilton, Susanna G.

AU - Hepburn, Theresa A.

AU - Lennon, Niall J.

AU - Joshi, Vandita

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AU - Mihindukulasuriya, Kathie

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AU - Wilczek-Boney, Katarzyna

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Evaluation of 16s rDNA-based community profiling for human microbiome research

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