Competition-cooperation mechanism between Escherichia coli and Staphylococcus aureus based on systems mapping

Caifeng Li; Lixin Yin; Xiaoqing He; Yi Jin; Xuli Zhu; Rongling Wu

doi:10.3389/fmicb.2023.1192574

Competition-cooperation mechanism between Escherichia coli and Staphylococcus aureus based on systems mapping

Front Microbiol. 2023 Nov 6:14:1192574. doi: 10.3389/fmicb.2023.1192574. eCollection 2023.

Authors

Caifeng Li¹, Lixin Yin¹, Xiaoqing He^{1

2

3

4}, Yi Jin^{1

2

3

4}, Xuli Zhu^{1

2

3

4}, Rongling Wu^{1

2

3

4}

Affiliations

¹ Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
² National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China.
³ Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China.
⁴ The Tree and Ornamental Plant Breeding and Biotechnology, Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China.

Abstract

Introduction: Interspecies interactions are a crucial driving force of species evolution. The genes of each coexisting species play a pivotal role in shaping the structure and function within the community, but how to identify them at the genome-wide level has always been challenging.

Methods: In this study, we embed the Lotka-Volterra ordinary differential equations in the theory of community ecology into the systems mapping model, so that this model can not only describe how the quantitative trait loci (QTL) of a species directly affects its own phenotype, but also describe the QTL of the species how to indirectly affect the phenotype of its interacting species, and how QTL from different species affects community behavior through epistatic interactions.

Results: By designing and implementing a co-culture experiment for 100 pairs of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), we mapped 244 significant QTL combinations in the interaction process of the two bacteria using this model, including 69 QTLs from E. coli and 59 QTLs from S. aureus, respectively. Through gene annotation, we obtained 57 genes in E. coli, among which the genes with higher frequency were ypdC, nrfC, yphH, acrE, dcuS, rpnE, and ptsA, while we obtained 43 genes in S. aureus, among which the genes with higher frequency were ebh, SAOUHSC_00172, capF, gdpP, orfX, bsaA, and phnE1.

Discussion: By dividing the overall growth into independent growth and interactive growth, we could estimate how QTLs modulate interspecific competition and cooperation. Based on the quantitative genetic model, we can obtain the direct genetic effect, indirect genetic effect, and genome-genome epistatic effect related to interspecific interaction genes, and then further mine the hub genes in the QTL networks, which will be particularly useful for inferring and predicting the genetic mechanisms of community dynamics and evolution. Systems mapping can provide a tool for studying the mechanism of competition and cooperation among bacteria in co-culture, and this framework can lay the foundation for a more comprehensive and systematic study of species interactions.

Keywords: Escherichia coli; Staphylococcus aureus; competition-cooperation mechanism; interspecific interaction; systems mapping.

Grants and funding

This research was supported by the Science and Technology Innovation 2030 Major Program (No. 2023ZD0405804) and the National Natural Science Foundation of China (31971398).