Genome-scale model-guided microbial engineering converts agricultural waste into biodegradable bioplastics

Every year, thousands of tons of radish by-products generated during kimchi production are discarded despite containing valuable carbon and nutrient resources. Researchers at the World Institute of Kimchi (WiKim) have developed a genome-scale model-guided microbial engineering strategy that enables these agricultural by-products to be converted into biodegradable bioplastics while rationally engineering microbial strains specifically for radish hydrolysate.

The study, published in Bioresource Technology, introduces an integrated engineering framework that combines transcriptomic analysis with a transcriptome-constrained genome-scale metabolic model (GEM) to identify metabolic engineering targets for enhanced bioplastic production. Rather than relying on conventional trial-and-error strain engineering, the approach predicts genetic modifications that redirect metabolic flux toward product biosynthesis, providing a new strategy for agricultural waste valorization and sustainable biomanufacturing.

Agricultural waste

South Korea’s kimchi industry processes approximately 132,000 metric tons of radish each year, generating an estimated 17,000 metric tons of inedible processing by-products. Nearly 94% of these by-products are currently disposed of as food waste or sent to waste-treatment facilities, resulting in both environmental burdens and disposal costs.

To evaluate agricultural waste as a sustainable feedstock, the research team led by Dr. Jung Eun Yang enzymatically converted radish by-products into radish hydrolysate and used it as the sole feedstock for Escherichia coli engineered to produce poly(3-hydroxybutyrate) (P(3HB)), a biodegradable bioplastic naturally degraded by microorganisms.

Efficient feedstock

Compared with conventional glucose medium, radish hydrolysate supported substantially higher P(3HB) accumulation, demonstrating that agricultural waste can serve as an efficient feedstock for microbial bioprocesses. The researchers therefore selected radish hydrolysate as the representative feedstock for subsequent transcriptomic profiling and integrated metabolic modeling.

Using comparative RNA sequencing (RNA-seq), the team characterized the transcriptional response of E. coli grown in radish hydrolysate. The transcriptomic data were subsequently integrated into a transcriptome-constrained genome-scale metabolic model (iML1515 GEM), enabling systematic prediction of metabolic flux redistribution and identification of gene knockout targets that enhance P(3HB) biosynthesis.

MICROBIOLOGY NEWS: Register with The Microbiologist for more free articles 

Guided by the model predictions, the researchers engineered an E. coli strain carrying simultaneous deletions of gltA and acnA. P(3HB) accounted for 71.95% of the engineered strain’s dry cell weight, representing a 78% increase over the parental strain and demonstrating the effectiveness of the genome-scale model-guided engineering strategy.

To evaluate industrial applicability, the engineered strain was further tested in fed-batch fermentation using radish hydrolysate as the sole feedstock. The process achieved a final P(3HB) concentration of 5.75 g/L with the polymer accounting for 75.60% of dry cell weight, demonstrating the feasibility of converting agricultural waste into biodegradable plastics through scalable microbial bioprocessing.

Sustainable bio-based manufacturing

Beyond demonstrating the use of radish hydrolysate for bioplastic production, the study establishes a genome-scale model-guided microbial engineering framework for agricultural waste valorization. Because the approach identifies engineering targets based on transcriptomic responses to individual feedstocks, it can potentially be applied to a wide variety of agricultural residues, including Chinese cabbage and other food-processing by-products, thereby supporting the development of circular agro-biorefineries and sustainable bio-based manufacturing.

“Our genome-scale model-guided strategy enables microbial strains to be engineered according to the metabolic characteristics of individual agricultural waste feedstocks,” said Dr. Jung Eun Yang, who led the study. “We believe this platform can significantly expand the utilization of agricultural by-products and accelerate the development of sustainable microbial bioprocesses for the circular bioeconomy.”