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Meet Your Microbiome, Your Body’s Superpower

6 min read  |  November 16, 2022  | 

A UHealth physician explains what works and what doesn’t work to restore gut health.

The old saying, “Out of sight, out of mind,” seems to hold for microbiome, those microscopic, but mighty, organisms living in your lower intestine. You can’t see or feel them, but they are hard at work, helping your body function.

As long as they’re healthy, we’re happy, and our gut health is balanced. Lose that balance, and those microbial benefactors falter. 

Contrary to popular opinion, restoring gut health isn’t as simple as popping probiotic supplements.

To restore or maintain your gut microbiome, get back to the basics of healthy living, says Morgan Allyn Sendzischew Shane, M.D. Dr. Shane is a gastroenterologist specializing in motility disorders at the University of Miami Health System. (Motility is the overall movement of the gastrointestinal tract.) 

Understanding microbiome

“As humans, we are more bacteria than human cells,” says Dr. Shane. 

The microbiome is a complex network of bacteria, fungi, and viruses. 

For the purposes of gut health, let’s focus on bacteria. 

You may have heard of “bad” and “good” bacteria. The good ones fight infection and illness and help digest our food. The bad ones make us sick and might kill us if left unchecked. We always have a mix of good and bad bacteria in our gut, but the goal, Dr. Shane says, is “homeostasis” – restoring our body’s bacterial balance. 

What happens when we’re out of balance

Unlike viruses such as COVID-19, most bacteria (except treatment-resistant superbugs) can be successfully treated with antibiotics. However, antibiotics don’t distinguish between good and bad bacteria, so their repeated use is like kryptonite to your microbiome superpower. 

“The job of antibiotics is to kill bacteria,” Dr. Shane says. 

The drugs aren’t selective; when they upset your microbiome balance, you may experience the following:  

  • Diarrhea
  • Nausea
  • Bloating
  • Temporary intolerance of certain foods, especially dairy
  • Yeast infections

Another cause of gastrointestinal trouble? “Frequent infections and illnesses can create changes or inflammation in the lining of your gut. For example, we see a lot of post-COVID gastrointestinal symptoms,” Dr. Shane says. 

Other factors that may diminish a healthy microbiome include:

  • Consuming highly processed or fried, fatty foods
  • Excessive alcohol consumption
  • Poor sleep hygiene

The problem with probiotic supplements

Advertised as a panacea for gastrointestinal health problems, probiotics pop up in everything from pills to pasta. Such products claim to maintain digestive balance, among other things. 

However, “Probiotics are a one size fits all approach. They don’t give you a wide selection of bacterial strains, which is what is needed, and they don’t necessarily contain the bacteria you personally may need.” 

Despite good intentions, probiotics can delay the repopulation of microbiome after a round of antibiotics, according to a 2018 study. Also, many supplements claiming to contain billions of live active probiotic cultures lack prebiotics, the dietary fibers that act as food for good bacteria. 

Another reason to save money on probiotic products is the stomach acid that aids digestion. 

“Many probiotic supplements die in the stomach due to the high acid environment. Often, they never even make it to the small intestine where they need to live,” says Dr. Shane.

She also discourages supplementing with additional unverified “gut health” supplements because “The FDA does not regulate the content of these supplements, and no one checks the credentials of the people promoting them. How we consume health information is critical. It’s important to be skeptical. ”

How can I build a healthy gut?

Fortunately, the human body is forgiving. There are several ways to improve your microbiome:

Limit antibiotics. 

You may be miserable with that cold or flu, but antibiotics won’t cure or shorten the duration of a viral infection.

During flu and cold season, be kind to your body: eat healthily, get enough rest, stay hydrated, wash your hands often, get vaccinated, avoid crowds, and wear a mask. If you take antibiotics for a bacterial infection, finish the full dose as your doctor prescribes.

Get your prebiotics and probiotics from food. 

Prebiotics are found in fiber-rich foods. Dr. Shane recommends bananas (greener, not overly ripe), asparagus, onions, leeks, and mushrooms in particular.

Probiotics occur in fermented foods such as sauerkraut, kimchi, pickles sold in the refrigerated section, pickled vegetables, kombucha, and plain, unsweetened Greek yogurt or kefir. (Read the labels on kombucha to avoid those with high sugar content.) 

Generally, the fewer processed foods you eat, the healthier your gut will be, so try to limit preservatives and additives such as emulsifiers.

This might require rethinking some favorite foods. If you love bread, buy fresh whole-grain varieties from the bakery; they have fewer preservatives and additives than loaves sold in the bread aisle. 

Cut back on drinking. 

Excessive alcohol use can cause diarrhea, inflammation of the gastrointestinal tract, and stomach ulcers. 

Get adequate sleep. 

Unless you are the parent of a newborn, it might be easier than you think. Try these tips to correct your sleep deficit. 

Get outdoors. 

Telling your kids to get off the couch and play outdoors helps their health.

“People who have more overall exposure to bacteria early on seem to have less autoimmune problems later in life. We don’t fully understand why, but spending time outside is important for many reasons,” Dr. Shane says. 

She cites the “hygiene hypothesis” that correlates increased urbanization and hygiene with an increase in autoimmune disorders. Turns out, a little dirt won’t hurt you. It’s never too late to have a happy childhood, so get outside whenever you can. 

Address underlying issues. 

Even without antibiotics, recurring illnesses and infections wreak havoc on health. Your body wants to stay balanced. Speak to your doctor if feeling unwell, chronically tired, or out of sorts.

Dr. Shane recommends partnering with a gastroenterologist or your primary care doctor to manage these conditions. Since diet can reveal clues as to when and why patients experience a variety of gastrointestinal symptoms, “I ask patients to keep a food diary for two weeks.” 

Although Dr. Shane says, “Microbiome is a complicated concept,” restoring our gut health doesn’t have to be. A few simple, healthy habits are more effective, and less expensive, than anything that comes in a bottle. 

To schedule a consultation with a UHealth specialist, call 305-243-8644.


Nancy Moreland is a regular contributor to UMiami Health News. She has written for several major health care systems and the CDC. Her writing also appears in the Chicago Tribune and U.S. News & World Report.


Tags: common probiotic, Dr. Morgan Allyn Sendzischew Shane, fruits and vegetables, unhealthy gut

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