A Survey of the 161 Bacterial Families That Live on Your Fruits and Veggies

The first-ever sequencing of the “produce microbiome” reveals that grapes, peaches and sprouts host the largest diversity of harmless bacteria

The first-ever sequencing of the produce microbiome reveals that grapes, peaches and sprouts host the largest diversity of harmless bacteria. Image via Wikimedia Commons

In recent years, research has upended one of the most intuitive ideas of modern science: that bacteria simply make us sick. Scientists have discovered that many types of bacteria living in and on the human body play a crucial role in its healthy functioning—and that these colonies are remarkably populous, with an estimated ten times as many bacterial cells as human ones in the average person.

Similarly, most research into the microorganisms living on fresh produce has focused on a few species of bacteria that cause disease, such as poisonous strains of E. coli, instead of the billions of harmless or even beneficial bacteria cells that live on fruits and vegetables.

Finally, though, the field is catching up: For the first time, researchers have sampled and sequenced the DNA of the hundreds of varieties of bacteria that harmlessly live on the produce you buy at the grocery store. Their study, published today in PLOS ONE, revealed 17 to 161 families of bacteria on each of the fruits and vegetables they tested, with grapes, peaches and sprouts hosting the largest diversity of bacteria.

The researchers—Jonathan Leff and Noah Fierer of the University of Colorado, Boulder—studied 11 types of produce in total: apples, grapes, lettuce, mushrooms, peaches, bell peppers, spinach, strawberries, tomatoes, alfalfa sprouts and mung bean sprouts. For each fruit or vegetable, they swabbed the surface, isolated the DNA from the swab, sequenced the DNA and analyzed which bacterial family it fell into.

All species host billions of individual bacterial cells, but the research showed that some tend to host a more limited diversity of bacteria. Most of the colonies living on spinach, tomatoes and strawberries, for example, all belonged to one particular family. Others, such as apples and peaches, not only carried a greater total number of bacterial families, but had bacterial colonies more evenly divided amongst each of the families.

The team also looked at the raw quantity of bacteria belonging to the Enterobacteriaceae family in particular, a broad group that encompasses both harmful and beneficial species. For many of the fruits and vegetables, they also compared conventionally grown samples to organic. As a whole, organic produce had lower amounts of bacteria in this family, but some organic vegetables (such as lettuce) actually had higher levels than conventional counterparts.

Research into breadth of bacteria on produce is still in fledgling stages, so it’s difficult to say what this all means. Scientists still aren’t sure what agricultural factors can affect the levels of bacteria on produce, or even which types of the bacteria identified are harmful, harmless, or beneficial.

There’s also the matter of how these types of bacteria interact with the colonies that already live inside our digestive tracts. In terms of nutrition, this dynamic could be crucial: Some of the bacteria living in us help us digest carbohydrates, while closely related strains can cause us to absorb excess levels of fat during digestion.

What this work does reveal is that when you bite into a juicy peach or tart grape, you’re simultaneously eating billions of bacterial colonies. Do they give a peach the ripe taste of summer or the grape its piquancy? Do these bacteria supplement the nutrition of our produce?  Further research, the authors note, will hopefully reveal more.

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