Developing metagenomic methods to monitor microbes in our food

18th November 2022

New genomics approaches are helping us learn more about the microbes that live on our food.

Researchers from the Quadram Institute have recently developed a new method to efficiently detect these microbes to improve our understanding of food safety and antimicrobial resistance. We caught up with the team to find out more.

“A range of microorganisms can be found on food, which may lead to spoilage, cause infectious disease or carry antimicrobial resistance genes.

Cuddly toys of microbes in a bowl, with a knife and fork either side

Monitoring microbes using metagenomics

Many methods can identify specific microorganisms on food, but these are time-consuming as they rely on growing cultures of the microorganisms. These tests look for individual species, so the costs increase with the number of microorganisms being tested.

A test that can sample and identify all of the microorganisms at once is more efficient in terms of both time and financial cost. Metagenomics can provide this.

Metagenomics involves sequencing all DNA on a sample to look at the microorganisms present. Few studies have applied this to food, as most foods contain the DNA of the source plants or animals, and this DNA vastly outnumbers the amount of microorganism DNA on food.

Filtering out food DNA

To get around this problem, we have improved a way to reduce the DNA of the food in a sample (the ‘host’ DNA). This leaves the DNA of microorganisms present, making them easier to detect.

Host DNA depletion methods have mostly been developed for clinical samples, but in our study, we developed a method that increases the proportion of DNA on food belonging to microorganisms 13-fold on average. The method preserves the DNA of microorganisms and works better on food than commercial host DNA depletion methods.

What microbes are on our food?

We tested our method using a number of different food types, including chicken, leafy greens, pork, prawns and salmon, to get an idea of the microorganism populations living on them.

The amount of different microorganisms varies amongst the same and different food types. However, we found the most common microorganism was Pseudomonas. This group includes many bacteria involved in food spoilage and future projects on why these bacteria are so successful at surviving on food should help improve the shelf-life of food.

Food and antimicrobial resistance

Bacteria that are resistant to antimicrobials can spread between the environment, animals, plants and humans via food.

As our method involves sequencing whole genomes, we can identify not just which species are there, but also any genes for antimicrobial resistance (AMR) they carry. We found that on average each gram of food contained over 100 million AMR genes. There was evidence that different food production methods result in increased AMR gene concentrations, such as with salmon and aquaculturing.

Microorganisms are found throughout the food chain, and the method we developed will help us to make the food chain safer by allowing us to understand the relationship between how food is produced, the microorganisms present and antimicrobial resistance.”

Related Targets

Targeting antimicrobial resistance

Antimicrobial Resistance

Targeting food safety

Food Safety

Related Research Groups


Alison Mather

Related Research Areas

Targeting microbes in the food chain

Microbes in the Food Chain