In few short years, CRISPR-Cas (clustered, regularly interspaced, short palindromic repeats (CRISPR)–CRISPR-associated protein) technology has shown a stunning progress from intriguing prokaryotic defense systems to a powerful and versatile biomolecular tools in applications ranging from genome editing to molecular imaging.

Although most of these progresses have been in eukaryotic system, it also offers promising tools for bacterial engineering. Since bacteria are ubiquitously known throughout the production and consumption of food, CRISPR technology has the potential to impact all classes of bacteria across the major domains of food spectrum, which includes pathogenic, commensal, fermentative, probiotic, and spoilage organisms. Furthermore, applications in food industry have lower regulatory hurdles than biomedical application and some of these markets are anticipated to produce earlier returns on investments.

The major application of CRISPR-Cas system in food industry comprises:

  • Genotyping of bacteria,
  • Vaccination against phages, and
  • Genome editing.

Firstly, CRISPR based genotyping of bacteria which offers a rapid, affordable, and high resolution means of typing bacterial strains within species that carry them. To date, CRISPR-based typing schemes have been reported in food borne pathogens such as Salmonella (EP2255011B1) and Escherichia coli (CN105112519A), industrial fermentation starter cultures such as S. thermophilus, probiotics such as Lactobacillus casei and spoilage organisms such as Lactobacillus buchneri, demonstrating the broad prospective of CRISPR-based bacterial genotyping across the spectrum.

Secondly, vaccination of industrial microbes which provide unique advantages against predatory bacteriophage. Specifically, the iterative process of spacers sequence corresponding to phages making further the acquisition of target-emerging phages. In the early 2000s, Philippe Horvath and Rodolphe Barrangou of Danisco (later acquired by DuPont) were first introduced to CRISPR while sequencing Streptococcus thermophilus (EP2126130B1). Danisco (DuPont) was the pioneer of commercial use of CRISPR technology (a total of 17 patent families filed till now), to enhance viral immunity in bacteria used to make yogurts and cheese, but other markets have been rapidly emerging.

Finally, genome editing using CRISPR-Cas systems via targeting any sequence in the genome offers promising applications towards defining minimal bacterial genomes, determining essential genes, and characterizing genetically heterogeneous bacterial populations. CRISPR-based genome editing has already been applied to organisms of interest across food science, including yeast, corn, rice, and tomatoes. BASF Plant Science has genetically modified crops using Cas9 for targeted engineering to improve growth under drought conditions, application of insecticide, low nutrition/fertilizer conditions, and also to improve the nutrition potential of food crops. Additionally, Dow Agrosciences along with Sangamo Biosciences (CA2908512A1) and Cellectis Plant Sciences (WO2014199358A1) are developing genetically modified crops using CRISPR-Cas9. Similarly, genome editing can improve yield in animal breeding through desirable alteration and selection of herd genetics. Recombinetics Inc. is using TALENs, ZFNs and Cas9 to enhance productivity in the livestock industry (EP2943060A1). Although, there is a huge potential to increase the disease-resistance of both crops & cattle, and the promising outcomes of genome editing using CRISPR-Cas systems, the practical implications of doing so are yet to be unanimously defined.

The message is clear, CRISPR-Cas technologies will drive research and development in many food products, and with all of its potential it is going to transform the future of food science across the globe.

Authors:

Dr. Sudhanshu Das from Ingenious e-Brain Solutions.