Scientists say a database created in a European project could improve food safety.

The database of food metagenomes was developed as part of the EU-funded MASTER project. Metagenomes are the genomic material from all microorganisms in an environment.

The curatedFoodMetagenomicData (cFMD) is a database of metagenomes from food. DNA sequencing technologies will help researchers tackle challenges like food waste, antimicrobial resistance, and food safety.

Microbes can positively impact food production, such as through food fermentation, or negatively impact food production, such as spoilage or foodborne disease.

Analysis of these microbes relied on traditional approaches requiring the growth of the microorganisms on agar in Petri dishes, with different agars used for different microorganisms.

Food safety benefits

Scientists say the use of high-throughput DNA sequencing-based methods could improve food testing. This method allows rapid, simultaneous testing for all microorganisms in parallel, including those that are difficult to grow.

Work included DNA testing of thousands of samples collected from European food processing facilities. The database means that data generated from DNA sequencing-based analysis of food samples can be rapidly and accurately analyzed to identify and control undesirable microorganisms.

The MASTER project involved 30 partners and was started in January 2019. It will last four years and use sequencing technologies to map microbiomes across a range of food and non-food environments. 

Project coordinator Professor Paul Cotter, head of food biosciences at Teagasc (the Irish Agriculture and Food Development Authority), said data represents 15 food categories from 52 countries.

“The cFMD contains data relating to 3,600 microbial species, of which 290 are novel species. It is free of charge and can be extensively used for microbiome studies and applications in food industries. For example, studying microbe movement along the food chain, studying the spread of antimicrobial resistance genes, detecting undesirable microbes, and investigating the transmission of microbes to humans. The availability of cFMD represents a major step toward a future where metagenomic sequencing could replace classical microbiology as a more accurate and faster food-chain microbe tracking tool.”

Related research

A study was published in the journal Cell. It was led by teams from the University of Trento and University of Naples Federico II in Italy, Teagasc of Ireland, the Spanish National Research Council and University of Leon in Spain, MATIS of Iceland, and FFoQSI in Austria, with other contributors.

Professor Danilo Ercolini from the Department of Agricultural Sciences at the University of Naples Federico II, said: “The availability of such a huge dataset including food metagenomes and food microbes genomes is going to represent an essential resource for many food scientists to exploit further the occurrence and role of microbes in food and food processing facilities with the final aim to improve food quality, safety, and sustainability.”

Most species of known concern for foodborne transmission were rarely found in sampled foods, but Listeria monocytogenes was detected once, and Clostridium perfringens three times.

Researchers detected hundreds of uncharacterized species in the food microbiome.

“Targeted isolation and functional characterization of these dietary microbes we detected only by metagenomics should be the next step to exploit further their role in food processing, quality, and safety. Our findings support molecular typing, which means developing food authenticity and origin certifications based on microbial specificity,” they said. 

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