Good and bad microbes in our food

Microbes are part of the food we eat and can influence our own microbiota (the set of microorganisms that live in our bodies). However, despite their importance, very little is known about the microbes in our food. Now, an international team of researchers has compiled a food microbiome database by analyzing the metagenomes (the term for all the genetic material of the set of microorganisms in an environment) of hundreds of foods.

The team includes, among others, Niccolò Carlino, from the University of Trento in Italy, Paul Cotter, from the Irish State Agency for Agriculture and Food Teagasc, and Abelardo Margolles, from the Institute of Dairy Products of Asturias (IPLA) dependent on the Spanish National Research Council (CSIC). Research staff from the University of Naples Federico II (Italy), the University of León (Spain), MATIS (Iceland) and FFoQSI (Austria), among other entities, also participated.

The team identified 10,899 food-associated microbes, half of which were unknown species, and showed that food-associated microbes accounted for 3% of the adult gut microbiome and 56% of the infant gut microbiome.

This new resource makes it possible to identify and control undesirable microorganisms, study the movement of microbes along the food chain and the spread of antibiotic resistance genes, and improve the healthy attributes of foods, among other applications.

This database, called CFMD (Curated Food Metagenomic Database), is the result of the largest study on food microbiomes carried out to date, and is freely accessible to facilitate its large-scale application by academia and industry.

“This resource will mark a milestone in food microbiology research,” says Abelardo Margolles. Researchers from three other CSIC centres have also participated in the MASTER consortium: the El Zaidín Experimental Station (EEZ), the Food Science Research Institute (CIAL, a joint centre of the CSIC and the Autonomous University of Madrid (UAM)) and the Institute of Agrochemistry and Food Technology (IATA).

“This resource will help researchers to tackle challenges that have been very difficult to address until now due to the scarcity of food metagenomes available in databases.”

“Food microbes can have both a positive impact on food production – for example, through fermentation – and a negative impact – on food spoilage or their involvement in the transmission of diseases,” explains Margolles.

“Traditionally, food microorganisms have been studied by culturing them in broths or Petri dishes, but this process is slow and not all microbes are cultivable,” he adds.

The CFMD database now makes it possible to analyse food metagenome data, based on DNA sequencing, quickly and accurately.

The CFMD database is the result of the work of the international MASTER consortium, which has analysed more than 2,500 food-associated metagenomes from 50 countries, including 1,950 metagenomes sequenced for the first time. It contains data on 3,600 microbial species, including more than 200 new species.

“Approximately two-thirds of the samples were dairy products and the facilities in which they are produced, and fermented beverages and meats, among other foods, were also analysed,” Margolles said.

Many of the food samples analysed came from cheese-making facilities. (Photo: Teagasc. CC BY-SA)

Microbial identity of artisanal cheeses

The CSIC’s work has focused on the analysis of artisanal cheeses from Asturias. “The environments of 28 cheese factories belonging to the Association of Artisanal Cheesemakers of the Principality of Asturias have been analysed, and it has been proven that the cheeses from each facility have unique characteristics,” reveals Margolles.

“This is important because the specificity and quality of local foods could be linked to their microbiome, and it even makes it possible to use the metagenome as a marker of food authenticity, representing a powerful tool to guarantee its traceability and origin,” he concludes.

The new database has been presented publicly in the academic journal Cell, under the title “Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome”. (Source: CSIC)