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CRISPR-Cas system based advancements in probiotics

In our quest to improve our health and lifestyle, probiotics have found their way into our diet in the form of fortification or as supplements. Probiotics microorganisms are live bacteria and yeasts, and are considered to be ‘soldiers’ helping us to fight pathogens and other harmful strains that might colonise our gut, and help restore a healthy gut microbiome, thus maintaining a healthy life.

According to Dr. Rodolphe Barrangou, Associate Professor from North Carolina State University ‘We can also gene edit probiotic strains to enhance our whole health: gut health, women’s health, skin health. For example, we could develop a probiotic that makes it easier for people with lactose intolerance to digest dairy products.’ (Dr. Rodolphe Barrangou: Gene Editing Could Improve Health — And Happiness, 2019).

In the current times, CRISPR-enabled gene editing has helped us achieve a quantum leap in molecular biology revolutionising the approaches of conventional probiotics which relied on using a mix of pre-determined ‘good’ bacteria. CRISPR offers the possibility of manipulating bacterial strains within our gut, thus creating unlimited opportunities in the field of probiotics.

In fact, of the possible reasons attributed to a microorganism’s probiotic nature, CRISPR-Cas gene loci are prominent. The endogenous CRISPR-Cas system is cited to be present in 40% of bacteria. In the field of probiotics, it is noteworthy that CRISPR, a mechanism originally discovered in bacteria and archaea as a part of their adaptive immunity, can be used to tweak their own genetic elements by subtly modifying and exploiting their endogenous CRISPR-Cas system or by using laboratory engineered CRISPR technology.

Bifidobacteria, Lactobacilli, and other Lactic Acid Bacteria (LAB) have been most popularly used probiotics and in targeted therapies against a host of diseases, including cancer. Hence these bacterial strains have also become the favourite choice of ‘good’ bacteria among scientists in their attempt to advance the field of probiotic through the incorporation of gene editing. CRISPR-mediated gene editing in bacteria can be achieved through the recombination of single-strand DNA (ssDNA) in combination with Cas9 nuclease. Through CRISPR, scientists aim to design probiotic microbes capable of unleashing more powerful and desired activities, including their improved rate of survival in our gut, increased bile salt hydrolase activities, fine-tuning immunomodulatory properties through expression/suppression of surface-associated proteins and other molecules, etc.

The use of CRISPR technology includes the designing probiotic bacterial strains that are more active and capable of achieving the desired outcome; and, eliminating specific bacterial strains through the delivery of CRISPR-Cas system into the target bacterial strains or through the design of special lytic bacteriophages. Interestingly, relying on techniques that use exogenous or endogenous CRISPR-Cas systems, the bacteria can be prompted to target its own chromosome, leading to self-destruction and elimination from the microbiome. Instead of initiating complete self-destruction, CRISPR technology can also be used to eliminate undesired genes related to bacterial pathogenicity. Finally, the CRISPR technology can also be used to modify gene expression in target bacteria without altering its genome. All this makes CRISPR a powerful technique to modulate the composition of the gut microbiome and their functional activities; and, simultaneously help to study the complex interplay between bacterial members comprising our gut microbiome.

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