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Table 2 Omics technologies-guided microbial manufacturing process optimization cases

From: Current advances for omics-guided process optimization of microbial manufacturing

Omics technology

Strain

Guiding role

Meaning

References

Metabolomics

Corynebacterium glutamicum

It found the bottleneck of carbon source utilization

Which laid a theoretical foundation for the subsequent use of pentose as a carbon source for fermentation

Kawaguchi et al. (2018)

Yarrowia Lipolytica

To elucidate the effect of the C/N ratio medium on lipid production

It found that high C/N ratio medium promoted long-chain fatty acids synthesis better

Yun et al. (2018)

Chromochloris zofingiensis

To elucidate the effect of the addition of gibberellic acid-3, sodium chloride and high C/N ratio on astaxanthin production

It provided the help for optimization of the medium composition for increase astaxanthin content

Chen et al. (2023)

Streptomyces

To elucidate the molecular mechanism of pH on the synthesis of candicidin

The step-by-step control strategy of pH in fermentation processes was put forward

Liu et al. (2018b)

Transcriptomics

Monascus

It found that carbon starvation could cause stress response in cells, and direct acetyl-CoA pigments synthesis

To provide a direction for subsequent fermentation optimization to improve pigment yield

Yang et al. (2015)

Thraustochytrids

To elucidate the regulatory mechanism of corn steep liquor for improving lipid and docosahexaenoic acid productivity

To provide a basis for using low-cost corn steep liquor as nitrogen source for fermentation

Wang et al. (2019)

P. purpureum

To elucidate the metabolic mechanism of polysaccharides and PUFAs were significantly improved under nitrogen stress

which was helpful for the design of medium and process control during under nitrogen stress fermentation

Ji et al. (2021)

Saccharomyces cerevisiae

To investigate the reasons for the significant difference on the carotenoid production in two different media (YPM, YPD)

It provided the key factors (Zn2+, Cu2+) in the optimization of medium for carotenoid production

Su et al. (2021)

Zymomonas mobilis

The Mg2+ deficiency in the medium were majorly related to stress response and energy conservation

The concentration of Mg2+ in the nitrogen source was critical for cell growth and ethanol fermentation

Li et al. (2020)

Streptomyces

pH shock increased yield by increasing ε-poly-L-lysine synthase activity and improving cellular respiration

It provided a reasonable explanation for the effect of pH on the synthesis of ε-poly-L-lysine

Pan et al. (2019)

Lipidomics

Mortierella alpina

To reveal the effects of types of nitrogen sources on the lipid metabolism

To provide an optimal direction for regulating the ratio of different components in lipid

Lu et al. (2019)

GSMN

Nostoc sp.

To elucidate PBPs biosynthesis's potential association in the cell

To provide a direction for subsequent fermentation optimization to improve PBPs yield

Saini et al. (2021)

P. thermoglucosidasius

To resolve a previously unclear bottleneck in anaerobic fermentation

To identifying the minimal required supplemented nutrients needed to sustain anaerobic growth

Mol et al. (2021)

Comparative transcriptomics and lipidomics

Aurantiochytrium sp.

To elucidate the effects of different temperatures (5 °C, 15 °C) treatments on the biosynthesis of long-chain polyunsaturated fatty acids

The accumulation of DHA was increased under 5 °C, the yield of eicosadienoic acid (20:2) increased at 15 °C

Song et al. (2022)

Genomics, comparative transcriptomics and proteomics

Rhodosporidium toruloides

To elucidate the molecular mechanism of nitrogen-limited starvation on the accumulation of oil

which was helpful for the design of medium and process control during nitrogen-limited fermentation

Zhu et al. (2012)

Transcriptomics, proteomics, metabolomics

Rhodosporidium toruloides

To elucidate the molecular mechanism of phosphate-limited starvation on the accumulation of lipids

To provide new substances for nutritionally limited production

Wang et al. (2018)

Proteomics, metabolomics

Phaffia rhodozyma

It found that succinate increased carotenoid production mainly due to increased acetyl-CoA utilization and cellular respiration rate

As a reference for the production of carotenoids from non-fermentative carbon sources

Martinez-Moya et al. (2015)

Transcriptomics, metabolomics

C. zofingiensis

To elucidate the molecular mechanism of 0.2 M NaCl maximize both TAG and astaxanthin contents

It provided an accumulation of biodiesel in algae under salt stress theoretical basis

Mao et al. (2020)

Methanotrophs

The changes of intracellular metabolism of cells to specific nutrient sources were determined

It provided a carbon source and nitrogen source optimization theoretical basis

Sugden et al. (2021)

R. glutinis ZHK

To elucidate the effects of different temperatures (16 °C, 32 °C) treatments on the biosynthesis of carotenoids, lipids and EPSs

To provide theoretical basis for optimizing temperature of fermentation to control the type of products

Zhao and Li (2022)

Zymomonas mobilis

To elucidate the effects of aerobic and anaerobic fermentation on type of products

which was beneficial to control oxygen content to improve accumulation of ethanol

Yang et al. (2009)

Rhodotorula sp.

To elucidate the molecular mechanism that low levels of cytoplasmic glycerol limited lipid production

The addition of glycerol to the fed-batch increased cell mass and lipid production

Zhao et al. (2021)

Transcriptomics, proteomics

Streptococcus thermophilus

To elucidate most remarkable growth phase changes were related to heterofermentation, glycolysis and peptidoglycan biosynthesis

which was helpful for the design of medium and provided the theoretical basis for high density fermentation

Qiao et al. (2019)

CHO cell

To elucidate the effects of different fermentation scales on cell productivity

The hypoxia was an important reason for limiting the scale-up of fermentation

Gao et al. (2016)