ArticleJournal of bacteriology2011
Core and panmetabolism in Escherichia coli.
Article in Journal of bacteriology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
33 citing papers in PubMed, 62 citations in OpenAlex.
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- Gene-level analysis of core carbohydrate metabolism across the Enterobacteriaceae pan-genome.Communications biology · 2025Article
- Gut Microbiota Dynamics in Hibernating and ActiveVeterinary sciences · 2025Article
- The role of bacterial metabolism in human gut colonization.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Review
- Limitations of sequence dissimilarity as a predictor of prokaryotic lineage.Open biology · 2025Review
- Genomic evidence of genetic diversity and functional evolution inFrontiers in microbiology · 2023Article
- Genomics and pathotypes of the many faces of Escherichia coli.FEMS microbiology reviews · 2022Article
- Phylogenetic background and habitat drive the genetic diversification of Escherichia coli.PLoS genetics · 2020Article
- Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial GenusmSystems · 2020Article
- Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens.Frontiers in cell and developmental biology · 2020Review
- MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.Briefings in bioinformatics · 2019Article
- Selective colonization ability of human fecal microbes in different mouse gut environments.The ISME journal · 2019Article
- High genomic diversity of multi-drug resistant wastewater Escherichia coli.Scientific reports · 2018Article
- Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes.PLoS genetics · 2018Article
- Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds.Frontiers in microbiology · 2018Article
- Metabolic network model guided engineering ethylmalonyl-CoA pathway to improve ascomycin production in Streptomyces hygroscopicus var. ascomyceticus.Microbial cell factories · 2017Article
- Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer.Journal of bacteriology · 2017Article
- Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.Cell systems · 2016Article
Corrections and comments
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Authors and funding
11 authors at 7 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Escherichia coli exhibits a wide range of lifestyles encompassing commensalism and various pathogenic behaviors which its highly dynamic genome contributes to develop. How environmental and host factors shape the genetic structure of E. coli strains remains, however, largely unknown. Following a previous study of E. coli genomic diversity, we investigated its diversity at the metabolic level by building and analyzing the genome-scale metabolic networks of 29 E. coli strains (8 commensal and 21 pathogenic strains, including 6 Shigella strains). Using a tailor-made reconstruction strategy, we significantly improved the completeness and accuracy of the metabolic networks over default automatic reconstruction processes. Among the 1,545 reactions forming E. coli panmetabolism, 885 reactions were common to all strains. This high proportion of core reactions (57%) was found to be in sharp contrast to the low proportion (13%) of core genes in the E. coli pangenome, suggesting less diversity of metabolic functions compared to that of all gene functions. Core reactions were significantly overrepresented among biosynthetic reactions compared to the more variable degradation processes. Differences between metabolic networks were found to follow E. coli phylogeny rather than pathogenic phenotypes, except for Shigella networks, which were significantly more distant from the others. This suggests that most metabolic changes in non-Shigella strains were not driven by their pathogenic phenotypes. Using a supervised method, we were yet able to identify small sets of reactions related to pathogenicity or commensalism. The quality of our reconstructed networks also makes them reliable bases for building metabolic models.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.