Explaining microbial phenotypes on a genomic scale: GWAS for microbes

• Published in: Briefings in functional genomics Vol. 12; no. 4; pp. 366 - 380
• Main Authors: Dutilh, Bas E, Backus, Lennart, Edwards, Robert A, Wels, Michiel, Bayjanov, Jumamurat R, van Hijum, Sacha A F T
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.07.2013
• Subjects: Genetic Association Studies; Genome-Wide Association Study - methods; Genomics - methods; functional genomics; random forest; genome-wide association studies; genotype–phenotype association; microbial genomics
• ISSN: 2041-2649; 2041-2657
• DOI: 10.1093/bfgp/elt008

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.