U.S. Department of EnergyOffice of Scientific and Technical Information
Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium
Abstract
This narrative was used for the 3-member community modeling using R2A medium for the bacteria isolated from Populus deltoides (PD). 10 bacteiral strains isolated from PD were co-cultured as a synthetic microbial community in R2A complex medium. After 15 passages, there were 3 members survived in R2A medium. The genome of each community member was sequenced and uploaded into KBase for genome annotation and metabolic modeling. To simulate the metabolic interactions among the finally surviving community members, the individual metabolic models of each strain were merged into a compartmentalized community model, and then the community model was gapfilled using R2A medium. The FBA modeling was performed and the metabolites exchange among community members was proposed. The publication by Jia Wang, Dana L. Carper, Leah H. Burdick, Him Shrestha, Manasa Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz can be found here: https://doi.org/10.1016/j.csbj.2021.03.034
- Authors:
-
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Department of Energy Systems Biology Knowledgebase (KBase)
- Publication Date:
- DOE Contract Number:
- AC05-00OR22725
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; community model, flux balance analysis, bacterial community, synthetic microbial community, plant-microbe interactions
- OSTI Identifier:
- 1777993
- DOI:
- https://doi.org/10.25982/73221.117/1777993
Citation Formats
Wang, Jia. Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium. United States: N. p., 2020.
Web. doi:10.25982/73221.117/1777993.
Wang, Jia. Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium. United States. doi:https://doi.org/10.25982/73221.117/1777993
Wang, Jia. 2020.
"Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium". United States. doi:https://doi.org/10.25982/73221.117/1777993. https://www.osti.gov/servlets/purl/1777993. Pub date:Thu Dec 31 23:00:00 EST 2020
@article{osti_1777993,
title = {Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium},
author = {Wang, Jia},
abstractNote = {This narrative was used for the 3-member community modeling using R2A medium for the bacteria isolated from Populus deltoides (PD). 10 bacteiral strains isolated from PD were co-cultured as a synthetic microbial community in R2A complex medium. After 15 passages, there were 3 members survived in R2A medium. The genome of each community member was sequenced and uploaded into KBase for genome annotation and metabolic modeling. To simulate the metabolic interactions among the finally surviving community members, the individual metabolic models of each strain were merged into a compartmentalized community model, and then the community model was gapfilled using R2A medium. The FBA modeling was performed and the metabolites exchange among community members was proposed. The publication by Jia Wang, Dana L. Carper, Leah H. Burdick, Him Shrestha, Manasa Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz can be found here: https://doi.org/10.1016/j.csbj.2021.03.034},
doi = {10.25982/73221.117/1777993},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Thu Dec 31 23:00:00 EST 2020},
month = {Thu Dec 31 23:00:00 EST 2020}
}