title: Explaining microbial phenotypes on a genomic scale: GWAS for microbes.
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.
authors.affiliation: CMBI, NCMLS, Radboud University Medical Centre. Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands. dutilh@cmbi.ru.nl
authors.forename: Bas E
authors.initials: BE
authors.lastname: Dutilh
authors.forename: Lennart
authors.initials: L
authors.lastname: Backus
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.forename: Michiel
authors.initials: M
authors.lastname: Wels
authors.forename: Jumamurat R
authors.initials: JR
authors.lastname: Bayjanov
authors.forename: Sacha A F T
authors.initials: SA
authors.lastname: van Hijum
mesh_terms: D056726:Genetic Association Studies; D055106:Genome-Wide Association Study / Q000379:methods*; D023281:Genomics / Q000379:methods*
keywords: functional genomics; genome-wide association studies; genotype–phenotype association; microbial genomics; random forest