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Abstract
This mini-review provides a perspective of traditional, emerging and future applications of lactic acid bacteria (LAB) and how genome editing tools can be used to overcome current challenges in all these applications. It also describes available tools and how these can be further developed, and takes current legislation into account. Genome editing tools are necessary for the construction of strains for new applications and products, but can also play a crucial role in traditional ones, such as food and probiotics, as a research tool for gaining mechanistic insights and discovering new properties. Traditionally, recombinant DNA techniques for LAB have strongly focused on being food-grade, but they lack speed and the number of genetically tractable strains is still rather limited. Further tool development will enable rapid construction of multiple mutants or mutant libraries on a genomic level in a wide variety of LAB strains. We also propose an iterative Design–Build–Test–Learn workflow cycle for LAB cell factory development based on systems biology, with ‘cell factory’ expanding beyond its traditional meaning of production strains and making use of genome editing tools to advance LAB understanding, applications and strain development.
Highlights
Lactic acid bacteria (LAB) are a phylogenetically diverse but functionally related group of bacteria comprising the families Aerococcaceae, Carnobacteriaceae, Enterococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae
LAB applications are rapidly expanding from food fermentations and probiotics to therapeutic agents for animals, plants and humans as well as platform production strains for chemicals and fuels
As the use of Genetically Modified Organisms (GMOs) in food products is controversial or not allowed by regulatory officials in many countries, the development of high-throughput genome editing tools for LAB has been limited compared to industrial strains such as Saccharomyces cerevisiae and Escherichia coli
Summary
Lactic acid bacteria (LAB) are a phylogenetically diverse but functionally related group of bacteria comprising the families Aerococcaceae, Carnobacteriaceae, Enterococcaceae, Lactobacillaceae, Leuconostocaceae and Streptococcaceae They are low-GC, Gram positive, facultatively anaerobic, non-sporulating and have a highly fermentative lifestyle, converting a range of sugars into mainly lactic acid. Their natural habitats range from plants and milk to major human and animal microbiota niches (Douillard and de Vos 2014). The development of high-throughput genome editing tools (as opposed to plasmid-based expression systems) for a wide variety of strains is crucial for both fundamental studies and applications to enable fast, targeted and stable genomic modifications
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