Table 1.
Genome-scale metabolic models to date. Under “Domain”, bacteria, eukaryote, and archaea are marked as “b”, “e”, and “a”, respectively.
| Organism | Domain | Model Details # rxns/# mets/# genes |
Refs | Demonstrated/Intended Applications |
|---|---|---|---|---|
| Lactobacillus plantarum | b | 643/531/721 | [19] | lactate [123] |
|
| ||||
| Lactococcus lactis | b | 621/422/358 | [20] | lactate [20], diacetyl [20] |
|
| ||||
| Streptococcus thermophilus | b | 522/---/429 | [22] | lactate, acetaldehyde |
|
| ||||
| Pseudomonas putida | b | 950/911/746 | [23] | polyhydroxyalkanoates [23, 24], bioremediation, biocatalytic chemicals, improvement of fossil fuel quality, promoting plant growth, pest control |
| Pseudomonas putida | 877/886/815 | [24] | ||
|
| ||||
| Clostridium acetobutylicum | b | 502/479/432 | [27] | acetone, butanol, ethanol, hydrogen |
| Clostridium acetobutylicum | 552/422/474 | [26] | ||
|
| ||||
| Methanosarcina barkeri | a | 509/558/692 | [28] | methane |
|
| ||||
| Desulfovibrio vulgaris | b | ---/---/--- | [29] | methane |
|
| ||||
| Methanococcus maripaludis | a | ---/---/--- | [29] | methane |
|
| ||||
| Acinetobacter baylyi | b | 875/701/774 | [31] | pollutant degradation, lipases, proteases, bioemulsifiers, cyanophycine, various biopolymers |
|
| ||||
| Geobacter metallireducens | b | 697/769/747 | [32] | reducing Fe(III), bioremediation of uranium, plutonium, technetium & vadium, fuel cell development |
|
| ||||
| Geobacter sulfurreducens | b | 523/541/588 | [33] | reducing Fe(III), bioremediation of uranium, plutonium, technetium & vadium [34], fuel cell development [34] |
|
| ||||
| Arabidopsis thaliana | e | ---/---/--- | [35] | photosynthetic plant cell, various secondary metabolites, flavonoid, polyamine metabolism |
|
| ||||
| Chlamydomonas reinhardtii | e | 259/113/174 | [36] | photosynthetic green algae, hydrogen production |
|
| ||||
| Halobacterium salinarum | a | 711/557/490 | [37] | producing bacteriorhodopsin |
|
| ||||
| Synechocystis sp | b | 831/704/633 | [38] | photosynthetic cyanobateria, ethanol production [38] |
|
| ||||
| Staphylococcus aureus | b | 640/571/691 | [41] | antibiotic target [41–44] |
| Staphylococcus aureus | 774/712/551 | [43] | ||
| Staphylococcus aureus (multiple strains) | 1444~97/1399~1437/522~47 | [44] | ||
|
| ||||
| Haemophilus influenzae | b | 461/451/412 | [1] | antibiotic target [1, 45] |
|
| ||||
| Pseudomonas aeruginosa | b | 883/760/1056 | [51] | antibiotic target [51] |
|
| ||||
| Mycobacterium tuberculosis | b | 849/739/726 | [46] | antibiotic target [42, 46–48, 50] |
| Mycobacterium tuberculosis | 939/828/661 | [47] | ||
|
| ||||
| Helicobacter pylori | b | 476/485/341 | [53] | antibiotic target [42, 53] |
|
| ||||
| Salmonella typhimurium | b | 1087/744/1038 | [54] | antibiotic target [54] |
| Salmonella typhimurium | 1964/1036/945 | |||
|
| ||||
| Neisseria meningitidis | b | 496/471/555 | [56] | vaccine development, antibiotic target |
|
| ||||
| Yersinia pestis | b | 1020/825/818 | [57] | vaccine development, antibiotic target |
|
| ||||
| Leishmania major | e | 1112/1101/560 | [58] | antibiotic target [58] |
|
| ||||
| Mycoplasma genitalium | b | 262/274/189 | [59] | antibiotic target [59] |
|
| ||||
| Porphyromonas gingivalis | b | 679/564/--- | [60] | control of negative inflammatory responses [60] |
|
| ||||
| Corynebacterium glutamicum | b | 446/411/446 | [61] | lactic and succinate [62], L-lysine [61], glutamate, ethanol |
| Corynebacterium glutamicum | 502/423/277 | [62] | ||
|
| ||||
| Bacillus subtilis | b | 1437/1138/1103 | [64] | antibiotics, industrial enzymes and proteins, nucleosides and vitamins |
|
| ||||
| Streptomyces coelicolor | b | 971/500/711 | [65] | secondary metabolites (antibiotics, immunosuppressants, anti-cancer agents) [66, 67] |
|
| ||||
| Homo sapiens | e | 3311/2766/1496 | [39] | biomarker of inborn error [70], understanding disease comorbidity toward diagnosis and prevention [69], identification of mutations causing defects in Leigh’s cells [124], predicting tissue- specific activity of metabolic genes [68] |
| Homo sapiens | 2823/2671/2322 | [40] | ||
|
| ||||
| Mus musculus | e | 1344/1042/--- | [75] | mouse hybridoma cells for enhanced production of monoclonal antibodies [75] |
|
| ||||
| Mannheimia succiniciproducens | b | 686/519/425 | [76] | succinate [76] |
|
| ||||
| Escherichia coli | b | 2077/1039/1260 | [92] | lycopene [79, 80], succinate [16, 81, 82], lactate [16, 83], malate [84], L-valine [85], L-threonine [86], additional amino acids [87], ethanol [88], hydrogen [17, 89], vanillin [17], 1,3-propanediol (PDO) [16], gene KO [94–96], antibacterial target [42] |
|
| ||||
| Saccharomyces cerevisiae (fully-compartmentalized) | e | 1412/1228/904 | [99] | ethanol [102, 103], succinate [104], glycerol [104], vanillin [104], sesquiterpene [105], gene KO [106–108] |
| Saccharomyces cerevisiae (lipids emphasized) | 1446/1013/800 | [100] | ||
| Saccharomyces cerevisiae (consensus model) | 1857/1168/832 | [101] | ||
|
| ||||
| Aspergillus niger | e | 1197/1045/871 | [112] | succinate [111], citrates and oxalates [112], additional organic acids, industrial enzymes, proteins (chymosin, human interferon) |
|
| ||||
| Aspergillus nidulans | e | 676/733/666 | [113] | model organism for studies of development biology & gene regulation, sharing many applicative properties of A. niger |
|
| ||||
| Aspergillus oryzae | e | 1053/1073/1314 | [114] | fermented sauces, industrial enzymes |
|
| ||||
| Buchnera aphidicola | b | 263/240/196 | [115] | symbiotes producing histidine [115] |
|
| ||||
| Rhizobium etli | b | 387/371/363 | [117] | symbiotic nitrogen fixation [117] |