ArticleBMC systems biology2014
A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors.
Article in BMC systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 40 citations in OpenAlex.
- Computational approaches to understanding Clostridioides difficile metabolism and virulence.Current opinion in microbiology · 2022Review
- Dual transcriptome based reconstruction of Salmonella-human integrated metabolic network to screen potential drug targets.PloS one · 2022Article
- Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile.Cell host & microbe · 2021Article
- Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis.mSystems · 2021Article
- Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence.NPJ systems biology and applications · 2020Article
- Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation.Scientific reports · 2020Article
- Vegetative Cell and Spore Proteomes ofJournal of proteome research · 2019Article
- Human Systems Biology and Metabolic Modelling: A Review-From Disease Metabolism to Precision Medicine.BioMed research international · 2019Review
- Network-Based Metabolism-Centered Screening of Potential Drug Targets inFrontiers in cellular and infection microbiology · 2019Article
- Article
- Metabolism the Difficile Way: The Key to the Success of the PathogenFrontiers in microbiology · 2019Review
- A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs).PLoS computational biology · 2018Article
- Biomedical applications of genome-scale metabolic network reconstructions of human pathogens.Current opinion in biotechnology · 2018Review
- Ethanolamine is a valuable nutrient source that impacts Clostridium difficile pathogenesis.Environmental microbiology · 2018Article
- Insights into metabolic osmoadaptation of the ectoines-producer bacterium Chromohalobacter salexigens through a high-quality genome scale metabolic model.Microbial cell factories · 2018Article
- Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis.BMC systems biology · 2017Article
- Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes.BMC systems biology · 2017Article
- Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects.BMC pharmacology & toxicology · 2017Article
- Article
- Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization.BMC systems biology · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundClostridium difficile is the leading cause of hospital-borne infections occurring when the natural intestinal flora is depleted following antibiotic treatment. Current treatments for Clostridium difficile infections present high relapse rates and new hyper-virulent and multi-resistant strains are emerging, making the study of this nosocomial pathogen necessary to find novel therapeutic targets.
resultsWe present iMLTC806cdf, an extensively curated reconstructed metabolic network for the C. difficile pathogenic strain 630. iMLTC806cdf contains 806 genes, 703 metabolites and 769 metabolic, 117 exchange and 145 transport reactions. iMLTC806cdf is the most complete and accurate metabolic reconstruction of a gram-positive anaerobic bacteria to date. We validate the model with simulated growth assays in different media and carbon sources and use it to predict essential genes. We obtain 89.2% accuracy in the prediction of gene essentiality when compared to experimental data for B. subtilis homologs (the closest organism for which such data exists). We predict the existence of 76 essential genes and 39 essential gene pairs, a number of which are unique to C. difficile and have non-existing or predicted non-essential human homologs. For 29 of these potential therapeutic targets, we find 125 inhibitors of homologous proteins including approved drugs with the potential for drug repositioning, that when validated experimentally could serve as starting points in the development of new antibiotics.
conclusionsWe created a highly curated metabolic network model of C. difficile strain 630 and used it to predict essential genes as potential new therapeutic targets in the fight against Clostridium difficile infections.
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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.