Metagenomic biomarker discovery and explanation

Nicola Segata; Jacques Izard; Levi Waldron; Dirk Gevers; Larisa Miropolsky; Wendy S. Garrett; Curtis Huttenhower

doi:10.1186/gb-2011-12-6-r60

Metagenomic biomarker discovery and explanation

Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S. Garrett, Curtis Huttenhower

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

8951 Scopus citations

Abstract

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/ .

Original language	English (US)
Article number	R60
Journal	Genome biology
Volume	12
Issue number	6
DOIs	https://doi.org/10.1186/gb-2011-12-6-r60
State	Published - Jun 24 2011
Externally published	Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/gb-2011-12-6-r60

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title = "Metagenomic biomarker discovery and explanation",

abstract = "This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/ .",

author = "Nicola Segata and Jacques Izard and Levi Waldron and Dirk Gevers and Larisa Miropolsky and Garrett, {Wendy S.} and Curtis Huttenhower",

note = "Funding Information: We would like to thank the entire Human Microbiome Project consortium, including the four sequencing centers (the Broad Institute, Washington University, Baylor College of Medicine, and the J Craig Venter Institute), associated investigators from many additional institutions, and the NIH Office of the Director Roadmap Initiative. This work was supported in part by grant DE017106 from the National Institute of Dental and Craniofacial Research (JI), NIH grants AI078942 (WSG) and Burroughs Wellcome Fund (WSG), and was funded by NIH 1R01HG005969 to CH.",

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doi = "10.1186/gb-2011-12-6-r60",

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AU - Segata, Nicola

AU - Izard, Jacques

AU - Waldron, Levi

AU - Gevers, Dirk

AU - Miropolsky, Larisa

AU - Garrett, Wendy S.

AU - Huttenhower, Curtis

N1 - Funding Information: We would like to thank the entire Human Microbiome Project consortium, including the four sequencing centers (the Broad Institute, Washington University, Baylor College of Medicine, and the J Craig Venter Institute), associated investigators from many additional institutions, and the NIH Office of the Director Roadmap Initiative. This work was supported in part by grant DE017106 from the National Institute of Dental and Craniofacial Research (JI), NIH grants AI078942 (WSG) and Burroughs Wellcome Fund (WSG), and was funded by NIH 1R01HG005969 to CH.

PY - 2011/6/24

Y1 - 2011/6/24

N2 - This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/ .

AB - This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/ .

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Metagenomic biomarker discovery and explanation

Abstract

ASJC Scopus subject areas

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