Bacterial genetic architecture of ecological interactions in co-culture by GWAS-taking Escherichia coli and Staphylococcus aureus as an example

Xiaoqing He, Yi Jin, Meixia Ye, Nan Chen, Jing Zhu, Jingqi Wang, Libo Jiang, Rongling Wu

Research output: Contribution to journalArticle

Abstract

How a species responds to such a biotic environment in the community, ultimately leading to its evolution, has been a topic of intense interest to ecological evolutionary biologists. Until recently, limited knowledge was available regarding the genotypic changes that underlie phenotypic changes. Our study implemented GWAS (Genome-Wide Association Studies) to illustrate the genetic architecture of ecological interactions that take place in microbial populations. By choosing 45 such interspecific pairs of Escherichia coli and Staphylococcus aureus strains that were all genotyped throughout the entire genome, we employed Q-ROADTRIPS to analyze the association between single SNPs and microbial abundance measured at each time point for bacterial populations reared in monoculture and co-culture, respectively. We identified a large number of SNPs and indels across the genomes (35.69 G clean data of E. coli and 50.41 G of S. aureus). We reported 66 and 111 SNPs that were associated with interaction in E. coli and S. aureus, respectively. 23 out of 66 polymorphic changes resulted in amino acid alterations.12 significant genes, such as murE, treA, argS, and relA, which were also identified in previous evolutionary studies. In S. aureus, 111 SNPs detected in coding sequences could be divided into 35 non-synonymous and 76 synonymous SNPs. Our study illustrated the potential of genome-wide association methods for studying rapidly evolving traits in bacteria. Genetic association study methods will facilitate the identification of genetic elements likely to cause phenotypes of interest and provide targets for further laboratory investigation.

Original languageEnglish (US)
Article number2332
JournalFrontiers in Microbiology
Volume8
Issue numberNOV
DOIs
StatePublished - Nov 27 2017

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Genome-Wide Association Study
Coculture Techniques
Single Nucleotide Polymorphism
Staphylococcus aureus
Escherichia coli
Genome
Genetic Association Studies
Population
Bacteria
Phenotype
Amino Acids
Genes

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Microbiology (medical)

Cite this

He, Xiaoqing ; Jin, Yi ; Ye, Meixia ; Chen, Nan ; Zhu, Jing ; Wang, Jingqi ; Jiang, Libo ; Wu, Rongling. / Bacterial genetic architecture of ecological interactions in co-culture by GWAS-taking Escherichia coli and Staphylococcus aureus as an example. In: Frontiers in Microbiology. 2017 ; Vol. 8, No. NOV.
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Bacterial genetic architecture of ecological interactions in co-culture by GWAS-taking Escherichia coli and Staphylococcus aureus as an example. / He, Xiaoqing; Jin, Yi; Ye, Meixia; Chen, Nan; Zhu, Jing; Wang, Jingqi; Jiang, Libo; Wu, Rongling.

In: Frontiers in Microbiology, Vol. 8, No. NOV, 2332, 27.11.2017.

Research output: Contribution to journalArticle

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