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Brief Funct Genomics. 2013 Jul;12(4):366-80. doi: 10.1093/bfgp/elt008. Epub 2013 Apr 26.

Explaining microbial phenotypes on a genomic scale: GWAS for microbes.

Author information

1
CMBI, NCMLS, Radboud University Medical Centre. Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands. dutilh@cmbi.ru.nl

Abstract

There is an increasing availability of complete or draft genome sequences for microbial organisms. These data form a potentially valuable resource for genotype-phenotype association and gene function prediction, provided that phenotypes are consistently annotated for all the sequenced strains. In this review, we address the requirements for successful gene-trait matching. We outline a basic protocol for microbial functional genomics, including genome assembly, annotation of genotypes (including single nucleotide polymorphisms, orthologous groups and prophages), data pre-processing, genotype-phenotype association, visualization and interpretation of results. The methodologies for association described herein can be applied to other data types, opening up possibilities to analyze transcriptome-phenotype associations, and correlate microbial population structure or activity, as measured by metagenomics, to environmental parameters.

KEYWORDS:

functional genomics; genome-wide association studies; genotype–phenotype association; microbial genomics; random forest

PMID:
23625995
PMCID:
PMC3743258
DOI:
10.1093/bfgp/elt008
[Indexed for MEDLINE]
Free PMC Article

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