Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism

PLoS Comput Biol. 2015 Oct 2;11(10):e1004452. doi: 10.1371/journal.pcbi.1004452. eCollection 2015 Oct.


A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm-based infections that are difficult to eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic cells. Developing treatments against biofilms requires an understanding of bacterial biofilm-specific physiological traits. Research efforts have started to elucidate the intricate mechanisms underlying biofilm development. However, many aspects of these mechanisms are still poorly understood. Here, we addressed questions regarding biofilm metabolism using a genome-scale kinetic model of the P. aeruginosa metabolic network and gene expression profiles. Specifically, we computed metabolite concentration differences between known mutants with altered biofilm formation and the wild-type strain to predict drug targets against P. aeruginosa biofilms. We also simulated the altered metabolism driven by gene expression changes between biofilm and stationary growth-phase planktonic cultures. Our analysis suggests that the synthesis of important biofilm-related molecules, such as the quorum-sensing molecule Pseudomonas quinolone signal and the exopolysaccharide Psl, is regulated not only through the expression of genes in their own synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules. Finally, we investigated why mutants defective in anthranilate degradation have an impaired ability to form biofilms. Alternative to a previous hypothesis that this biofilm reduction is caused by a decrease in energy production, we proposed that the dysregulation of the synthesis of secondary metabolites derived from anthranilate and chorismate is what impaired the biofilms of these mutants. Notably, these insights generated through our kinetic model-based approach are not accessible from previous constraint-based model analyses of P. aeruginosa biofilm metabolism. Our simulation results showed that plausible, non-intuitive explanations of difficult-to-interpret experimental observations could be generated by integrating genome-scale kinetic models with gene expression profiles.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Biofilms / growth & development*
  • Computer Simulation
  • Genome, Bacterial / genetics*
  • Kinetics
  • Metabolome / genetics*
  • Models, Biological*
  • Proteome / genetics
  • Proteome / metabolism
  • Pseudomonas aeruginosa / physiology*


  • Bacterial Proteins
  • Proteome

Grant support

The authors were supported by the U.S. Army Network Science Initiative, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD ( The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.