Dr. Joseph Murray takes the adage “You are what you to eat” to a whole new level — a lower level. As a gastroenterologist at Mayo Clinic in Rochester, Murray studies “anything that ails you from your mouth to the other end.”

In addition to being an expert in Celiac disease and swallowing disorders, he has a “keen interest in what we feed ourselves and the bugs inside us.”

We talked to Murray about the increasing interest in the gut, good bugs vs. bad bugs, food vs. supplements, the possible dangers of elimination diets and how “brugs” may be the next frontier in treating autoimmune diseases.

Q: How do you think of the gut?

A: One analogy is the big brain/little brain, with our mind being the big brain and the gut our little brain. But I think of us as a gut — with a few well-developed appendages.

Q: Sounds like a gastroenterologist talking. What’s in this gut?

A: We are essentially a bag of bugs. We have bugs on us and in us, and we have evolved with those bugs. They help mature and develop our immune systems. They also prevent bad bugs from taking root.

Q: So these bugs are important. How do we take care of them?

A: When we feed ourselves, we feed the bugs inside us. Our bugs are what we feed them. We need to think about how we tend to them, how we grow and train them. A lot of people think a plant-based diet may be good for us.

Q: What do you think?

A: Here’s the single most important piece of nutritional advice I can give: Eat less.

Q: That’s it?

A: Eat less. Probably eat more plants. Eat less saturated fats and more things with healthy fiber, like oatmeal. And don’t go overboard on any one thing.

Q: Why do you think interest in the gut has skyrocketed?

A: When people experience things that make them feel not well, they look at what they can control, things they can do themselves. For the last 10 years or so, people have been turning to diets to help themselves improve how they feel, how they perform.

Q: Can diets help?

A: Yes, but I’m very worried about fads because they’re not based on science. We don’t want people to drastically shift their diets on ideas that are unproven. Take grain-free diets. There are studies that show eating healthy whole grains seems to be associated with good cardiovascular health.

Q: Are you concerned about elimination diets?

A: When people go on a restrictive diet, they avoid something like gluten. And then they feel a little better for a while. But then that wears off, so they avoid dairy, too. Soon, they’re on such a restrictive diet that it’s nutritionally deficient and unsustainable.

If you make a dietary change and the benefit isn’t durable, don’t stick with it. And certainly don’t double down on it.

Get medical advice. Talk to your doctor about what it is you’re trying to address.

Q: Fermented foods are hugely popular. If I eat sauerkraut and drink kombucha, will I be healthy?

A: We don’t know. We do know that fermented foods have evolved over centuries, and that they may reduce the risk from other types of bad bugs.

Q: What about supplements?

A: If there’s evidence that a certain food or group of foods is good for you, then eat that food. Don’t try to distill it down into a pill form.

Q: Why is food better than a pill?

A: When we eat a food with probiotics in it, that food helps reduce the amount of acid in our stomachs. If you take a supplement, the acid in our stomachs can kill some of the good bugs.

And, often, what a food contains is so much more complicated. Take yogurt, for example. When you eat yogurt, you get more than probiotics. It has milk in it (which protects the probiotics from the stomach acids), magnesium, calcium and whatever it is in the milk that the probiotic bugs have been working on. When you take lactobacillus, that’s all you get.

Q: Where is gut science headed?

A: We’re studying how we can manipulate the bacteria in our guts — by adding to them, feeding them — to tame our autoimmune system to help us overcome or treat diseases like rheumatoid arthritis. We have powerful drugs to treat that, but what if we could use the bacteria instead?

This isn’t realized yet, but we’re trying to see if “brugs” (a bug that acts like a drug) can change how our immune system works.