Exploring the microbiome of the foods we eat

Microbes are part of the foods we eat and can even influence our own microbiome, but until now, very little has been known about these microbes.

Researchers have now developed a ‘food microbiome’ database by sequencing the metagenomes of over 2500 different foods, including dairy and fermented beverages and meats. They identified over 10,000 food-associated microbes, half of which were previously unknown species, and showed that food-associated microbes account for around 3% of the adult and 56% of the infant gut microbiome on average.

“This is the largest survey of microbes in food,” said co-senior author and computational microbiologist Nicola Segata of the University of Trento and the European Institute of Oncology. “We can now start to use this reference to better understand how the quality, conservation, safety and other characteristics of food are linked with the microbes they contain.”

Traditionally, microbes in food have been studied by culturing them one by one in the lab, but this process is slow and time-consuming, and not all microbes can be easily cultured. To characterise the food microbiome more comprehensively and efficiently, the researchers used metagenomics, a molecular tool that enabled them to simultaneously sequence all the genetic material within each food sample. Metagenomics is often used to characterise the human microbiome or analyse environmental samples but hasn’t previously been used to investigate food at a large scale.

“Food microbiologists have been studying foods and testing for food safety for well over a hundred years now, but we’ve underutilised modern DNA sequencing technologies,” said co-senior author and microbiologist Paul Cotter of Teagasc, APC Microbiome Ireland and VistaMilk Ireland. “This is the starting point for a new wave of studies in the field where we make full use of the molecular technology available.”

Altogether, the team analysed 2533 food-associated metagenomes from 50 countries, including 1950 newly sequenced metagenomes. These metagenomes came from a variety of food types, of which 65% were dairy sources, 17% were fermented beverages and 5% were fermented meats.

These metagenomes comprised genetic material from 10,899 food-associated microbes categorised into 1036 bacterial and 108 fungal species. Similar foods tended to harbour 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 didn’t 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 flavour or preservation. Knowing which microbes ‘belong’ in different types of food could help producers — both industrial and small-scale — to 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 ‘local’ foods.

“One thing that was striking is that some microbes are present and performing similar functions in even quite different foods, and at the same time, we showed that foods in each local facility or farm have unique characteristics,” Segata said. “This is important because it could further improve the idea of the specificity and the quality of local foods, and we could even use metagenomics to authenticate foods coming from a given facility or location.”

Understanding the food microbiome could also have implications for human health, as some of the microbes we eat could become stable members of our own microbiomes. To examine overlaps between food-associated microbes and the human microbiome, the team compared their new database with 19,833 previously sequenced human metagenomes. They showed that food-associated microbial species compose around 3% of the gut microbiome of adults and more than 50% of the gut microbiomes 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 those microbes adapted to become part of the human microbiome,” Segata said. “It might seem like only a small percentage, but that 3% can be extremely relevant for their function within our body. With this database, we can start surveying at a large scale how the microbial properties of food could impact our health.”

The study has been published in the journal Cell and the database is available as an open-access resource.

Image credit: iStock.com/Andrii Lysenko