A Multiomics Approach Using Metabolomics and Lipidomics

Importance of the Topic

The ability to monitor metabolic and lipidomic changes in microorganisms is vital for optimizing fermentation processes in food, biotechnology and energy industries.
By integrating metabolomics and lipidomics, researchers can gain a comprehensive view of cellular responses to culture conditions, ultimately improving production of high value-added compounds such as the sulfur-containing metabolite ergothioneine.

Goals and Study Overview

This study applied a multiomics strategy to evaluate how different sulfur sources (thiosulfate vs. sulfate) influence metabolite profiles and membrane lipid composition in Escherichia coli over a 216-hour cultivation period.
Key objectives included tracking sulfur-related metabolites and phospholipids at defined time points to understand the interplay between primary metabolism and lipid biosynthesis.

Methodology and Instrumentation

• Culture conditions: Jar fermenter with minimal medium supplemented with 50 mM thiosulfate or 100 mM sulfate
• Sampling: Time points at 0, 24, 48, 72, 96, 120, 168 and 216 hours
• Extraction: Bligh–Dyer method to isolate hydrophilic metabolites and phospholipids
• Chromatography and MS: LCMS-8060 triple quadrupole system

• Primary metabolites: PFPP column, linear gradient of 0.1 % formic acid in water vs. acetonitrile
• Phospholipids: C8 column with ammonium formate and acetonitrile/2-propanol gradient

Main Results and Discussion

• Identification of 49 primary metabolites and 56 phospholipid species
• Thiosulfate supplementation led to a pronounced rise in cysteine, γ-glutamylcysteine and downstream sulfur metabolites after 72 hours, compared to sulfate
• Phosphatidylethanolamine (PE) and phosphatidylserine (PS) levels increased differentially; PE accumulated earlier suggesting prioritized membrane assembly
• Correlation between serine availability, PS biosynthesis and cysteine production highlights metabolic channeling under sulfur limitation

Benefits and Practical Applications

• Multiomics profiling enables real-time monitoring of metabolic fluxes and membrane remodeling
• Insights facilitate rational strain engineering and process optimization for enhanced yields of target metabolites
• Approach supports quality control and scale-up in industrial bioprocesses

Future Trends and Applications

• Expansion of targeted MRM libraries for broader metabolite coverage
• Integration with genomics and flux analysis for predictive metabolic modeling
• Adoption of high-throughput platforms and artificial intelligence for automated data interpretation
• Application to diverse microbial systems and co-culture fermentations

Conclusion

This multiomics study demonstrates how varying sulfur sources steer both metabolite pools and membrane lipid composition in E. coli.
The combined use of metabolomics and lipidomics on a triple quadrupole LC-MS platform offers deep insight into cellular adaptation, guiding future bioprocess enhancements.

References

• Iwao Ohtsu and Yusuke Kawano, Headquarters for International Industry-University Collaboration, University of Tsukuba, sample provision.
• Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries and Food Industry, Ministry of Agriculture, Forestry and Fisheries of Japan, funding support.