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

Consumers expect that ingesting probiotics will promote a healthy, diverse and balanced population of microbes in the gut. We have heard a lot about the importance of the gut microbiome – the collective term for the enormous microbial community within the gut – to a well-functioning body and brain. In fact they may even affect our mood and appetite, because what we eat directly impacts our microbiome, and vice versa.

Lactic acid bacterial strains (LABs) are commonly used as probiotics. They are found everywhere in the environment, including human breast milk. LABs are some of the first to colonise newborn babies and are important for the development of the baby’s gut and immune system.

The great probiotics race

As their name suggests, these bacteria 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 drinks. But 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.

Fonterra discovered and owns two of the top five probiotic strains in the world. It also has a “library” of 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.

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.

Harnessing the power of hybrid whole genome sequencing

A dose of Kiwi ingenuity

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. Shalome knew that ESR had MinION long-read sequencers and was evaluating their use for whole genome sequencing of bacteria. The MinION is a small handheld device developed by Oxford Nanopore Technologies Ltd, which requires less DNA and is much cheaper than the ‘Rolls Royce’ PacBio that Fonterra had been sending their samples to overseas.

ESR scientists Angela Cornelius and Lucia Rivas came up with the idea to cross-map MinION readouts with the data produced by an Illumina machine to create a near-complete genome. “Combining MinION long-read sequence data with Illumina short-read sequence data to generate high quality genomes has already provided valuable insights into outbreaks of human disease caused by bacteria and the MinION’s larger brother, GridION, has been the workhorse for sequencing Covid-19 in New Zealand”, says Angela. “This project was undertaken to evaluate the ability to generate high quality genomes from a small set of LABs using Illumina and MinION data.”

The research team, involving Fonterra, Massey University and ESR, started by testing the accuracy of Illumina-MinION hybrids against five already sequenced LAB strains and the results exceeded all hopes. They quickly established an efficient workflow where DNA was extracted from the LAB of interest, sequenced on the MinION, and the data combined with short-read sequencing data previously obtained using Illumina technology. This was used to build hybrid genomes that were equivalent to (and in some cases better than) the Illumina-PacBio hybrids. These high quality, near-complete genomes were suitable for safety assessment of LABs at a quarter of the cost and with a much quicker turn-around-time.

The benefit of combining resources

With the results validated by overseas experts in LAB genomics, this development will help Fonterra and other companies become more competitive in the growing probiotics market and is a method the New Zealand food industry can use for similar applications.

In fact, this small study was so successful that ESR is now using the higher capacity GridION so that they can run more samples at a time. “We went to the GridION because Fonterra wanted to run more than 200 isolates through so it was faster to do it on the GridION”, says Lucia. “ESR is one of the lead providers of sequencing for the NZ food industry. We are investigating MinION applications to help with rapid sequencing for the food industry and looking to collaborate with the the NZ Food Safety Science & Research Centre,” she adds.

Director of the NZ Food Safety Science & Research Centre, Professor Phil Bremer of University of Otago, says 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.

This story was originally written for Food NZ magazine by Dr Catherine McLeod, former director of the NZ Food Safety Science & Research Centre, Dr Lucia Rivas of ESR, Dr Angela Cornelius of ESR and science writer Glenda Lewis and has been adapted with the authors’ permission.

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  • Food science
  • Health science
  • Genome Sequencing