Currently, microbial manufacturing is widely used in various fields, such as food, medicine and energy, for its advantages of greenness and sustainable development. Process optimization is the committed step enabling the commercialization of microbial manufacturing products. However, the present optimization processes mainly rely on experience or trial-and-error method ignoring the intrinsic connection between cellular physiological requirement and production performance, so in many cases the productivity of microbial manufacturing could not been fully exploited at economically feasible cost. Recently, the rapid development of omics technologies facilitates the comprehensive analysis of microbial metabolism and fermentation performance from multi-levels of molecules, cells and microenvironment. The use of omics technologies makes the process optimization more explicit, boosting microbial manufacturing performance and bringing significant economic benefits and social value. In this paper, the traditional and omics technologies-guided process optimization of microbial manufacturing are systematically reviewed, and the future trend of process optimization is prospected.
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http://dx.doi.org/10.1186/s40643-023-00647-2 | DOI Listing |
Food Res Int
January 2025
Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; Yunnan Key Laboratory for Food Advanced Manufacturing, 650500 Kunming, China; International Green Food Processing Research and Development Center of Kunming City, Kunming 650500, China. Electronic address:
The formation of flavor in fermented vegetables is directly associated with the interactions among the resident microbial strains. This study explored the cooperative dynamics between Lactobacillus plantarum and Rhodotorula mucilaginosa in a simulated cabbage juice system. The obtained results indicated that the co-cultivation of these strains accelerated fermentation kinetics and enhanced lactic acid production.
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January 2025
Renewable Carbon and Biology System (ReCABS) Laboratory, Department of Biotechnology, Engineering School of Lorena, University of São Paulo (EEL-USP), Lorena 12602-810, SP, Brazil. Electronic address:
Food security issues are becoming more pressing due to the world's rapid population expansion and climate change, which also drive up demand for nutrient-dense commodities like meat and cereals. Conventional agricultural practices, which depend on pesticides, fertilizers, and antibiotics, are exacerbating environmental problems, such as antibiotic resistance. Precision fermentation has become a game-changing technique that uses microorganisms to create high-value food ingredients more efficiently and with less negative environmental impact.
View Article and Find Full Text PDFJ Cheminform
January 2025
Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
Predicting EC numbers for chemical reactions enables efficient enzymatic annotations for computer-aided synthesis planning. However, conventional machine learning approaches encounter challenges due to data scarcity and class imbalance. Here, we introduce CLAIRE (Contrastive Learning-based AnnotatIon for Reaction's EC), a novel framework leveraging contrastive learning, pre-trained language model-based reaction embeddings, and data augmentation to address these limitations.
View Article and Find Full Text PDFAntibiotics (Basel)
December 2024
Oral Health Centre, School of Dentistry, University of Queensland, Herston, QLD 4006, Australia.
Biofilms are structured microbial communities that adhere to various abiotic and biotic surfaces, where organisms are encased in an exo-polysaccharide matrix. Organisms within biofilms use various mechanisms that help them resist external challenges, such as antibiotics, rendering them more resistant to drugs. Therefore, researchers have attempted to develop suitable laboratory models to study the physical features of biofilms, their resistance mechanisms against antimicrobial agents, and their gene and protein expression profiles.
View Article and Find Full Text PDFAdv Colloid Interface Sci
January 2025
Department of Biotechnology, School of Applied Sciences and Technology, BLDE (Deemed to be University), Bangaramma Sajjan Campus, Vijayapura 586103, India; Department of Basic Sciences, Faculty of Engineering and Technology, CMR University, Bangalore 562149, India. Electronic address:
Biosurfactants are biodegradable, non-toxic, and environmentally beneficial substances that are produced by microorganisms. Due to their chemical characteristics and stability in various environmental circumstances, biosurfactants are low-molecular-weight, surface-active molecules of great industrial importance. The choice of the producer microbe, kind of substrate, and purification technique determine the chemistry of a biosurfactant and its production cost.
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