ABOVE: Researchers characterized the microbiome of over 2,500 food samples. ©istock, fcafotodigital
A simple salad made up of crunchy lettuce and onions topped with juicy tomatoes shares the plate with an army of ingredients invisible to the human eye—a thriving world of microscopic life. While researchers described microbes in foods like yogurt, cheese, and meat, communities of microbes in diverse foods remained uncharacterized. 1-3
Now, a team of researchers have curated the largest-ever database of microorganisms from more than 2,500 different foods.4 The collection, published in Cell, includes over 500 new microbial species and provides researchers a resource to study how food-associated microbes impact human health.
Microbes are everywhere in a food’s life cycle, from enhancing flavors and extending shelf life to driving spoilage. “Food microbiologists have been studying microbes in food for hundreds of years,” said Nicola Segata, a computational microbiologist at the University of Trento and a study coauthor. “But with modern techniques, there is really an opportunity to survey not only the microbes that are easier to grow, but all of them, and also be able to check the microbes present in less studied foods.”
Using shotgun metagenomics, one such modern method for sequencing all the genetic material within a sample, Segata’s team analyzed microbial DNA from foods from 50 countries.5 They compiled the data with existing sequencing data to create the food microbiome database.
Using computational methods to assemble the metagenomes from the sequencing data, the researchers reconstructed over 10,000 genomes of food-associated microbes, which they categorized into more than 1,100 species. Segata found that around half of these species were previously unknown. While most of the newly identified microbes were found in exotic foods—an alcoholic beverage called Mexican pulque, an African palm wine, and a Korean fermented fish—common items like vegetables and coffee harbored new species as well. When Segata and his team compared the genomes of these newly identified microbes to those of other unknown species found in animals, soil, water, and plants, they found that almost half of the unknown food-associated species are not found in any other environment.
The researchers also identified less desirable species in some food samples, demonstrating that metagenomic surveys can help investigate food safety. While they rarely found known disease-causing microbes like Listeria monocytogenes and Clostridium perfringens in their samples, other potentially pathogenic strains of microbes like Staphylococcus aureus were more common. They also came across spoilage-associated microbes in some samples.
“[Now] we have an idea which microbes you should expect to find in a given food,” said Segata, who added that this provides a basis to test foods for potential spoilage and quality control.
“The more we know about the good bacteria, we can control the bad bacteria,” said Josephine Wee, a food microbiologist at Pennsylvania State University. This knowledge can also have implications in extending the shelf lives of food to avoid wastage by understanding microbes responsible for spoilage, she added.
Next, the researchers explored whether these food-associated microbes are found in the human microbiome by comparing the new database with previously sequenced human metagenomes. In adults, they found an overlap in three percent of the microbial species.
However, Segata cautioned that this does not necessarily mean that the microbes in human guts are coming from the food. “It can be that at some point in human history, some microbes from the food colonized our gut and then got adapted to our gut,” he explained. “And then these microbes were exchanged by direct contact between individuals, like pathogens, rather than directly from food.”
Wee agreed. “But the potential link is really interesting, because that means we can protect ourselves from certain things,” she said. “We can [potentially] shape our human microbiome just by our food habits.”
“While the strength in the study lies in the 2,500 foods, I think a big limitation is the [food source] diversity,” she said. A majority of the foods tested are of European origin, she noted. She suspects that fermented foods from older civilizations like Asia and the Middle East may have a higher biodiversity than those from Europe and America.
“We need to look at more different countries, continents, and local communities,” said Segata. “They hold a tremendous diversity of food microbes that are extremely important to survey.”
- Islam SMR, et al. Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh. Sci Rep. 2021;11(1):22667.
- Wolfe BE, et al. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell. 2014;158(2):422-433.
- Hellmann SL, et al. Identification and quantification of meat product ingredients by whole-genome metagenomics (All-Food-Seq). Eur Food Res Technol. 2019;246(1):193-200.
- Carlino N, et al. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. Cell. 2024.
- Quince C, et al. Shotgun metagenomics, from sampling to analysis. Nat Biotechnol. 2017;35(9):833-844.