ArticleNucleic acids research2018
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 381 papers, 2 of them syntheses that pooled it.
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Who cites it
381 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.Nature microbiology · 2026Pooled it
- Antimicrobial resistance crisis: could artificial intelligence be the solution?Military Medical Research · 2024Pooled it
- Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies.Gut microbes · 2026Article
- Bridging the gap:Gut microbes · 2026Review
- Metabolic flux analysis revealed key roles of ArcB in ADI pathway and IlvC in BCAA biosynthesis duringVirulence · 2026Article
- Cross-feeding enables robust coexistence between four bacterial species.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Integrative Proteomics and Genome-Scale Modeling Elucidate Metabolic Flux Shifts inInternational journal of molecular sciences · 2026Article
- Community Interactions and Extracellular Riboflavin Are Associated with Oral Biofilm-Mediated Medical Stainless Steel Corrosion.Microorganisms · 2026Article
- BioEMMA: Automated Generation of Model-Specific Escher-Compatible Maps from KEGG Pathways.Biology · 2026Article
- Obligate cross-feeding of metabolites is common in soil microbial communities.Nature microbiology · 2026Article
- Decoding microbial metabolic complementarity from individual traits to community structuring.Ecology · 2026Article
- Systems Biology and Structure-Based In Silico Evaluations of Quercetin-Psychobiotic Interactions for the Management of Depression.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Causal AI digital twin for bioprocess bottleneck diagnosis via metabolic flexibility and rigidification maps.iScience · 2026Article
- Article
- MAAMOUL: metabolic network-based discovery of microbiome-metabolome shifts in disease.Bioinformatics (Oxford, England) · 2026Article
- Environmental formermSystems · 2026Article
- AlphaGEM enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining.Nature communications · 2026Article
- Untargeted Blubber Metabolomics Reveals Biochemical Signatures Associated with Physiological Status in Live, Free-Ranging Bottlenose Dolphins.Metabolites · 2026Article
- Functional roles of degraders and non-degraders in anaerobic trophic networks converting lignocellulose into monocarboxylates.NPJ biofilms and microbiomes · 2026Article
- Multi-omic characterization of a soil microbial consortium reveals critical role of succinate and glutamate metabolism during calcium carbonate precipitation.BMC biotechnology · 2026Article
321 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-scale metabolic models are instrumental in uncovering operating principles of cellular metabolism, for model-guided re-engineering, and unraveling cross-feeding in microbial communities. Yet, the application of genome-scale models, especially to microbial communities, is lagging behind the availability of sequenced genomes. This is largely due to the time-consuming steps of manual curation required to obtain good quality models. Here, we present an automated tool, CarveMe, for reconstruction of species and community level metabolic models. We introduce the concept of a universal model, which is manually curated and simulation ready. Starting with this universal model and annotated genome sequences, CarveMe uses a top-down approach to build single-species and community models in a fast and scalable manner. We show that CarveMe models perform closely to manually curated models in reproducing experimental phenotypes (substrate utilization and gene essentiality). Additionally, we build a collection of 74 models for human gut bacteria and test their ability to reproduce growth on a set of experimentally defined media. Finally, we create a database of 5587 bacterial models and demonstrate its potential for fast generation of microbial community models. Overall, CarveMe provides an open-source and user-friendly tool towards broadening the use of metabolic modeling in studying microbial species and communities.
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