Work

Metabolic modeling of host-microbe interactions

Year: 2025

Type: article

Abstract: Host-microbe interactions play an integral role in the function and survival of eukaryotes, influencing various processes ranging from metabolism to immune regulation. As our understanding of these interactions deepens, there is a growing shift toward integrative approaches that consider both host and microbial genotypic potential. However, capturing the complexity and dynamic nature of these relationships remains a significant challenge. Genome-scale metabolic models (GEMs) offer a powerful framework to investigate host-microbe interactions at a systems level. By simulating metabolic fluxes and cross-feeding relationships, GEMs enable the exploration of metabolic interdependencies and emergent community functions. These models can be applied independently or in conjunction with experimental data, supporting hypothesis generation and systems-level insights into host-microbe dynamics. In this review, we examine recent applications of GEMs to host-microbe studies, with a focus on how they reveal reciprocal metabolic influences. We also discuss the current technical challenges, highlight available tools and methodological strategies, such as model reconstruction, data integration, and simulation and analysis steps, and outline future directions for advancing host-microbe interaction study using GEMs.

Source: Computational and Structural Biotechnology Journal

DOI: 10.1016/j.csbj.2025.10.006

Authors: Natchapon Srinak, Florian Krüger, Christoph Kaleta, Jan Taubenheim

Institutions: Christian-Albrechts-Universität zu Kiel, University Hospital Schleswig-Holstein

Language: English

Topic: Microbial Metabolic Engineering and Bioproduction

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,230

Funders: Deutsche Forschungsgemeinschaft, Bundesministerium für Bildung und Forschung