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How Your Gut Microbiome Impacts Your Health

Gut health is an important element of your overall physical and mental health

A person sifts through a food mixture containing chopped up carrots, shallots and other vegetables

We’ve all had a “gut feeling.” And while that popular saying is based on our intuition and instinct, our gut truly does play a role in our health and how we feel and function.


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“Gut health” has become a trendy term in recent years. Our gut microbiome describes the microbes and their genetic material found in our gastrointestinal tract. And we know the bacteria in our gut affect everything from our digestion to our mental health.

“Gut health is really important,” says registered dietitian Kristin Kirkpatrick, RD. “There is so much attention and research on the microbiome and gut health now that experts often refer to it as the ‘second brain.’”

Digestive disease researcher and registered dietitian Gail Cresci, PhD, RD, and Kirkpatrick discuss the gut microbiome and how it can affect your health.

What is the gut microbiome?

You may think your gut microbiome is in your stomach, but it’s located in your large and small intestines.

“It contains all the microbes that reside within our intestinal tract,” says Dr. Cresci. “And those microbes are comprised of bacteria, fungi, yeast and viruses.”

And we’re not talking about a few hundred microbes — it’s estimated that about 100 trillion microbes are found inside the human body, with many of them residing in our gut.

As you ingest food, the gastric acid found in your stomach destroys a lot of the pathogens you consume.

“We are consuming microbes all the time through our food and water,” says Dr. Cresci. “But the ones that escape that gastric acid then move down to your intestinal tract.”

The goal is to have a healthy gut microbiome. Factors like your diet, infections and certain medications can affect its balance. Having an unhealthy gut microbiome can lead to certain diseases and affect your mental health.

Importance of your gut microbiome

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Your intestinal tract is your largest immune system organ, with about 80% of your immune-producing cells living there.

“What we’ve learned over the years is that there’s a lot of crosstalk between your gut microbiome and your body,” says Dr. Cresci.

Your gut microbiome plays a role in digestion, metabolism and inflammation. As an infant, your gut microbiome helps develop your gut immune system, and then as an adult, it helps maintain it.

“There are certain gut microbes that can produce small molecules and that can also help synthesize certain vitamins, enzymes and hormones that are needed in our body,” notes Dr. Cresci.

Research is ongoing on how the gut microbiome works in tandem with parts of the body like your brain, heart, liver and lungs.

Symptoms of an unhealthy gut microbiome

An imbalance of healthy and unhealthy microbes and their function is known as gut dysbiosis.

“We’ve noticed that people with different mental health issues or mood disorders have gut dysbiosis, meaning there’s alterations in the composition of the gut microbiome and its function,” says Dr. Cresci.

Dr. Cresci warns that not all symptoms of an unhealthy gut microbiome are the same for everyone.

Some common symptoms may include:

If you have gut dysbiosis, it may be linked with other conditions like:

  • Diabetes.
  • Obesity.
  • Inflammatory bowel disease (IBD).
  • Irritable bowel syndrome (IBS).


“Your gut health is so important because studies really do indicate that our gut health plays a huge role in our overall health,” says Kirkpatrick. “It impacts our risk of chronic conditions, our ability to manage our weight, even our immune system.”

How to improve your gut microbiome

Here are a few ways you can improve your gut microbiome.

Eat a variety of colorful fruits and vegetables

Start by focusing on eating a variety of fruits and vegetables. You want to have “microbial diversity,” which will lead to better gut health.

So, how do we achieve that?

“It’s really looking at variety in our diet,” says Kirkpatrick. “If someone tells me they eat kale all day, I think that’s a great habit to have but it’s only one color. It’s only one type of nutrient they’re getting with the kale. So, we need to add more color to our diet. We need to add more variety.”

Think about having a plate full of colorful produce. For example, make a salad that includes kale with other vegetables and fruits like peppers, tomatoes and berries.

Add fiber to your diet

Another vital part of your diet is making sure you’re eating enough fiber. It’s recommended that women eat 25 grams of fiber per day and men 35 grams of fiber per day.

Fiber helps keep your bowel movements regular, but also helps lower cholesterol and keeps your blood sugar levels from spiking. High-fiber foods include whole-wheat pasta, chickpeas, lentils and berries.

“You want to have soluble and insoluble fiber,” says Kirkpatrick. “Soluble fiber swells in water, for example, oats from oatmeal. And insoluble fiber like nuts don’t swell. We want both of those types of it.”

Dr. Cresci also suggests eating a diet low in animal meat and simple sugars and watching how much processed foods and refined sugar you consume.


Eat fermented foods

Consider adding fermented foods like yogurt, kimchi and kombucha to your diet.

These fermented foods help introduce good bacteria into your gut microbiome and can lower your intestine’s pH level. By doing so, it can decrease the chance that bad bacteria survive.

By having good bacteria in your gut microbiome, it also produces essential vitamins like B12 and K.

Reduce stress

Your stress level can impact your gut health.

“We’re learning more how stress can impact the gut microbiome,” says Dr. Cresci. “That means psychological stress, physical stress and metabolic stress.”

How can you work on reducing your stress levels? Turn to relaxation techniques like deep breathing and meditation to help lower your stress and anxiety. You can also try to exercise regularly and prioritize sleep.

Maintain a regular eating schedule

In addition to eating a well-balanced diet, it’s also important when you eat.

“You have a circadian rhythm, but your microbiome has a circadian rhythm, too,” explains Dr. Cresci. “If you’re eating late at night, your microbiome is not likely geared up to metabolize those nutrients as well.”

Try to stick to eating your meals at the same time each day.

Avoid taking certain medications long term

Sometimes, taking antibiotics is unavoidable, notes Dr. Cresci.

“But antibiotics will destroy the pathogens and attack the good microbes in the gut, too,” she adds.

Dr. Cresci also warns against taking over-the-counter acid-reducing agents long-term.

“By doing so, you elevate the pH in your stomach,” she says. “That allows any ingested pathogens to have a better chance to survive, which can alter the microbiome.”


Consider probiotic and prebiotic supplements

You can get the benefits of probiotics and prebiotics from the foods that you eat. But you can also use a supplement.

Prebiotics, which can be found naturally in artichokes, apples and green bananas, are a type of fiber that supports the growth of healthy bacteria.

Probiotics are live good bacteria that can maintain or help get to a healthy, balanced gut microbiome. There are two popular types of bacteria commonly found in supplement form: Lactobacillus and Bifidobacterium.

It’s important to know that these supplements are fragile. Many require refrigeration to protect them from heat, oxygen, light and humidity, which can break down their effectiveness.

Look for supplements that have a seal of approval from testing agencies like Consumer Reports or Consumer Labs.

And there are many strains of probiotics, so it’s key to find one that works for the condition you’d like to treat. Some may provide relief if you have IBS or diarrhea. Others can help boost your immune system or reduce inflammation.

Overall, researchers are just beginning to understand how vital your gut microbiome is in relation to how the rest of your body functions. Even small changes in your diet and lifestyle can have a positive effect on your gut health.

“You have to look at where you are, what you’re willing to do in order to improve gut health,” advises Kirkpatrick. “A lot of times what happens is you feel the benefits so quickly that it’s easy to go on to the next step.”


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