Metagenomic Biomarker Discovery and Explanation

Authors

Nicola Segata, Harvard University
Jacques Izard, Harvard UniversityFollow
Levi Waldron, Harvard University
Dirk Gevers, Broad Institute of the Massachusetts Institute of Techology and Harvard University
Larisa Miropolsky, Harvard University
Wendy S. Garrett, Harvard University
Curtis Huttenhower, Harvard UniversityFollow

ORCID IDs

Izard https://orcid.org/0000-0002-5904-5436

Document Type

Article

Date of this Version

6-24-2011

Citation

Genome Biology (2011) 12: R60

http://genomebiology.com/2011/11/6/R60

Comments

License: CC BY 2.0

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/.

Includes supplemental materials.