Metabolic flux methods applied to different organisms. Isotopic tracers used in the experiments, techniques and software for data analysis are reported as well. When authors did not use “omics” software to analyse data the abbreviation “ns” is reported for “not specified”a.
| Flux methods & isotopomers | Organisms | Techniques | Software data analysis | Ref. |
|---|---|---|---|---|
| 13 C-MFA | ||||
| 80% unlabelled Glc and 20% [U-13C] Glc | S. cerevisiae, S. bayanus var. uvarum, S. exiguus, S. servazzii, Z. rouxii, S. kluyveri K. thermotolerans K. lactis K. marxianus var. marxianus, P. angusta, D. hansenii, P. sorbitophila, C. tropicalis, Y. lipolytica | GC-MS | METAFoR | 38 |
| [1-13C] Glc or a mix of 20% [U-13C] Glc and 80% unlabelled Glc | E. coli | GC-MS | METAFoR | 39 |
| 5 mM Glc + 5 mM [2-13C] acetate, 5 mM [1-13C] Glc + 5 U/L insulin and 5 mM Glc + [3-13C] pyruvate | Rat hearts | GC-MS along with 13C-NMR (400 MHz) | ns | 40 |
| 0%, 0.5%, 1%, 2% and 10% of [1-13C] Glc mixture | C. glutamicum | GC-C-IRMS | MATLAB | 41 |
| 13C sodium acetate; 13C sodium hydrogen carbonate | Chlamydomonas reinhardtii | GCxGC-TOF-MS | MetMax and GMD | 36 |
| [1-13C] Glc; 99% [6-13C] Glc | C. glutamicum | MALDI-TOF MS | 42 | |
| [1,2-13C] Glc, [1,6-13C] Glc | E. coli | GC-MS | METRAN | 43 |
| [5-13C] glutamine and [U-13C] glutamine | Brown adipocyte cells | GC-MS | METRAN and ISA | 34 |
| [1-13C] Glc | C. glutamicum | GC-MS | OpenFLUX | 44 |
| [1-13C] Glc, or a mix of 20% [U-13C] Glc and 80% naturally labelled Glc | E. coli, B. subtilis | GC-MS | SUMOFLUX, INCA | 45 |
| 25 mM 1 : 1 mixture of [U-13C] Glc and [1-13C] Glc | A549 lung carcinoma cell line | GC-MS | METRAN | 35 |
| 2 g L−1 NaH13CO3 and 5 g L−1 Glc (U-13C6 or 1-13C1) | Synechocystis sp. PCC 6803 | GC-MS | MATLAB | 46 |
| 20% [1,3-13C]-glycerol and 80% unlabeled glycerol | Pichia pastoris X-33 strain | GC-MS | OpenFLUX | 37 |
| [1,2-13C] Glc | Co-culture of E. coli Δpgi and Δzwf | GC-MS | METRAN | 47 |
| [l-13C] Glc and [U-13C] ethanol | S. cerevisiae strain CEN.PK-113.7D | LC-MS | MATLAB | 48 |
| 500 g L−1 1 : 1 mixture of [1-13C] Glc and [U-13C] Glc | E. coli strain WYK050 | LC-MS/MS | MATLAB | 49 |
| A mixture of 80% [1-13C] Glc and 20% [U-13C] Glc | B. subtilis strain BSB168 trp+ | LC-MS/MS | 13CFLUX | 50 |
| [1-13C] Glc and [U-13C] Glc | E. coli strain K-12 MG1655 | LC-MS/MS | MATLAB and INCA | 51 |
| [l-13C] Glc | Corynebacterium glutamicum | 1H-13C NMR | ns | 52 |
| [U-13C] Glc 10% and natural labeled Glc 90% | B. subtilis | 1H-13C NMR | ns | 53 |
| 13.9 mM of a mixture of either 20% [U-13C]-Glc and 80% [1-13C]-Glc or [U-13C]-Xyl and 80% [1-13C]-Xyl | E. coli Pzwf1.1, Pzwf1.2, Pzwf1.3, Pzwf1.4 and E. coli Pzwf1, Pzwf2, Pzwf3, Pzwf4 | 1H-13C NMR | influx_s | 54 |
| [1,2-13C] Glc | Mammalian cells | 1H-13C NMR coupled with GC-MS | ns | 55 |
| 90% unlabelled Glc and 10% uniformly labeled [U-13C] Glc | Synechocystis | 1H-13C NMR coupled with GC-MS | ns | 56 |
| [13C2] glycine, [13C3] serine and [3-13C] serine | A. gossypii B2 | GC-MS, LC-MS, and NMR | OpenFLUX | 57 |
| [U-13C] Glc 10%, [1-13C] Glc 40% and 50% unlabelled Glc | Chinese Hamster Ovary (CHO) cells | 2D [13C, 1H] COSY | 13C-Flux | 58 |
| 50 mM [1-13C] Glc | Actinobacillus succinogenes | GC-MS, 1H-13C NMR | 13C-Flux | 59 |
| 20% [U-13C] Glc and 80% unlabelled Glc | Escherichia coli | 3D TOCSY-HSQC | ns | 60 |
| FBA | ||||
| [1-13C] Glc | Geobacillus thermoglucosidasius M10EXG | Based on GC-MS data | SimPheny Software from Genomatica | 61 |
| Chinese Hamster Ovary (CHO) cells | Based on 2D [13C, 1H] COSY data | 13C-Flux | 58 | |
| 13 C-INST-MFA | ||||
| [1,6-13C] Glc | Rat brain (in vivo) | 13C-NMR | ns | 62 |
a
Ns = not specified, Glc = glucose; GC-C-IRMS = gas chromatography-combustion-isotope ratio mass spectrometry; GCxGC-TOF-MS = two-dimensional gas chromatography coupled to time-of-flight mass spectrometry; GMD = Golm metabolome database; Glc = glucose; Xyl = xylose.