ArticleMetabolomics : Official journal of the Metabolomic Society
Recon 2.2: from reconstruction to model of human metabolism.
Article in Metabolomics : Official journal of the Metabolomic Society. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 152 papers.
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152 citing papers in PubMed, 328 citations in OpenAlex.
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- Metabolic modeling elucidates phenformin and atpenin A5 as broad-spectrum antiviral drugs against RNA viruses.Communications biology · 2025Article
- Metabolic modelling reveals the aging-associated decline of host-microbiome metabolic interactions in mice.Nature microbiology · 2025Article
- Genome-scale models in human metabologenomics.Nature reviews. Genetics · 2025Review
- Advances in functional analysis of the microbiome: Integrating metabolic modeling, metabolite prediction, and pathway inference with Next-Generation Sequencing data.Journal of microbiology (Seoul, Korea) · 2025Review
- Longitudinal Metabolomics Data Analysis Informed by Mechanistic Models.Metabolites · 2024Article
92 more citing papers are in PubMed but not listed here.
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25 authors at 11 institutions in 5 countries.
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Abstract
introductionThe human genome-scale metabolic reconstruction details all known metabolic reactions occurring in humans, and thereby holds substantial promise for studying complex diseases and phenotypes. Capturing the whole human metabolic reconstruction is an on-going task and since the last community effort generated a consensus reconstruction, several updates have been developed.
objectivesWe report a new consensus version, Recon 2.2, which integrates various alternative versions with significant additional updates. In addition to re-establishing a consensus reconstruction, further key objectives included providing more comprehensive annotation of metabolites and genes, ensuring full mass and charge balance in all reactions, and developing a model that correctly predicts ATP production on a range of carbon sources.
methodsRecon 2.2 has been developed through a combination of manual curation and automated error checking. Specific and significant manual updates include a respecification of fatty acid metabolism, oxidative phosphorylation and a coupling of the electron transport chain to ATP synthase activity. All metabolites have definitive chemical formulae and charges specified, and these are used to ensure full mass and charge reaction balancing through an automated linear programming approach. Additionally, improved integration with transcriptomics and proteomics data has been facilitated with the updated curation of relationships between genes, proteins and reactions.
resultsRecon 2.2 now represents the most predictive model of human metabolism to date as demonstrated here. Extensive manual curation has increased the reconstruction size to 5324 metabolites, 7785 reactions and 1675 associated genes, which now are mapped to a single standard. The focus upon mass and charge balancing of all reactions, along with better representation of energy generation, has produced a flux model that correctly predicts ATP yield on different carbon sources.
conclusionThrough these updates we have achieved the most complete and best annotated consensus human metabolic reconstruction available, thereby increasing the ability of this resource to provide novel insights into normal and disease states in human. The model is freely available from the Biomodels database (http://identifiers.org/biomodels.db/MODEL1603150001).
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