Microbes are a part of the food we consume and can affect our own microbiome, yet our knowledge about the microbes present in our food is still limited. Researchers have now created a database focusing on the ‘food microbiome’ by sequencing the metagenomes of 2,533 different foods. In the process, they discovered 10,899 food-associated microbes, with half of these being unknown species. Their findings indicate that food-related microbes represent about 3% of the adult gut microbiome and 56% of the infant gut microbiome, on average. The study was published on August 29 in the journal Cell, and the database is available to the public.
Microbes are a part of the food we consume and can affect our own microbiome, yet our knowledge about the microbes present in our food is still limited. Researchers have now created a database focusing on the “food microbiome” by sequencing the metagenomes of 2,533 different foods. In the process, they discovered 10,899 food-associated microbes, with half of these being unknown species. Their findings indicate that food-related microbes represent about 3% of the adult gut microbiome and 56% of the infant gut microbiome, on average. The study was published on August 29 in the journal Cell, and the database is available to the public.
“This represents the largest survey of microbes in food,” states co-senior author and computational microbiologist Nicola Segata from the University of Trento and the European Institute of Oncology in Milan. “With this reference, we can better understand how food properties, such as quality, preservation, and safety, relate to the microbes present within them.”
Historically, researchers have studied food microbes by growing them individually in the lab. However, this method is slow and not every microbe can be easily cultured. To study the food microbiome more effectively, the researchers utilized metagenomics, a technique that allows them to sequence all the genetic material in each food sample at once. While metagenomics has been widely used to analyze the human microbiome and environmental samples, it hasn’t been applied to food on a large scale before.
“Food microbiologists have been examining food safety and quality for more than a century, but we have not fully utilized modern DNA sequencing technologies,” explains co-senior author and microbiologist Paul Cotter of Teagasc, APC Microbiome Ireland, and VistaMilk Ireland. “This is just the beginning of a new era in our field, taking full advantage of available molecular technology.”
The research team analyzed 2,533 food-associated metagenomes from 50 different countries, which included 1,950 newly sequenced metagenomes. The samples covered a range of food types, with 65% coming from dairy, 17% from fermented drinks, and 5% from fermented meats.
The metagenomes contained genetic material from 10,899 food-associated microbes, classified into 1,036 bacterial and 108 fungal species. Similar types of food were found to contain similar microbes; for example, microbial communities within different fermented drinks were more alike compared to those found in fermented meat. However, there was more variety among dairy products, likely due to the larger array of dairy items examined.
While the researchers did not detect many known harmful bacteria within the food samples, they did find some microbes that could negatively affect food flavor or preservation. Identifying which microbes are appropriate for various food types can assist both large-scale and smaller producers in creating more reliable and appealing products. Furthermore, this knowledge may aid food regulators in determining acceptable and questionable microbes in specific food types and in verifying the authenticity of “local” foods.
“One noteworthy finding was that certain microbes exhibit similar functions across different foods, while at the same time, foods from each local facility or farm show unique traits,” Segata remarks. “This is crucial because it can enhance our understanding of the uniqueness and quality of local foods, and we could even use metagenomics to verify foods originating from particular facilities or areas.”
Understanding the food microbiome may also impact human health, as some microbes we ingest could become stable components of our own microbiomes. To explore the connections between food-associated microbes and the human microbiome, the research team compared their new database with 19,833 previously sequenced human metagenomes. Their analysis revealed that food-associated microbial species make up about 3% of the adult gut microbiome and over 50% of the gut microbiomes in newborns.
“This indicates that portions of our gut microbes may be directly obtained from food, or that historically, human populations gained these microbes from their diet and adapted them into their microbiomes,” explains Segata. “While this may seem like a small percentage, that 3% can play a significant role in our body’s functioning. With this database, we can begin large-scale assessments of how the microbial characteristics of food could affect our health.”
The study emerged as a key output from the MASTER EU consortium, an initiative funded by the EU involving 29 partners across 14 countries with the goal of characterizing microbes throughout the entire food supply chain.
“In the future, we want to investigate the diversity of these food microbiomes in relation to various foods, cultures, lifestyles, and populations,” adds Cotter.
