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Transforming Europe’s food supply through the power of the microbiome

A better understanding of microbial communities could bring profound benefits to the agri-food sector. The EU-funded MASTER project has developed a wide range of microbiome products, foods, services and processes. These innovations are helping improve the quantity, quality, safety and sustainability of our food and farms.

©ovocheva #319484629 source: 2023

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What do climate change, aquaculture, food supply and human health have in common? All of them stand to benefit from microbiomes, according to the project coordinator of MASTER.

“The overall aim of the project is to take a global approach to developing concrete microbiome products, foods, feeds, services and processes with a high potential for improving the quantity, quality and safety of food,” says Paul Cotter, head of biosciences and senior principal research officer at Ireland’s Teagasc Food Research Centre.

As Cotter explains, the microbiome is the collection of all the microorganisms that live in a given environment. The gut microbiome – including bacteria, archaea, fungi and viruses – plays an important role in digesting the food we eat, protecting us against disease and producing the vitamins that help us stay healthy.  

But microbiomes can also be found across multiple food chains, many of which are interconnected. These include microbiomes associated with farm animals and plant crops, the microorganisms living in physical environments such as soil and water, and those used directly for fermentation of bread, alcohol and other products.

“By harnessing the power of these microbiomes, through new technologies and groundbreaking research, we can enhance the health and resilience of fish, plants, soil, animals and humans – bringing about a revolutionary change within our food chains,” adds Cotter, who served as the project coordinator. 

Breeding a better bovine

By mining microbiome data and developing big data tools to identify the interrelations between microbiomes, the MASTER project has delivered key improvements to the food chain, supporting the delivery of Europe’s farm to fork strategy.

One of those improvements is enabling cattle breeders to produce animals that emit less methane. This line of research investigated the role of diet, host genetics, feed efficiency, and rumen microbiome on environmental outputs in beef cattle.

Over the course of several years, researchers collected methane data from over 1 500 bovines and performance data on more than 3 000 feed intakes. This information was combined to create the first-ever database for breeding bulls based on their offspring’s methane output.

“Essentially, what this means is that we can now actually select cattle for reduced methane output,” notes Stuart Kirwan, a fellow researcher at Teagasc.

“There is also a potential to combine this advancement with other developments from the MASTER project to further reduce methane outputs in the future,” adds Cotter.

Keeping pathogens out of aquaculture

The project’s work also helped make aquaculture more sustainable by developing a solution to rapidly detect fish pathogens.

“Aquaculture, or the rearing of fish or other aquatic organisms in large tanks or in sea pens, has the potential to sustainably produce high-quality food in large amounts,” says René Groben, microbiology project manager at Matís, one of the project’s 29 partners.

One of the key challenges facing aquatic farming, however, is pathogens that spread rapidly among high-density populations. The MASTER project developed a monitoring system capable of providing fish farmers fast and reliable information about the occurrence, severity and type of pathogens present in a farm, and whether measures need to be taken to protect the health of the fish stock and consumers.

According to Groben, the advantages of this solution are many. “It can identify all microorganisms together, and it works with a wide range of aquaculture-related sample types, including water samples, fish tissues, and the biofilter from tanks,” he explains. These tests can also be carried out on-site, meaning results can be obtained in hours, a significant improvement on the days or weeks that traditional testing methods require.

Delivering healthier, more sustainable foods

Other innovations to come out of the MASTER project include new technology to detect pathogens in soil, technologies for selective enrichment of bacterial DNA from plants, and strategies for the enhanced biopreservation of seafood and meat.

Furthermore, the project validated a procedure for mapping microbiomes in the food industry, promoting process optimisation, reducing waste and improving food quality and safety. Researchers even succeeded at mapping the interconnections between food products, nutrients, microorganisms and the human gut – laying the foundation for dietary recommendations that use gut microbiome modulation to improve our overall health.

While diverse, each of these outcomes will result in healthier, more sustainably produced foods that offer a higher level of quality, safety and shelf life. “These outcomes will have major implications, enhancing our understanding of the microbiomes associated with food chains and addressing key societal challenges such as food and nutrition security, health and well-being, food waste management, and climate change adaptation and mitigation,” concludes Cotter.

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Project details

Project acronym
Project number
Project coordinator: Ireland
Project participants:
United Kingdom
Total cost
€ 12 136 475
EU Contribution
€ 11 855 115
Project duration

See also

More information about project Master

All success stories