Bayesian community-wide culture-independent microbial source tracking

被引：1221

作者：

Knights, Dan ^{[2
]}

Kuczynski, Justin ^{[3
]}

Charlson, Emily S. ^{[4
,5
]}

Zaneveld, Jesse ^{[3
]}

Mozer, Michael C. ^{[2
]}

Collman, Ronald G. ^{[4
]}

Bushman, Frederic D. ^{[4
]}

Knight, Rob ^{[6
,7
]}

Kelley, Scott T. ^{[1
]}

机构：

[1] San Diego State Univ, Dept Biol, San Diego, CA 92182 USA

[2] Univ Colorado, Dept Comp Sci, Boulder, CO 80309 USA

[3] Univ Colorado, Dept Mol Cellular & Dev Biol, Boulder, CO 80309 USA

[4] Univ Penn, Sch Med, Dept Med, Philadelphia, PA 19104 USA

[5] Univ Penn, Sch Med, Dept Microbiol, Philadelphia, PA 19104 USA

[6] Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA

[7] Howard Hughes Med Inst, Chevy Chase, MD USA

来源：

NATURE METHODS | 2011年 / 8卷 / 09期

基金：

美国国家卫生研究院;

关键词：

BACTERIAL; SEQUENCES; DIVERSITY;

D O I：

10.1038/nmeth.1650

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Contamination is a critical issue in high-throughput metagenomic studies, yet progress toward a comprehensive solution has been limited. We present SourceTracker, a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments. We applied SourceTracker to microbial surveys from neonatal intensive care units (NICUs), offices and molecular biology laboratories, and provide a database of known contaminants for future testing.

引用

页码：761 / U107

页数：5

共 23 条

[1] PCR-induced sequence artifacts and bias: Insights from comparison of two 16S rRNA clone libraries constructed from the same sample [J].

Acinas, SG ;

Sarma-Rupavtarm, R ;

Klepac-Ceraj, V ;

Polz, MF .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2005, 71 (12) :8966-8969

[2] Latent Dirichlet allocation [J].

Blei, DM ;

Ng, AY ;

Jordan, MI .

JOURNAL OF MACHINE LEARNING RESEARCH, 2003, 3 (4-5) :993-1022

[3] Random forests [J].

Breiman, L .

MACHINE LEARNING, 2001, 45 (01) :5-32

[4] QIIME allows analysis of high-throughput community sequencing data [J].

Caporaso, J. Gregory ;

Kuczynski, Justin ;

Stombaugh, Jesse ;

Bittinger, Kyle ;

Bushman, Frederic D. ;

Costello, Elizabeth K. ;

Fierer, Noah ;

Pena, Antonio Gonzalez ;

Goodrich, Julia K. ;

Gordon, Jeffrey I. ;

Huttley, Gavin A. ;

Kelley, Scott T. ;

Knights, Dan ;

Koenig, Jeremy E. ;

Ley, Ruth E. ;

Lozupone, Catherine A. ;

McDonald, Daniel ;

Muegge, Brian D. ;

Pirrung, Meg ;

Reeder, Jens ;

Sevinsky, Joel R. ;

Tumbaugh, Peter J. ;

Walters, William A. ;

Widmann, Jeremy ;

Yatsunenko, Tanya ;

Zaneveld, Jesse ;

Knight, Rob .

NATURE METHODS, 2010, 7 (05) :335-336

[5] Bacterial Community Variation in Human Body Habitats Across Space and Time [J].

Costello, Elizabeth K. ;

Lauber, Christian L. ;

Hamady, Micah ;

Fierer, Noah ;

Gordon, Jeffrey I. ;

Knight, Rob .

SCIENCE, 2009, 326 (5960) :1694-1697

[6]

Dufrene M, 1997, ECOL MONOGR, V67, P345, DOI 10.1890/0012-9615(1997)067[0345:SAAIST]2.0.CO

[7]

[8] Search and clustering orders of magnitude faster than BLAST [J].

Edgar, Robert C. .

BIOINFORMATICS, 2010, 26 (19) :2460-2461

[9] The influence of sex, handedness, and washing on the diversity of hand surface bacteria [J].

Fierer, Noah ;

Hamady, Micah ;

Lauber, Christian L. ;

Knight, Rob .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (46) :17994-17999

[10] Alternative estimate of source distribution in microbial source tracking using posterior probabilities [J].

Greenberg, Joshua ;

Price, Bertram ;

Ware, Adam .

WATER RESEARCH, 2010, 44 (08) :2629-2637

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