When it comes to apples, most of the microbes turn out to be in the core, central part which most people don’t eat because it is fibrous—full of fiber and microbes. If you eat only the flesh and skin, you miss out on 90 percent of the bacteria, some of which are the same species sold in expensive pills at Whole Foods. As I’ve argued in the past, if you eat the apple from bottom to top, the fibrous “core” is barely noticeable. The seeds of the apples had the most microbes of any part. They do contain trace amounts of cyanide, but adults should have no problem with a single daily core.
At Rutgers University, the professor of food science Donald Schaffner does not eat apple cores. But he is intrigued by the idea—and by the apple bacterial counts. His team has been counting microbes in food for years. Their main concern has been looking for disease-causing bacteria. The diversity of microbes in an apple comes as news even to him—and the numbers would have seemed impossible to him not long ago.
“This microbiome research is blowing things wide open in terms of complexity,” he told me. When the Rutgers lab started studying foods, the only way to look for microbes was to culture bacteria. It turns out that this was detecting only a small percentage of microbes, since not all of them grow on agar. Newer technology allows scientists to test for DNA, and this has revealed orders of magnitude more microbes on and in our food than previously imagined.
“We’ve known for a long time that there are organisms in fermented foods that have benefits,” said Schaffner, who had just eaten yogurt, “but there is a lot more to it than that.”
Each week his research team samples foods in the dining hall at Rutgers. They bring, for example, an egg back to the lab and mix it in with some dilution and put it into a “stomacher,” a sort of glorified sack that that churns and shakes to simulate the action of the food being partly digested in the stomach. Then the team tests the slurry for bacteria—what’s there that would make it through the acidic barrier of the stomach. Produce consistently has more organisms than other foods.
“As long as it’s not spoiled, that may not be a bad thing,” says Schaffner. “You always want to limit human pathogens, but you also want to look at the overall microbiota.”
If the stomach machine test found lots of microbes in a salad that would be expected; it would only be a problem if a disease-causing species like E. Coli appeared. By contrast, even a small number of bacteria on a hard-boiled egg suggests something is awry. “One of the foods I passed up on the breakfast buffet this morning is hard boiled eggs,” he said. These should be relatively microbe free, but this is often not the case. They represent “an excellent environment for growing bacteria.”
Short of food poisoning, the idea that foods with naturally higher bacterial counts could be good for human health is promising. It also offers a plausible explanation for why what we already knew to be true is indeed true. If fresh produce can be considered a probiotic food, that would only be cause to double-down on the old nutritional wisdom: Eat a “balanced” diet, full of fresh fruits and vegetables, nuts and seeds, et cetera. If you do all that, except for specific cases, the average person shouldn’t need supplemental microbes.
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, MD, is a staff writer at The Atlantic. He hosts the video series If Our Bodies Could Talk and is the author of a book by the same title. | More