NEW YORK (CBSNewYork) – Here’s some shocking news for almost every person who eat apples – we’ve probably been doing it wrong.

It turns out some important nutrients are in the parts of the apple we hardly ever eat, CBS2’s Dr. Max Gomez reports.

That old Welsh proverb – an apple a day keeps the doctor away – came from the accurate belief that apples are healthy and nutritious.

But a new Austrian study says we’re missing out on important probiotics by not eating all of the apple, stem and all!

You don’t have to search far to find YouTube videos of people eating apples. They all pretty much eat them the same way although they take different routes to the finish line.

But that’s not what we mean by eating an apple the wrong way. Here’s what some experts recommend.

“I eat the core. The whole piece, I eat the whole thing the skin, the seed, the only thing that I don’t eat is the stem,” Ramundo Seguro said.

Ramundo may be on to something.

A new study in the journal “Frontiers in Microbiology” says the core and stem contain the highest concentration of the good, gut health-promoting bacteria usually called probiotics.

Those good bacteria, and each person has trillions of them in their gut, form what’s called the microbiome. It’s a part of our body that’s been shown to affect everything from our mental health to our immune system.

The trouble is everyone’s microbiome is different.

“So lately there has been a lot of buzz around a healthy gut and the brain and gut connection. We really don’t know how to test for a healthy microbiome. We don’t know what that looks like,” Sharon Zarabi from Lenox Hill Hospital said.

The registered dietician explained that most of the good stuff we associate with apples, fiber, vitamins, and antioxidants are actually in the skin and pulp.

Eating the core and stem may give you more probiotics – but there’s a downside.

“When you eat through the seeds of the apple there is some cyanide which can be toxic to the body,” Zarabi warned.

You’d have to eat many apples to be in serious danger from this. Healthy or not, CBS2 found few apple core eaters ready to dig in.

“No usually don’t eat the core,” one person said.

“Nope I don’t want to eat that core,” another person declared.

The study found little difference between organic and conventionally grown apples when it came to the number of bacteria, but organic apples had a greater variety of bacteria.

Again, that might be important or they might not.

So eat the core if you like, just don’t expect it to magically heal your gut. The cyanide risk is very small and only becomes an issue if you crush or chew the seeds.