Bridging the Gap between Fluxomics and Industrial Biotechnology

Table 1

Recent application of fluxomics of nonmodel microbes to bioproduct synthesis.

Species	Product	Substrate	Model description	Results from study	Reference
Corynebacterium glutamicum	Lysine	Glucose (sucrose, fructose)	^13C-MFA	MFA models (combining transcriptome, metabolome analysis) have been developed to study fluxes under different cultivation modes (minibioreactor, batch, fed-batch) using various carbon sources.	[107]
Corynebacterium glutamicum	Methionine	Glucose	^13C-MFA only focuses on flux distribution in the methionine pathway.	The C. glutamicum mutant (mcbR) showed no overproduction of methionine, but accumulation of homolanthionine.	[108]
Corynebacterium glutamicum	Glutamate	Glucose	^13C-MFA (focus on anaplerotic pathways)	The flux from phosphoenolpyruvate to oxaloacetate catalyzed by phosphoenolpyruvate carboxylase (PEPc) was active in the growth phase, whereas pyruvate carboxylase was inactive.	[109]
Actinobacillus succinogenes	Succinate formate and acetate	Glucose NaHCO3	^13C-MFA (via NMR and GC-MS) and enzyme assay	The model indicated (1) NADPH was produced primarily by transhydrogenase and/or by NADP-dependent malic enzyme (2) oxaloacetate and malate were converted to pyruvate (3) the effects of NaHCO3 and H2 on metabolic fluxes were quantified.	[110, 111]
Geobacillus thermoglucosidasius	Ethanol	Glucose	FBA and ^13C-MFA	The model characterized the ethanol production under three oxygen conditions. The FBA analysis pointed out several gene targets for improving ethanol production.	[19]
Clostridium acetobutylicum	Butanol	Glucose	Genome-scale-FBA	The engineered strain was able to produce 154 mM butanol with 9.9 mM acetone at pH 5.5, resulting in a butanol selectivity (a molar ratio of butanol to total solvents) of 0.84.	[112]
Penicillium chrysogenum	Penicillin	Gluconate/glucose	^13C -MFA (focus on pentose phose phase pathway and glycolysis)	The model determined the pentose-phosphate pathway split ratio and estimated NADPH metabolism.	[113]
Synechocystis sp. PCC6803	Hydrogen	CO2	FBA	The results included H2 photoproduction, strategies to avoid oxygen inhibition, and analysis of hetero-, auto-, and mixotrophic metabolisms.	[114, 115]
Synechocystis sp. PCC6803	Light energy & Biomass	Glucose/CO2	^13C-MFA and dynamic ^13C -MFA	The model analyzed heterotrophic, autotrophic and mixotrophic metabolisms.	[34, 58]
Chlamydomonas reinhardtii	Light energy & Biomass	CO2	FBA model including three metabolically active compartments	The model indicated that heterotrophic growth had a low biomass yield on carbon, while mixotrophical and autotrophical growth had higher carbon utilization efficiency.	[116]
Zymomonas mobilis	Ethanol	Glucose/xylose	FBA with various biological objectives	Model analyzed the metabolic boundaries of Z. mobilis. The study indicated that ethanol and biomass production depend on anaerobic respiration stoichiometry and activity.	[117]
Zymomonas mobilis	Ethanol	Glucose/fructose/ xylose	^13C–MFA via 1H-NMR 31P-NMR spectroscopy	The model characterized the intracellular metabolic state during growth on glucose, fructose and xylose in defined continuous cultures.	[118]
Coculture (Desulfovibrio vulgaris and Methanococcus maripaludis)	CH4	Lactate	FBA analysis of microbial consortia	The model predicted the ratio of D. vulgaris to M. maripaludis cells during growth. It was possible to eliminate formate as an interspecies electron shuttle, but H2 transfer was essential for syntrophic growth.	[55]
Community (oxygenic phototrophs, filamentous anoxygenic phototrophs, and sulfate-reducing bacteria).	Biomass and nitrogen fixation	CO2	FBA and elementary mode analysis	The model predicted and described relative abundances of species, by-products, and the metabolic interactions.	[54]
Phaffia rhodozyma and Haematococcus pluvialis	Astaxanthin	Glucose with (peptone & yeast extract)	FBA analysis of mix culture	The two major astaxanthin-producing microorganisms exhibited elevated yields (2.8-fold) under mixed culture conditions compared to pure culture.	[119]