This article has been reviewed according to Science X's editorial process and policies. Editors have highlighted the following attributes while ensuring the content's credibility: 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 hydrolyzate.
The study, published in the journal 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. South Korea's kimchi industry processes approximately 132,000 metric tons of radish each year (145,000 tons), generating an estimated 17,000 metric tons of inedible processing by-products (18,700 tons).
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 hydrolyzate and used it as the sole feedstock for engineered Escherichia coli to produce poly(3-hydroxybutyrate) (P(3HB)), a biodegradable bioplastic naturally degraded by microorganisms.
Compared with a conventional glucose medium, radish hydrolyzate supported substantially higher P(3HB) accumulation, demonstrating that agricultural waste can serve as an efficient feedstock for microbial bioprocesses. The researchers therefore selected radish hydrolyzate 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 hydrolyzate.
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. 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 hydrolyzate 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. Beyond demonstrating the use of radish hydrolyzate for bioplastic production, the study establishes a genome-scale model-guided microbial engineering framework for agricultural waste valorization.
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