Explaining microbial phenotypes on a genomic scale: Gwas for microbes

Bas E. Dutilh, Lennart Backus, Robert A. Edwards, Michiel Wels, Jumamurat R. Bayjanov, Sacha A.F.T. Van Hijum

Research output: Contribution to journalArticlepeer-review

30 Citations (Scopus)

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.

Original languageEnglish
Article numberelt008
Pages (from-to)366-380
Number of pages15
JournalBriefings in Functional Genomics
Volume12
Issue number4
DOIs
Publication statusPublished - Jul 2013
Externally publishedYes

Bibliographical note

The Author 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Keywords

  • Functional genomics
  • Genome-wide association studies
  • Genotype-phenotype association
  • Microbial genomics
  • Random forest

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