What question did this study set out to answer?

To develop a tutorial for constructing metabolic models of iron-oxidizing bacteria using KBase tools.

January 18, 2026Microbiology Resource Announcements0 citationsOpen Access

Modeling neutrophilic iron-oxidizing bacteria: a KBase narrative resource describing newly integrated metabolic reactions

GTGracee K. TotheroBiotechnology Institute JAJames AngPacific Northwest National Laboratory FLFilipe LiuArgonne National Laboratory

Key Points

To develop a tutorial for constructing metabolic models of iron-oxidizing bacteria using KBase tools.
Utilized the ModelSEED2 framework for metabolic modeling.
Integrated iron oxidation capabilities into the framework.
Conducted omics analyses to support predictions of metabolic behavior.
Successfully constructed stoichiometric models of bacteria involved in iron oxidation.
Demonstrated improved predictions of physiological dynamics and metabolic fluxes related to iron oxidation.

Abstract

ABSTRACT We present a KBase tutorial narrative demonstrating construction of stoichiometric metabolic models of iron-oxidizing bacteria. The tutorial describes an extended ModelSEED2 framework, which includes support for iron oxidation. These capabilities complement omics analyses by enabling predictions of physiological dynamics, metabolic fluxes, and the role of iron oxidation in environmental systems.

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