Cited by 304Microbial Metabolic Engineering and BioproductionGene Regulatory Network AnalysisBioinformatics and Genomic Networks

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Reconstructing organisms in silico: genome-scale models and their emerging applications

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Fang, Xin, Lloyd, Colton J., Palsson, Bernhard O.·2020·Nature Reviews Microbiology

DOI 10.1038/s41579-020-00440-4PMC PMC7981288

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Abstract

Escherichia coli is considered to be the best-known microorganism given the large number of published studies detailing its genes, its genome and the biochemical functions of its molecular components. This vast literature has been systematically assembled into a reconstruction of the biochemical reaction networks that underlie E. coli's functions, a process which is now being applied to an increasing number of microorganisms. Genome-scale reconstructed networks are organized and systematized knowledge bases that have multiple uses, including conversion into computational models that interpret and predict phenotypic states and the consequences of environmental and genetic perturbations. These genome-scale models (GEMs) now enable us to develop pan-genome analyses that provide mechanistic insights, detail the selection pressures on proteome allocation and address stress phenotypes. In this Review, we first discuss the overall development of GEMs and their applications. Next, we review the evolution of the most complete GEM that has been developed to date: the E. coli GEM. Finally, we explore three emerging areas in genome-scale modelling of microbial phenotypes: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses.

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Additional file 9 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
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Additional file 3 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
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Additional file 6 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558351
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Additional file 11 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
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Additional file 1 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
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Additional file 7 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
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Additional file 10 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558363
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Additional file 5 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
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Additional file 1 of Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii
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Additional file 8 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558357
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Additional file 6 of Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii
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Additional file 4 of Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii
Yao, H., Dahal, S., & Yang, L. (2024) · Figshare · doi:10.6084/m9.figshare.26562172
Additional file 7 of Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii
Yao, H., Dahal, S., & Yang, L. (2024) · Figshare · doi:10.6084/m9.figshare.26562181
Additional file 3 of Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii
Yao, H., Dahal, S., & Yang, L. (2024) · Figshare · doi:10.6084/m9.figshare.26562169
Additional file 2 of Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii
Yao, H., Dahal, S., & Yang, L. (2024) · Figshare · doi:10.6084/m9.figshare.26562166
Additional file 4 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558345
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Additional file 2 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558339
Self-citation
TROPPO: tissue-specific reconstruction and phenotype prediction using omics data
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Authors: Fang, X., Lloyd, C. J., & Palsson, B. O.
Affiliations: University of California San Diego (US)
ORCID: Fang, Xin
Lloyd, Colton J.
Palsson, Bernhard O.
Venue: Nature Reviews Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2020-09-21
Volume: 18
Issue: 12
Pages: 731-743
ISSN: 1740-1526 (ISSN-L)
1740-1534
DOI: 10.1038/s41579-020-00440-4
PMC: PMC7981288
OpenAlex: W3087744872
Cited by: 292
References: 142
Citations by year: 2026: 34 · 2025: 49 · 2024: 66 · 2023: 60 · 2022: 35 · 2021: 47 · 2020: 1
FWCI: 3.42
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature Reviews Microbiology (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
Funders: National Institute of General Medical Sciences (R01GM057089)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords: genome-scale metabolic models, Escherichia coli, metabolic network reconstruction, pangenome analysis, proteome allocation, phenotype prediction
MeSH terms: Firmicutes, Bacillota, Whole Genome Sequencing, Thermotoga, Cyanobacteria, Computer Simulation, Escherichia coli, Models, Genetic, Phenotype, Stress, Physiological, Genome, Bacterial, Proteobacteria, Genomics, Actinobacteria, Gene Regulatory Networks, Metabolic Networks and Pathways

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Reconstructing organisms in silico: genome-scale models and their emerging applications

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