But fresh produce and grains also give us more than fiber. An exciting, emerging idea is that fruits and vegetables are healthier than the sum of their parts, not just because of nutrients and fibrous skeletons, but because they contain microbes themselves.

That might seem like a bad thing. But it actually builds on a story I wrote last week about how the immune system, gut microbes, and the food we eat all work in harmony to influence weight gain and loss. The closest thing to practical advice from scientists was to maintain a “diverse biome.” But how do people actually do that? Many readers wrote to ask for more concrete advice. (“Sounds like you still want us to take probiotics every day?”; “What’s the best probiotic?”; “Can I buy your microbiome?”)

Doctors have insisted for decades that unnecessary antibiotics should be avoided, to prevent the evolution of antibiotic-resistant superbugs. Upsetting one’s own personal microbial diversity adds yet another reason. Fermented foods of course contain bacteria, and their consumption has been linked to some health benefits. Beyond that, many people believe it’s necessary to turn to supplements. Even Harvard Medical School’s website tells patients as much, advising that “there are two ways to get more good bacteria into your gut: fermented foods and dietary supplements.”

But supplements are an enormous and barely regulated industry. Even the best clinical trials are limited and short-term. Taking a probiotic supplement of Akkermansia was found last month to have some metabolic benefits—but the same bacteria are also associated with multiple sclerosis. Such things are not to be wantonly introduced into everyone’s guts, but used strategically in specific populations with specific needs—more like a drug than a food.

For all of human history, the gut microbiome has gone without bacterial pills. Fermented foods have been part of many cuisines around the world, but our ancestors didn’t live on kombucha. There had to be another source.

And, it turns out, there is: fresh produce.

In a study from July in Frontiers in Microbiology, researchers found that the average apple contains about 100 million bacteria. Most are inside, not on the skin. They came from many different taxa—as opposed to the probiotic-supplement pills, which tend to be only one type of bacteria. Of the millions of bacteria in any given apple, very rarely are any the sort that cause diseases; most are innocuous or even beneficial.

The idea, the apple researchers explain, is that these bacteria join and interact with the trillions of microbes that are in our guts already—which are vital to our digestion and metabolic health, and the functioning of our immune systems. Food is the main way that our gut biomes are populated throughout our lives, and microbe-rich foods seem to be important to maintaining diversity. The researchers suggest that microbial profiles could eventually become standard information on nutrition labels (currently limited to fats, proteins, carbohydrates, vitamins, and minerals).