ArticleProceedings of the National Academy of Sciences of the United States of America2013
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 176 papers.
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Who cites it
176 citing papers in PubMed.
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- Multiplexed CRISPR base editing enables pulse-activated irreversible biocontainment of engineered bacteria.Nucleic acids research · 2026Article
- High-throughput generation and comparison of genome-scale metabolic models reveal strain-specific metabolic diversity in 439mSystems · 2026Article
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- Identification of specific metabolic capacities associated with major extraintestinal pathogenicJournal of bacteriology · 2026Article
- Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models.mSystems · 2026Article
- Describing and Designing Microbial Community Metabolic Models In Silico: A Comprehensive Protocol Utilizing FLYCOP.Methods in molecular biology (Clifton, N.J.) · 2026Article
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- Genome-scale Metabolic Modeling Guided Escherichia coli Engineering for De Novo Biosynthesis of Chrysanthemic Acid.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- From Single Organisms to Communities: Modeling Methanotrophs and Their Satellites.Microorganisms · 2025Review
- A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation.PLoS biology · 2025Article
- Rare metabolic gene essentiality is a determinant of microniche adaptation in Eschherichia coli.PLoS pathogens · 2025Article
- Multi-strain Analysis ofbioRxiv : the preprint server for biology · 2025Article
- PMkbase (version 1.0): an interactive web-based tool for tracking bacterial metabolic traits using phenotype microarrays made interoperable with sequence information and visualizing/processing PM data.Microbiology spectrum · 2025Article
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- Use of genome-scale metabolic reconstructions of avian pathogenicMicrobial genomics · 2025Article
- Experimental systems are essential for strengthening ecological modeling of microbiomes beyond observational data.mSystems · 2025Review
116 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
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Abstract
Genome-scale models (GEMs) of metabolism were constructed for 55 fully sequenced Escherichia coli and Shigella strains. The GEMs enable a systems approach to characterizing the pan and core metabolic capabilities of the E. coli species. The majority of pan metabolic content was found to consist of alternate catabolic pathways for unique nutrient sources. The GEMs were then used to systematically analyze growth capabilities in more than 650 different growth-supporting environments. The results show that unique strain-specific metabolic capabilities correspond to pathotypes and environmental niches. Twelve of the GEMs were used to predict growth on six differentiating nutrients, and the predictions were found to agree with 80% of experimental outcomes. Additionally, GEMs were used to predict strain-specific auxotrophies. Twelve of the strains modeled were predicted to be auxotrophic for vitamins niacin (vitamin B3), thiamin (vitamin B1), or folate (vitamin B9). Six of the strains modeled have lost biosynthetic pathways for essential amino acids methionine, tryptophan, or leucine. Genome-scale analysis of multiple strains of a species can thus be used to define the metabolic essence of a microbial species and delineate growth differences that shed light on the adaptation process to a particular microenvironment.
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