Jan 31, 2014

Predicting bacterial growth conditions from bacterial physiology

BioRxiv : the Preprint Server for Biology
Viswanadham SridharaClaus O Wilke


Bacterial physiology reflects the environmental conditions of growth. A widely studied problem in systems biology is to predict bacterial phenotype from growth conditions, using mechanistic models such as flux balance analysis (FBA). However, the inverse prediction of growth conditions from phenotype is rarely considered. Here we develop a computational framework to carry out this inverse prediction on a computational model of bacterial physiology. We use FBA to calculate bacterial phenotypes from growth conditions in E. coli , and then we assess how accurately we can predict the original growth conditions from the phenotypes. Prediction is carried out via regularized multinomial regression. Our analysis provides several important physiological and statistical insights. First, we show that by analyzing metabolic end products we can consistently predict growth conditions. Second, prediction is reliable even in the presence of small amounts of impurities. Third, flux through a relatively small number of reactions per growth source ( ∼ 10) is sufficient for accurate prediction. Fourth, combining the predictions from two separate models, one trained only on carbon sources and one only on nitrogen sources, performs better than model...Continue Reading

  • References
  • Citations


  • We're still populating references for this paper, please check back later.
  • References
  • Citations


  • This paper may not have been cited yet.

Mentioned in this Paper

Metabolic Process, Cellular
Biochemical Pathway
Nitrogen Utilization
Cell Growth
Metabolic Pathway

About this Paper

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Related Papers

International Journal of Food Microbiology
Aline MetrisJózsef Baranyi
Current Opinion in Microbiology
Adam M Feist, Bernhard O Palsson
Proceedings of the National Academy of Sciences of the United States of America
Jong Myoung ParkSang Yup Lee
© 2020 Meta ULC. All rights reserved