ArticleeLife2023
Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models.
Article in eLife, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- BioEMMA: Automated Generation of Model-Specific Escher-Compatible Maps from KEGG Pathways.Biology · 2026Article
- High-throughput generation and comparison of genome-scale metabolic models reveal strain-specific metabolic diversity in 439mSystems · 2026Article
- Global perspectives on Klebsiella epidemiology and biology: conference report on the KLEBS 2024 symposium.npj antimicrobials and resistance · 2026Article
- Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models.mSystems · 2026Article
- A public resource of 15 genomically characterized representative strains ofMicrobial genomics · 2026Article
- Exploring the IS-capades ofMicrobial genomics · 2026Article
- Evidencing strain-dependency of metabolic pathways within 1,494 lactic bacteria genomes with thePeerJ · 2026Article
- A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation.PLoS biology · 2025Article
- Evaluation of Genome-Scale Model Reconstruction Strategies forMetabolites · 2025Article
- Use of genome-scale metabolic reconstructions of avian pathogenicMicrobial genomics · 2025Article
- Genome-scale models in human metabologenomics.Nature reviews. Genetics · 2025Review
- Wild-Type Domestication: Loss of Intrinsic Metabolic Traits Concealed by Culture in Rich Media.Microbial ecology · 2024Article
- Variation in the response to antibiotics and life-history across the majorMicrobiology spectrum · 2024Article
- A validated pangenome-scale metabolic model for theMicrobial genomics · 2024Article
- State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs.Microorganisms · 2023Review
- Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models.eLife · 2023Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolic capacity can vary substantially within a bacterial species, leading to ecological niche separation, as well as differences in virulence and antimicrobial susceptibility. Genome-scale metabolic models are useful tools for studying the metabolic potential of individuals, and with the rapid expansion of genomic sequencing there is a wealth of data that can be leveraged for comparative analysis. However, there exist few tools to construct strain-specific metabolic models at scale. Here, we describe Bactabolize, a reference-based tool which rapidly produces strain-specific metabolic models and growth phenotype predictions. We describe a pan reference model for the priority antimicrobial-resistant pathogen,
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