The microbiome of the food we eat

The food we eat contains microbes that can affect both the quality of the food and the human microbiome, that is, the collection of microorganisms that live on and in humans. Until now, however, we knew little about what microbes are in foods. An international research team coordinated by the Cibio Department of the University of Trento has created a "food microbiome" database with the metagenomes of 2,533 different foods. This helped the researchers identify 10,899 food-associated microbe genomes, half of which belong to previously unknown species. Research has also shown that food-associated microbes account on average for up to 3% of adult gut microbiome and 56% of the gut microbiome of children. The study was published on 29 August in "Cell".

"This is the largest survey of microbes in food ever carried out," says Nicola Segata, co-senior author of the study and computational microbiologist at the University of Trento and the European Institute of Oncology (Ieo) in Milan. “Now, we can use this data to better understand how the quality, conservation, safety, and other characteristics of foods are linked to the microbes they contain.”

Traditionally, microbes in food are cultured one by one in the laboratory, in a very slow process that is not suitable for all types of microorganisms. To characterize the food microbiome more comprehensively and efficiently, Segata's research team and the international team relied on metagenomics, a molecular tool that allows the simultaneous sequencing of the entire genetic material of a food sample. Overall, they have analysed over 2,500 metagenomes from 50 countries, including 1,950 metagenomes that have been sequenced for the first time.

They identified 10,899 food-associated microbe genomes, which were categorized into 1,036 bacterial species and 108 fungal species. The research team also observed that similar foods tend to harbour similar but not identical microbes, with greater variety among dairy products.

The researchers have identified few potentially pathogenic bacteria, including some which are less desirable because of their impact on the flavour or preservation of foods. This information could be useful to improve the quality of what we eat, but also help food regulators or those who have to determine the identity and origin of food products.

"It is surprising – continues Segata – that some microbes are present and perform similar functions in very different foods. At the same time, we have shown that foods that come from a specific facility or farm have unique characteristics. This could help determine the specificities and quality of a single production area. We could also use metagenomics to identify foods from a certain place and a certain production process".

Understanding the food microbiome could also have implications for human health as some of the microbes we eat could become permanent members of our microbiome. To examine the overlaps between food-associated microbes and the human microbiome, the team compared the new database with 19,833 previously sequenced human metagenomes. They showed that food-associated microbial species make up about 3% of the adult gut microbiome and over 50% of the gut microbiome of newborns. “This suggests that some of our gut microbes may be acquired directly from food, or that historically human populations got these microbes from food and then these microbes adapted to become part of the human microbiome,” Segata explains. "This might seem a small percentage, but that 3% can be extremely relevant for function and role within our body. With this database we can begin to study on a large scale how the microbial properties of food affect our health."

The study was one of the main results of the MASTER consortium (Microbiome Applications for Sustainable food systems through Technologies and EnteRprise), an initiative funded by the European Union that includes 30 partners from 14 countries and aims to characterize the presence and function of microbes throughout the entire food chain.

The research was supported by Horizon H2020, the Italian Ministry of Foreign Affairs and International Cooperation, the European Research Council, the National Cancer Institute of the National Institutes of Health, the Spanish Ministry of Science and Innovation, the Science Foundation Ireland and the Irish Department of Agriculture, Food and the Marine.