TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria

Tothero, Gracee K [Department of Earth Sciences, University of Delaware, Newark, DE, USA; Delaware Biotechnology Institute, Newark, DE, USA] (ORCID:0000000177923880); Weisenhorn, Pamela [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000318445502); Liu, Filipe [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000187012984); Faria, José P [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000193027250); Henry, Christopher [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000180589123); Chan, Clara S [Department of Earth Sciences, University of Delaware, Newark, DE, USA; Delaware Biotechnology Institute, Newark, DE, USA] (ORCID:0000000318104994)

doi:10.25982/200793.58/2556864

DOE OSTI · 2556864

TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria

Tothero, Gracee K [Department of Earth Sciences, University of Delaware, Newark, DE, USA; Delaware Biotechnology Institute, Newark, DE, USA] (ORCID:0000000177923880)·Weisenhorn, Pamela [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000318445502)·Liu, Filipe [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000187012984)·Faria, José P [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000193027250)·Henry, Christopher [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000180589123)·Chan, Clara S [Department of Earth Sciences, University of Delaware, Newark, DE, USA; Delaware Biotechnology Institute, Newark, DE, USA] (ORCID:0000000318104994)

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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.

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Tothero, Gracee K [Department of Earth Sciences, University of Delaware, Newark, DE, USA; Delaware Biotechnology Institute, Newark, DE, USA] (ORCID:0000000177923880), Weisenhorn, Pamela [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000318445502), Liu, Filipe [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000187012984), Faria, José P [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000193027250), Henry, Christopher [Argonne National Laboratory, Lemont, IL, USA] (ORCID:0000000180589123), Chan, Clara S [Department of Earth Sciences, University of Delaware, Newark, DE, USA; Delaware Biotechnology Institute, Newark, DE, USA] (ORCID:0000000318104994). 2025-04-15. TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria. https://doi.org/10.25982/200793.58%2F2556864

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