Integrative Metabolic Modelling of Bacterial Systems in Microbiome Contexts: From Genomes to Community Functions
A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbiomes".
Deadline for manuscript submissions: closed (31 December 2025) | Viewed by 1158
Special Issue Editor
Special Issue Information
Dear Colleagues,
The rapid growth of multi-omics and metagenomic data is transforming our understanding of microbiomes across natural, clinical, and industrial environments. In this evolving landscape, metabolic modelling of individual bacterial strains and microbial communities has become a key tool for linking genomic potential to ecological and functional roles. This Special Issue invites original research articles and reviews that explore the integration of genome-scale metabolic models (GEMs) within microbiome research. We particularly welcome studies focused on the reconstruction of metabolic networks, phenotype prediction, simulation of interspecies interactions, and the rational design of synthetic consortia. Contributions that combine experimental data, computational approaches, artificial intelligence, or automated genome annotation and pathway prediction tools are highly encouraged. Topics of interest include, but are not limited to, metabolic modelling of bacteria isolated from complex environments (e.g., soil, gut, marine ecosystems); integrated approaches for model construction from metagenomes and MAGs (metagenome-assembled genomes); computational exploration of cross-feeding and trophic interactions within microbial communities; experimental validation of in silico predictions in natural or synthetic microbiomes; development of bioinformatics tools to automate metabolic modelling in microbiome studies.
Dr. Arianna Basile
Guest Editor
Manuscript Submission Information
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Keywords
- microbiome
- multi-omics
- microbial communities
- metabolic modelling
- bioinformatics tools
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