Bayesian community-wide culture-independent microbial source tracking

Dan Knights; Justin Kuczynski; Emily S. Charlson; Jesse Zaneveld; Michael C. Mozer; Ronald G. Collman; Frederic D. Bushman; Rob Knight; Scott T. Kelley

doi:10.1038/nmeth.1650

Bayesian community-wide culture-independent microbial source tracking

Dan Knights, Justin Kuczynski, Emily S. Charlson, Jesse Zaneveld, Michael C. Mozer, Ronald G. Collman, Frederic D. Bushman, Rob Knight, Scott T. Kelley

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1084 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	761-765
Number of pages	5
Journal	Nature Methods
Volume	8
Issue number	9
DOIs	https://doi.org/10.1038/nmeth.1650
State	Published - Sep 2011
Externally published	Yes

Bibliographical note

Funding Information:
We acknowledge funding from US National Institutes of Health (R01HG4872, R01HG4866, U01HL098957 and P01DK78669), the Crohn’s and Colitis Foundation of America and the Howard Hughes Medical Institute, and B. Prithiviraj for helpful insight into previous related work.

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abstract = "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.",

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AU - Kuczynski, Justin

AU - Charlson, Emily S.

AU - Zaneveld, Jesse

AU - Mozer, Michael C.

AU - Collman, Ronald G.

AU - Bushman, Frederic D.

AU - Knight, Rob

AU - Kelley, Scott T.

N1 - Funding Information: We acknowledge funding from US National Institutes of Health (R01HG4872, R01HG4866, U01HL098957 and P01DK78669), the Crohn’s and Colitis Foundation of America and the Howard Hughes Medical Institute, and B. Prithiviraj for helpful insight into previous related work.

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Bayesian community-wide culture-independent microbial source tracking

Abstract

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