Largest database of microbial genomes from food developed

A study also led by the Department of Agriculture at the University of Naples Federico II has developed a key database for characterizing foods from metagenomic data, opening up new scenarios for improving food quality, safety and sustainability.

The largest database of metagenomes from foods was developed by the EU-fundedMASTER project. The related scientific article titled"Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome" was published Aug. 29, 2024 in the journal Cell.

The curatedFoodMetagenomicData (cFMD) resource represents a key database for the study of food-derived metagenomes (the term defining genomic material from all microorganisms in an environment). A tool that will make it possible to address global challenges such as food waste and antimicrobial resistance, while increasing food safety through the study of the microorganisms that characterize an environment.

Microorganisms in food can have both a positive impact on food production, as in the case of cheese and alcoholic beverage production, and a negative impact, as in the case of spoilage or foodborne illness. Until recently, the analysis of these microorganisms relied mainly on traditional approaches. The application of DNA sequencing-based methods has the potential to transform food analysis, enabling rapid and simultaneous analyses of all microorganisms in parallel, including those that are difficult to culture.

The database represents a major achievement for microbiome research in food. It was made possible by sequencing approximately 2,000 samples collected from food companies throughout Europe, which when added to existing global collections brought the total analysis to 2,500. The open-access resource will facilitate the study of food microorganisms globally on a large scale in both academic and industrial settings.

The MASTER Project

MASTER, which stands for "Microbiome Applications for Sustainable food systems through Technologies and EnteRprise," is a project funded by the European Union under Horizon 2020. Started in January 2019, it involved 29 partners with the goal of characterizing microbiomes in diverse food and non-food environments using innovative sequencing technologies. The study was led by teams from the University of Naples Federico II and the University of Trento (Italy), in collaboration with Teagasc (Ireland), Superior Council of Scientific Research and University of León (Spain), MATIS (Iceland) and FFoQSI (Austria), in addition to many other partners.

MASTER project coordinator Professor Paul Cotter (Teagasc, Ireland) says, "cFMD is a large database of food metagenomic data, representative of 15 food categories from 50 countries. cFMD contains data on 3,600 different microbial species, of which 290 are novel species. It is freely available to be used for microbiome studies and applications in the food industry. For example, to study the microbial component throughout the food chain, study the spread of antibiotic resistance genes, detect unwanted microorganisms, and investigate the possible transmission of microorganisms to humans. The availability of cFMD represents an important development toward a future in which metagenomic sequencing could replace classical microbiology as a more accurate and rapid tool for tracking microorganisms along the food chain."

Professor Danilo Ercolini, Director of the Department of Agriculture at the University of Naples Federico II says, "The availability of such a vast database, including metagenomes and genomes from food, will be a very important resource for studying the presence and role of microorganisms in food and food processing, with the ultimate goal of improving food quality, safety and sustainability." Prof. Edoardo Pasolli of the same department adds, "cFMD will be the basis for the development of even more comprehensive metagenomic databases from foods, which can be supplemented with particular types of foods or geographical areas that are still underrepresented."

Professor Nicola Segata of the University of Trento adds, "This resource is also critical for understanding how the food microbiome might influence human health, as some of the microorganisms we introduce in our diet could become stable members of our microbiome. We found that food-associated microbial species make up about 3 percent of the gut microbiome in the adult population, suggesting that some of our gut microorganisms could be acquired directly from food, or that historically, human populations obtained these microbes from foods and then these microbes adapted to become part of the human microbiome. Thus, foods are also crucial to our health because of the microorganisms they provide to our microbiome."

The article"Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome" is published in Cell and available online: https://cell.com/cell/fulltext/S0092-8674(24)00833-X DOI: 10.1016/j.cell.2024.07.039