TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria
- Department of Earth Sciences, University of Delaware, Newark, DE, USA; Delaware Biotechnology Institute, Newark, DE, USA
- Argonne National Laboratory, Lemont, IL, USA
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.
- Research Organization:
- Department of Earth Sciences, University of Delaware, Newark, DE, USA; Delaware Biotechnology Institute, Newark, DE, USA; Argonne National Laboratory, Lemont, IL, USA
- Sponsoring Organization:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- DOE Contract Number:
- AC02-06CH11357
- OSTI ID:
- 2556864
- Country of Publication:
- United States
- Language:
- English
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