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In Silico Reconstructions

Please visit the Virtual Metabolic Human database for all our reconstructions of human and gut microbial metabolism.

AGORA2

Please cite: Heinken et al, Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine, Nat Biotech, 2023, https://doi.org/10.1038/s41587-022-01628-0.

The reconstructions can be downloaded here: 

https://www.vmh.life/files/reconstructions/AGORA2/

Organ-resolved, sex-specific whole-body metabolic reconstructions (Harvey and Harvetta).

Please cite: Thiele, I., Sahoo, S., Heinken, A., Hertel, J., Heirendt, L., Aurich, M.K., Fleming, R.M.T., "Personalized whole-body models integrate metabolism, physiology, and the gut microbiome", Molecular Systems Biology, 16:e8982 (2020).

- male WBM

- female WBM 

Please cite: Thiele, I., Sahoo, S., Heinken, A., Hertel, J., Heirendt, L., Aurich, M.K., Fleming, R.M.T., "Personalized whole-body models integrate metabolism, physiology, and the gut microbiome", Molecular Systems Biology, 16:e8982 (2020).

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Microbial Metabolic Reconstructions

Heinken et al., "A systematic interrogation of the distinct metabolic potential in gut microbiomes of inflammatory bowel disease patients with dysbiosis",  Systems Biology & Applications (2020).

InputFiles.

ComputedFluxes.

ConstrainedMicrobiomeModels_Set1.

ConstrainedMicrobiomeModels_Set2.

818 curated gut microbial metabolic reconstructions​

  • The latest version can also be downloaded from github: Link

  • Please cite:  Magnusdottir, S., Heinken, A., Kutt, L., Ravcheev, D.A., Bauer, E., Noronha, A., Greenhalgh, K., Jaeger, C., Baginska, J., Wilmes, P., Fleming, R.M.T., Thiele, I., ''Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota'', Nature Biotechnology, 35(1):81-89 (2017)

Bacteroides thetaiotaomicron.

  • Please cite: Heinken et al., "Systems-level characterization of the host-microbe metabolic symbiosis in the mammalian gut", Gut Microbes, 4(1):1-13 (2013)

Collection of 11 human gut microbe reconstructions in SBML format.

  • Please cite the original references listed in the included readme file.

Faecalibacterium prausnitzii.

  • Please cite “Heinken, A. et al. A functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. J Bacteriol, 196(18):3289-302 (2014).

Pseudomonas aeruginosa.

  • Please cite: Sigurdsson, G. et al.,"A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm", PLoS One, 7(4): e34337 (2012).

Synechocystis sp. PCC6803.

  • Please cite: Nogales, J.et al., "Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis.", PNAS, 109(7):2678-83 (2012).

Thermotoga maritima. 

  • Please cite: Nogales et al., "An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production", Int J Hydrogen Energ, 37(17), 12205–12218 (2012).

Draft metabolic reconstructions for 301 gastro-intestinal microbe models. 

  • Please cite Bauer et al., "Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires". Microbiome, 3(1):1-13, 2015.

Eukaryotic Biochemical Models

Human metabolic reconstruction, Recon 2.

  • Please cite: Thiele et al., "A community-driven global reconstruction of human metabolism", Nat Biotechnol. 2013.

Human small intestinal enterocytes. 

  • Please cite: Sahoo et al., "Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells", Human Mol Genet, 22(13):2705-2722.

Human cardiac myocyte mitochondrial metabolic reconstruction. 

  • Please cite: Thiele et al., "Candidate metabolic network states in human mitochondria: Impact of diabetes, ischemia, and diet.", J Biol Chem, 280(12):11683-11695 (2005).

Mus musculus. 

  • Please cite: Heinken et al., "Systems-level characterization of the host-microbe metabolic symbiosis in the mammalian gut", Gut Microbes, 4(1):1-13 (2013).

Host-Microbe Biochemical Models

Bacteroides thetaiotaomicron - Mus musculus co-growth model. 

  • Please cite: Heinken et al., "Systems-level characterization of the host-microbe metabolic symbiosis in the mammalian gut", Gut Microbes, 4(1):1-13 (2013).

Global human reconstruction Recon2 joined with a model community of 11 human gut microbes (in total 25 models are provided).

  • SI Table S7.

  • Please cite: Heinken and Thiele. "Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework". Gut Microbes, 6(2):120-130, 2015.

Model community of 11 gut microbes joined pairwise with and without small intestinal enterocyte.

  • Please cite: Heinken and Thiele, "Anoxic conditions promote species-specific mutualism between gut microbes in silico". Appl Environ Microbiol, 10.1128/AEM.00101-15, 2015.

Multi-Scale Biochemical Models

Expression matrix (E-Matrix) for E. coli. 

  • Please cite: Thiele, I., et la., "Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: A knowledge base, its mathematical formulation, and its functional characterization.", PLoS Comp Biol, 5(3):e1000312 (2009).

Hybrid model of levodopa gastrointestinal absorption.

  • Please cite Ben Guebila and Thiele, “Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients.”, NPJ Syst Biol Appl, doi:10.1038/npjsba.2016.13

Metabolism & Expression matrix (ME-Matrix) for E. coli: minimal medium glucose, aerobic conditions, wildtype.

  • Please cite: Thiele et al., "Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage", PLoS One, 7(9):e45635 (2012).

Toll-like receptor signalling model. 

  • Please cite: Aurich and Thiele, "Contextualization procedure and modeling of monocyte specific TLR signaling", PLoS ONE 7(12): e49978 (2012).

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