05.09.2024: The first comprehensive database of food metagenomes has been developed by the EU-funded MASTER project. The CuratedFoodMetagenomicData (cFMD) resource is a milestone database system that includes thousands of metagenomes from different foods. The study “Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome” was recently published in the prestigious journal Cell.
The cFMD resource is a milestone database of metagenomes (the collective term for all of the genomic material from all of the microorganisms in an environment) from food that will enable DNA sequencing technologies to operate at their peak potential, helping researchers tackle global challenges, like food waste and antimicrobial resistance, while increasing food safety.
Food microbes can have both a positive impact on food production, such as through food fermentation, or a negative impact, such as spoilage or foodborne disease. Until recently, analysis of these microbes has relied heavily on traditional approaches requiring the growth of these microorganisms on agar in Petri dishes, with different agars used for different microorganisms. The application of high throughput DNA sequencing-based methods has the potential to transform food testing as it allows the rapid, simultaneous testing for all microorganisms in parallel, including those that are difficult to grow.
The cFMD database is a major development for microbiome research as it has added 1,950 food samples to the existing global library bringing the sample selection up to 2,500. As an open access resource, this facilitates the large-scale application of this technology worldwide by academics and industry.
MASTER Project
MASTER stands for Microbiome Applications for Sustainable food systems through Technologies and EnteRprise, and is a European Union’s Horizon 2020 funded, 29 partner, project that kicked off in January 2019 to map microbiomes across a range of food and non-food environments with pioneering sequencing technologies. The study was led by teams from the University of Trento and University of Naples Federico II (Italy), Teagasc (Ireland), Spanish National Research Council and University of Leon (Spain), MATIS (Iceland) and FFoQSI (Austria), with many other contributors.
Coordinator Paul Cotter says: "The cFMD is a large curated database of foods metagenomic data, representing 15 food categories from 52 countries. The cFMD contains data relating to 3,600 different microbial species, of which 290 are novel species. It is available free of charge, to 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.”
“The availability of such a huge dataset including food metagenomes and food microbes genomes is an incredibly important resource for many food scientists to further exploit the occurrence and role of microbes in food and food processing facilities with the final aim to improve food quality, safety and sustainability,” says Martin Wagner, Scientific Director of FFoQSI and Vice-Head of Clinical Department for Farm Animals and Food Systems Safety at Vetmeduni. "The consortium has built a basis to understand how the food microbiome could impact human health as some of the microbes we eat could become stable members of our own microbiomes. We found that food-associated microbial species compose around 3% of the gut microbiome of adults, suggesting that some of our gut microbes may be acquired directly from food, or that historically, human populations got these microbes from food and then those microbes adapted to become part of the human microbiome. Food is thus crucial for our health also for the microbes they provide for our own microbiome," says Martin Wagner.
The overall aim of MASTER was to take a global approach to the development of microbiome products (strains, strain mixtures, modulators, kits), foods/feeds, services (bioinformatics analysis, high throughput sequencing) or processes (standard operating procedures, fermentations, testing in real-time of all microbes in a sample) with high commercial potential, to benefit society through improving the quantity, quality and safety of food, across multiple food chains, including marine, plant, soil, rumen, meat, brewing, fruit and vegetable waste, and fermented foods. This was achieved through mining microbiome data relating to the food chain, developing big data management tools to identify inter-relations between microbiomes across food chains, and generating applications which promote sustainability, circularity and contribute to waste management and climate change mitigation.
MASTER scientists harnessed microbiome knowledge to significantly enhance the health and resilience of fish, plants, soil, animals and humans. Through applying cross-sectorial and transdisciplinary expertise, MASTER has provided capacity building and training, improving professional skills and competencies in the food sector and the bioeconomy.
