A new, open-source database called curatedFoodMetagenomicData (cFMD) is now available for the collection of food microbial data to support the use of metagenomics in food science. It currently includes the metagenomes of 2,533 foods, comprising more than 10,000 microbes, approximately half of which were previously unknown.

Microorganisms play a fundamental role in food safety, quality, and production yield. The relevance of characterizing food-associated microbial communities to improve foods and understand their impact on human health is increasingly recognized, but, until the present research, much of this diversity has been left unexplored.

The researchers who created the database used modern metagenomics sequencing tools to compile the initial dataset. In total, the team analyzed 2,533 food-associated metagenomes from 50 countries, including 1,950 newly sequenced metagenomes.

The metagenomes were sourced from a variety of foods, 65 of which were dairy, 17 percent were fermented beverages, and 5 percent were fermented meats. Fermentation of raw plants, dairy, and meat is a dynamic process that can enhance the quality, diversity, and safety of food products by controlling potentially harmful bacteria and improving organoleptic properties and health-promoting features.

The metagenomes were made of genetic material from 10,899 food-associated microbes categorized into 1,036 bacterial and 108 fungal species. Similar foods tended to harbor similar types of microbes; for example, the microbial communities in different fermented beverages were more similar to each other than to the microbes in fermented meat, but there was more variation between dairy products, likely due to the larger number of dairy products surveyed.

Though the researchers did not identify many overtly pathogenic bacteria in the food samples, they did identify some microbes that might be less desirable due to their impact on food flavor or preservation. Knowing which microbes belong to different types of food could help industry produce more consistent and desirable products. It could also help food regulators define which microbes should and should not be in certain types of food and to authenticate the identity and origins of foods.

Additionally, the findings suggest that human gut microbes may be acquired directly from food, or that historically, human populations adopted microbes from food, which then adapted to become part of the human microbiome. A comparison between the new database with 19,833 previously sequenced human metagenomes showed that food-associated microbial species compose around 3 percent of the gut microbiome of adults and more than 50 percent of the gut microbiomes of newborns.

The study was one of the main outputs from the MASTER EU consortium, an EU-funded initiative spanning 29 partners across 14 countries that aims to characterize the presence and function of microbes throughout the entire food chain.