Next-gen probiotics: Genetic engineering paves way for microbiome innovation

(All image credit: North Carolina State University).

21 Jul 2022 --- Researchers from US-based North Carolina State University are analyzing ways to improve the human gut bacterium Bifidobacterium to enhance genetic engineering and improve probiotics. According to researchers, Bifidobacterium is important but challenging to define and is utilized in many probiotics that support healthy microbiomes.

“The strategies we established in the paper open new opportunities for probiotic enhancement and genome engineering,” Echo Pan, functional genomics Ph.D. student at North Carolina State University, tells NutritionInsight.

“For example, we can fine-tune the carbohydrate metabolism to enhance the utilization of Human Milk Oligosaccharides (HMOs) in breast milk by Bifidobacterium, which is highly associated with a healthy infant microbiome.”

“We can also perform cell surface engineering to modulate the molecular interplay with host epithelial and immune cells to control inflammation. Moreover, we can engineer probiotics to deliver therapeutics, either enzymes or small molecules, directly to the target sites.”

Therefore, the study may open up new opportunities for developing next-generation probiotics by highlighting the necessity of creating customized CRISPR-based genome engineering techniques for various bacterial strains.

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a group of DNA sequences present in bacteria genomes.

Utilizing novel tools
To arrive at their conclusions, the researchers used both a portable CRISPR effector that was manufactured and the bacterium’s built-in CRISPR-Cas system.

The CRISPR-based editing tool has various applications for understanding the genetic characteristics of bifidobacteria.Bacteria can resist attacks from opponents like viruses due to CRISPR-Cas adaptive immune systems. Scientists have modified these systems to remove or replace particular genetic code sequences.

“Unlike other genetically tractable bacteria, genomic engineering in Bifidobacterium is hindered by different factors. For example, limited molecular tools developed for Bifidobacterium are known to be enriched with restriction and modification (R-M) systems.”

“Altogether, these limiting factors hamper our ability to genetically manipulate this important genus, and novel molecular tools will enable the engineering of Bifidobacterium strains with enhanced probiotic efficacy and the development of biotherapeutic applications.”

Bifidobacterium possesses many native CRISPR-Cas systems, one of which is a type I-G system that has received little research.

“Bifidobacterium and Lactobacillus are the top two genera in commercial probiotics, and they are commonly found in the human gut microbiome. Bifidobacterium has been linked to various potential health benefits, including preventing enteropathogenic infection via producing short-chain fatty acids, alleviating irritable bowel syndrome and enhancing the host immune system.”

Variations within bacteria strains
In separate experiments, the researchers resensitized a Bifidobacterium strain to the common antibiotic – tetracycline – using this internal system and a portable Cas effector known as a cytosine base editor. Natural antibiotic resistance is seen in many microorganisms.

Pan adds that bacteria may pass on antibiotic resistance to other bacteria in the gut, “Restoring antibiotic sensitivity is conceptually and practically crucial.”

Bifidobacterium has been linked to various potential health benefits, including irritable bowel syndrome alleviation.Additionally, the researchers discovered very small variations in the bacterial strains known as single nucleotide polymorphisms (SNPs), which appeared to reflect significant variations in the phenotypes, or traits, of the strains.

“A relatively unexpected but practically important finding from our study is that probiotic strains that are 99.9% genetically identical can be fundamentally different in their performances,” Pan details.

She asserts that researchers can begin to appreciate how the epigenome significantly influences the genome biology and cellular function in probiotic bacteria.

“In today’s world where we understand the importance of personalized medicine and nutrition, the individualized deployment of genome editing strategies for each bacterial strain sometimes is necessary for successful genome engineering, particularly for genetically recalcitrant bacteria such as Bifidobacterium.”

Impact on the microbiome sector
The results from this paper highlighted that CRISPR-based genome engineering in non-canonical bacteria remains challenging, explains Pan.

“We are working closely with our industry collaborator, IFF, one of the largest probiotic suppliers in the world, to study the Bifidobacterium strains in their proprietary portfolio to understand the underlying molecular mechanisms of the probiotic benefits.”

“This research has raised more questions such as how we can better streamline the genome modification process and how the epigenome affects the functions of Bifidobacterium, all of which our lab is actively working on,” she concludes.

By Nicole Kerr

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