Are you what you eat? Biggest-ever catalogue of food microbes finds out

You are what you eat — at least when it comes to the microbiome. A catalogue of microorganisms from more than 2,500 cheeses, meats and other foods suggests that a small portion of each person’s microbiome comes from the food they eat. The study1 is the largest-ever compendium of bacteria, fungi and other microbes found in foods.
Some microbes are an essential ingredient of fermented foods — from salami to sauerkraut and kimchi to kefir. Other microorganisms in fermented and unfermented foods could be important to their taste and other properties such as how quickly they spoil, says microbiologist Nicola Segata at the University of Trento, Italy, who co-led the work, published in Cell on 29 August.
Segata and his colleagues sequenced microbial DNA from nearly 2,000 foods and collated these data with almost 600 existing food microbiomes. Most of the foods were fermented — Segata was sure to include samples of Gorgonzola cheese, one of his favourites — but the study also included fresh meat, fish, fruit and vegetables.
Similar foods tended to harbour similar microbes, although a closer look revealed some intriguing patterns. Lactic acid-making bacteria including Lactobacillus were especially prevalent in dairy products, but the composition varied. Dutch blue cheese harboured different Lactobacillus species from Italian fontina and mozzarella, for instance. Microbes from coffee, kombucha and pu’er — a fermented tea from Yunnan, China — resembled those in alcoholic beverages.
Nearly every microbiome study uncovers organisms that have never been seen before, and this one was no different. About half the microbes the researchers identified were new. Pulque — a sour agave wine drunk in Mexico — was especially rich in this microbial dark matter, as were African palm wine and cheese brine.
When the researchers compared the food microbiomes with thousands of microbiomes from human guts and mouths, they found a degree of overlap. About 3% of the microbe species in adults’ guts, 8% of children’s and more than 50% of newborns’ were also found in food. This doesn’t necessarily mean that these microbes all came from foods people ate, Segata says: the overlap could also reflect instances in the past when food microbes became established in peoples’ guts and began circulating between humans. The food microbes in newborns’ microbiomes tended to be associated with dairy but are also found in breast milk.
None of these findings is especially surprising, says Benjamin Wolfe, a microbiologist at Tufts University in Medford, Massachusetts. But the study lays the groundwork for detailed research into why various microbes — and communities of microbes — are in particular foods. He’s also intrigued by all the unknown microbes in what we eat. Mining these, Wolfe says, could lead to new kinds of food with novel properties.