NEW ZEALAND – Fonterra, a global dairy nutrition company, has invented a genome sequencing device, the MinION, that can spit out DNA results from probiotic at a fast pace and a quarter of the cost, enhancing food safety.

Probiotics are specific strains of live bacteria or yeast proven to have a beneficial effect on health. These are commonly consumed in yoghurts and fermented milk drinks, or taken as supplements in capsule form.

Lactic acid bacterial strains (LABs)​ are commonly used as probiotics. They are found everywhere in the environment, including human breast milk.

As their name suggests, LABs make lactic acid as a by-product of fermentation – this gives yoghurt its tangy taste. They provide taste, texture and nutritional benefits to a wide range of foods and beverages.

Global regulations around probiotics are strict and safety is paramount. Probiotic preparations must contain live microbes which are proven to provide a positive health effect in a defined dose.

As a part of the safety assessment for any new probiotic strain, the DNA make-up or “whole genome sequence” of each strain must be examined to confirm the bacterial species and the absence of undesirable traits such as transferable antibiotic resistance (which would rule them out as probiotics).

Whole genome sequencing may also provide valuable clues to a strain’s potential health benefits. However, these assessments require high-quality (complete or near-complete) genomes, which can only be achieved using a combination of sequencing methods.

For Fonterra’s LAB strains, this meant sending DNA samples overseas because one of the sequencing machines they required wasn’t available in New Zealand. The process was expensive and results took months.

To overcome this problem, Dr Shalome Bassett,​ Principal Scientist at Fonterra, approached the NZ Food Safety Science & Research Centre, ESR, and Massey University to help find a local solution.

Combined sequencing technologies

Together, the team with funding from the Ministry for Business, Innovation and Employment, devised a successful strategy that involved combining sequencing technologies available in New Zealand, which previously had not been used with LABs.

This included using a low-cost, handheld sequencer called the MinION (Oxford Nanopore Technologies),​ the same technology used to sequence New Zealand’s Covid-19 samples, as reported by Stuff.

The MinION is only 10 and a half centimetres high and just over three centimetres wide, generating results in hours.

They found that by combining data from locally available sequencers, the high-quality genomes needed for these important assessments were easily achievable, dramatically reducing the cost and turn-around time. The results were validated by overseas experts in LAB genomics.

This development helps Fonterra and other New Zealand companies to be more competitive in the burgeoning global probiotics market, and will lead to faster progress towards new probiotic products.

“Along with our research partners, we wanted to develop this genome sequencing capability in New Zealand for use by other New Zealand food companies. This would provide everyone with greater food safety and quality assurance and protection of New Zealand’s reputation, as well as better health,” said Bassett

According to Professor Phil Bremer, Director of the NZ Food Safety Science & Research Centre,​ this research shows what can be achieved when industry, government and science pool resources and expertise, and how whole genome sequencing can be used far more widely than tracking the sources and evolution of pathogens such as Covid-19.

Fonterra discovered and commercialized two of the world’s top probiotic strains. It has a “library” with over 40,000 different LABs, most of which have yet to be tested for their potential as probiotics. These may have health benefits never seen before.

It is the only dairy company in the world which manufactures its own starter cultures that it uses in its factories to create everyone’s favourite dairy products, like yoghurt and cheese, according to Bassett.

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