Scientists use metagenomics to unlock “largest survey of microbes in food”

02 Sep 2024 --- International researchers created an open-access database of the “food microbiome” by sequencing the metagenomes of 2,533 different foods. They note that the database expands knowledge on food microbiomes and their role in shaping the human microbiome and supports future uses of metagenomics for food safety and authorization. 

The team identified 10,899 metagenome-assembled genomes, grouped in 1,036 prokaryotic (single-celled organisms without a nucleus) and 108 eukaryotic (organisms with a nucleus) species, of which 320 taxa were previously undescribed. 

The food genome groups accounted for an average of 3% of the adult gut microbiome and 56% of the infant gut microbiome. 

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

Power of metagenomics

The researchers leveraged metagenomics to overcome challenges in traditional microbe research. This molecular tool enabled them to sequence all the genetic material within each sample simultaneously. Traditionally, researchers study food microbes by culturing them one by one in the lab, which is a slow and time-consuming process and not all microbes can be cultured. 

Metagenomics is commonly used to characterize the human microbiome or environmental samples, but it hasn’t previously been used to analyze food products on a large scale. 

“Food microbiologists have been studying foods and testing for food safety for well over a hundred years now, but we’ve underutilized modern DNA sequencing technologies,” details 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.”

The researchers examined the microbes in various dairy and fermented foods, including sauerkraut, kimchi and pickles.The team analyzed 2,533 food-associated metagenomes from 50 countries, which included 1,950 newly sequenced metagenomes. The metagenomes came from various food types, including dairy (65%), fermented beverages (17%) and fermented meats (5%). 

The researchers note that similar foods often harbor similar types of microbes. For example, microbial communities in fermented beverages were more identical than microbes in fermented meat. At the same time, the team found a more significant variation between dairy products, likely due to the large number of products included in the research. 

The study, published in Cell, was one of the main outputs of the Master EU consortium. This EU-funded initiative includes 29 partners from 14 countries and aims to characterize the presence and function of microbes throughout the entire food chain. 

“In the future, we want to explore the diversity of these food microbiomes concerning different foods, cultures, lifestyles and populations,” says Cotter.

Human gut microbiome

The researchers underscore that a better understanding of the food microbiome could have implications for human health. Some food microbes could become stable members of the human microbiome. The team compared the new database with 19,833 previously sequenced human metagenomes to examine overlaps between food-associated microbes. 

They conclude that food-associated microbial species compose around 3% of the gut microbiome of adults, 5% in seniors and 3% of children of school ages, but around 56% 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,” explains Segata. 

“It might seem like only a small percentage, but 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.”

With the database, researchers can expand knowledge of food microbe’s role in the human microbiome.Scientific research underscores the benefits of consuming fermented foods. Last year, experts revealed that eating foods with a higher microbial concentration can lead to modest health improvements. Additionally, another study revealed that the fermented beverage kombucha can lower blood sugar spikes. 

Improving food quality

The researchers also investigated potential pathogens, concluding that most species of known concern for foodborne transmission “were rarely found in our sampled foods.” 

At the same time, they found microbes that may be less desirable due to their impact on flavor or preservation of food. They explain that knowing which microbes are typically in different food types may help manufacturers produce more consistent and desirable products. 

Moreover, the database could help food regulators define which microbes should and shouldn’t be in certain food products and authenticate the identity and origins of local foods. 

“One striking thing is that some microbes are present and perform 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,” says Segata. 

“This is important because it could further improve the specificity and the quality of local foods, and we could even use metagenomics to authenticate foods coming from a given facility or location.”

By Jolanda van Hal