Fermented foods: Study identifies lactic acid bacteria in kimchi with robust defense system

02 Nov 2023 --- Researchers at the World Institute of Kimchi have isolated lactic acid bacteria (LAB) strains from kimchi with high levels of resistance to phages — viruses that infect and replicate within bacteria. The team sourced the Pediococcus inopinatus strain from Mukeunji — a long-term fermented kimchi that is in the final stage of fermentation.

According to the researchers, the isolated P. inopinatus strain has a better defense system against gene invasion than Lactiplantibacillus plantarum, a bacteria strain commonly used in probiotics that is also present in kimchi. They suggest that P. inopinatus may have an immune role against mammalian viruses as well, though further research is needed.

“We are planning to study the antiviral activity and analyze the immune spectrum of P. inopinatus, and we expect that the excellent antiviral ability of these kimchi LAB strains can be used not only in food but also in the pharmaceutical industry,” says Dr. Hae Choon Chang, president of the World Institute of Kimchi and the corresponding author of the study. 

To determine the genetic traits of the identified LAB, the research team collected 34 samples of kimchi that were fermented for over six months at temperatures between -2 and 10℃ from all over South Korea. In over 88% of the analyzed samples, P. inopinatus was the dominant species. 

Kimchi is a lactic acid-fermented vegetable product. The researchers note that, unlike fermented dairy products produced in a sterilized-closed fermentation system, kimchi is created through spontaneous fermentation. This is initiated by various microorganisms in the product’s raw materials in a non-sterilized-open fermentation system. 

As a result, various LABs are involved in kimchi fermentation. Which strain is dominant and when they’re dominant depends on the environment. 

The researchers conducted a genetic analysis of kimchi LABs to determine their bacterial defense system.Genetic assessment 
The researchers conclude that the dominance of P. inopinatus in long-term fermented kimchi produced across different regions and recipes suggests that “this LAB species has characteristics that enable it to survive in prolonged fermentation conditions.”

Through a comparative genetic analysis of 29 strains of six genera of kimchi LAB, the researchers determined that P. inopinatus had a relatively large number of genes related to CRISPR (clustered regularly interspaced short palindromic repeat) — the hallmark of a bacterial defense system that forms the basis for CRISPR-Cas9 genome editing technology. 

“P. inopinatus possesses a unique, well-developed CRISPR system that can defend against viral invasions,” explains Chang.

Compared to other LAB strains, P. inopinatus possesses additional copies of the csa3 gene — the gene coding for cas genes, which play a role in fighting viruses that infect bacteria. 

According to the researchers, the “high expression levels of CRISPR-related genes in a bacteriophage-free environment is expected to rapidly induce the defense system when bacteriophages invade.” 

Because of the active expression of cas genes, P. inopinatus strains store much more genetic information about phages. This means that after a phage infection, the strain will be more effective in preventing additional infections with a similar phage. 

When comparing the genetic features of P. inopinatus with L. plantarum, the researchers found that the latter had fewer CRISPR system genes, making it less effective in defending against phage invasion. 

Kimchi and other fermented foods are increasingly heralded for their health benefits.Power of fermentation 
Along with other fermented foods, kimchi has been heralded for its health benefits. For example, one study found that fermented food consumption is associated with lower blood pressure, BMI, waist circumference and blood plasma glucose levels. 

As fermented foods like kimchi contain live microbes that contribute to gut health and overall well-being, scientists and industry players look toward the possibility of adding these foods to dietary recommendations to ensure that consumers reap their benefits. 

The kimchi industry uses LAB as a starter to produce a standardized product with better sensory qualities. However, as these starters risk infection from phages, phage-resistant LAB strains are crucial. 

The health benefits of LABs and probiotics are increasingly the topic of research, especially regarding their support of gut and immune health. For example, earlier this year, researchers found that the LAB Lactococcus lactis could support early recovery of smell and taste dysfunction in COVID-19 patients and reduce the viral load. 

Additionally, research has suggested that probiotics may fight off mercury absorption in the gut while also supporting the nutritional intake function of iron and other minerals. 

By Jolanda van Hal