U.S. Department of EnergyOffice of Scientific and Technical Information
TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria
Abstract
In this tutorial narrative, we introduce a novel template developed to enable the creation of stoichiometric genome-scale metabolic models for iron-oxidizing bacteria. We demonstrate the development of this template by applying it to Sideroxydans lithotrophicus ES-1, and validate our model using transcriptomic data (Published in Zhou et al., 2022 AEM). Below, we further show that our template facilitates the modeling of mixotrophic iron-oxidizing bacteria and metagenome-assembled genomes (MAGs), by applying our template to the MAG of the mixotrophic iron oxidizer Leptothrix ochracea (Published in Tothero et al, 2024). This work represents the first instance of a generalized and adaptable template for modeling diverse iron-oxidizing microbial systems, expanding the accessibility and applicability of metabolic modeling in this field.
- Authors:
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- Department of Earth Sciences, University of Delaware, Newark, DE, USA; Delaware Biotechnology Institute, Newark, DE, USA
- Argonne National Laboratory, Lemont, IL, USA
- Publication Date:
- DOE Contract Number:
- AC02-06CH11357
- Research Org.:
- Department of Earth Sciences, University of Delaware, Newark, DE, USA; Delaware Biotechnology Institute, Newark, DE, USA; Argonne National Laboratory, Lemont, IL, USA
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Subject:
- genome-scale model; iron-oxidizing bacteria; metabolic modeling
- OSTI Identifier:
- 2556864
- DOI:
- https://doi.org/10.25982/200793.58/2556864
Citation Formats
Tothero, Gracee K, Weisenhorn, Pamela, Liu, Filipe, Faria, José P, Henry, Christopher, and Chan, Clara S. TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria. United States: N. p., 2025.
Web. doi:10.25982/200793.58/2556864.
Tothero, Gracee K, Weisenhorn, Pamela, Liu, Filipe, Faria, José P, Henry, Christopher, & Chan, Clara S. TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria. United States. doi:https://doi.org/10.25982/200793.58/2556864
Tothero, Gracee K, Weisenhorn, Pamela, Liu, Filipe, Faria, José P, Henry, Christopher, and Chan, Clara S. 2025.
"TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria". United States. doi:https://doi.org/10.25982/200793.58/2556864. https://www.osti.gov/servlets/purl/2556864. Pub date:Tue Apr 15 00:00:00 EDT 2025
@article{osti_2556864,
title = {TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria},
author = {Tothero, Gracee K and Weisenhorn, Pamela and Liu, Filipe and Faria, José P and Henry, Christopher and Chan, Clara S},
abstractNote = {In this tutorial narrative, we introduce a novel template developed to enable the creation of stoichiometric genome-scale metabolic models for iron-oxidizing bacteria. We demonstrate the development of this template by applying it to Sideroxydans lithotrophicus ES-1, and validate our model using transcriptomic data (Published in Zhou et al., 2022 AEM). Below, we further show that our template facilitates the modeling of mixotrophic iron-oxidizing bacteria and metagenome-assembled genomes (MAGs), by applying our template to the MAG of the mixotrophic iron oxidizer Leptothrix ochracea (Published in Tothero et al, 2024). This work represents the first instance of a generalized and adaptable template for modeling diverse iron-oxidizing microbial systems, expanding the accessibility and applicability of metabolic modeling in this field.},
doi = {10.25982/200793.58/2556864},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Apr 15 00:00:00 EDT 2025},
month = {Tue Apr 15 00:00:00 EDT 2025}
}