How Your Gut Microbiome Is Affecting Your Health

healthy woman doing heart symbol on her belly button at outdoor

Did you know that the average human body has 10 times more bacteria than human cells, and that over 4,000 different species of bacteria reside just in your gut?

Otherwise known as “gut microbiome,” the bacteria in our gut aren’t all bad. In fact, this has become a hot area of research and information, with great potential effect on our overall health.

If you’ve never heard about the microbiome before, soon you won’t be able to escape it. Fortune Magazine declared 2015 the Year of the Microbiome, calling poop the center of a medical revolution. The National Institute of Health has spent $173 million on its Human Microbiome Project – established in 2008 – which hopes to uncover the role of the microbiome in health, nutrition, immunity, and disease.

What is It?

The bacteria in our gut perform a number of functions – training our immune system, helping with food digestion, and manufacturing vitamins, says Lisa Cimperman, a registered dietician and spokesperson for the Academy of Nutrition and Dietetics. “Recent research has indicated that our gut bacteria may play a key role in the development of various autoimmune diseases (such as inflammatory bowel disease and rheumatoid arthritis), irritable bowel syndrome, and even influence our likelihood of being obese,” she says.

Research is also starting to link gut microbiota with metabolic syndrome and other non-intestinal disorders, says Gail Cresci, a registered dietician and member of the Department of Gastroenterology and Hepatology and Department of Pathobiology at the Cleveland Clinic. There’s now a link between the gut-brain that’s being realized, she adds.

Desiree Nielsen, registered dietician, member of the Bio-K+ Advisory Board, and author of Unjunk Your Diet, expands on this. “Maintaining a healthy, functioning gut environment – with the help of the microbiota – supports a well functioning nervous system and it is known that the microbiota can influence the levels of neurotransmitters such as serotonin.” A healthy microbiome can play a critical role in affecting mood. “In my opinion,”  Dr. Raphael Kellman,  author of  The Microbiome Diet,  says,  “it works better than antidepressants.”

Gut Bacterial Changes

Many factors affect gut bacteria, which even differ from person to person. Cimperman says some of them include:

  • Age
  • Antibiotic use
  • Exercise
  • Diet pattern (i.e. vegetarian, vegan, meat eater)
  • Alcohol intake
  • Environmental exposures (pets, others in the house)

When it comes to antibiotics, Cresci recommends taking a probiotic supplement during and up to 14 days after a course.

Interestingly, any changes to your physical, emotional, or dietary state can begin to alter the microbiota (gut flora) in as little as 24 hours, says Nielsen, “It takes sustained lifestyle change to maintain these alterations,” she says. But within a week of making changes, many people will start noticing an effect in how they feel.

Prebiotics and Probiotics

Our gut bacteria feed off the fiber we consume, so a diet high in whole grains, fruits, and vegetables best supports a balance of healthy gut bacteria, says Cimperman. She says fiber is considered a “prebiotic,” which means it is food for our gut bacteria.

Increasing the fermentable prebiotic fibers in your diet means choosing foods such as onions, garlic, sunchokes, chicory, asparagus, and legumes, says Nielsen. “There is some new evidence that prebiotics may be enough to help support mood,” she says.

Kiwis, leeks, radishes, and jicama are other prebiotic foods mentioned by Dr. Kellman in his book, The Microbiome Diet.

Another type of foods contains probiotics, which Cresci describes as “live microbial substances that when consumed in adequate amounts have beneficial effects on the host.” She cautions that many dietary supplements that claim to be probiotics don’t actually meet the criteria. In order to be considered a probiotic, a bacterial strain must be isolated from a human, be resistant to acid and bile, survive an intestinal process, be safe for human consumption, and be clinically validated with research studies.

Yogurt, kefir, sauerkraut, and other fermented foods contain probiotics, with yogurt not surprisingly being one of the most popular options. Cimperman says to look for yogurts labeled as containing “live and active cultures.” She recommends buying plain yogurt and adding fresh fruit or a little bit of honey, to control the amount of added sugars. “Keep in mind that plain, unsweetened yogurt will have about 12 grams of naturally occurring milk sugars,” she says.

If you eat fermented foods in the hopes of introducing good bacteria into your body, you’ll have to eat them in large amounts daily – a cup or more a day – to have an impact over time, says Nielsen.


Diet plays an extensive role as a risk factor for many diseases. It should make sense that highly refined and processed food (think junk food, fast food, candy and sweets) doesn’t have the fiber your body needs to maintain a healthy gut microbiome, Cimperman says. “Likewise, high protein diets that eliminate complex carbs (like those found in whole grains and fruits) may also lack the necessary fiber to support an optimal balance of bacteria in your gastrointestinal tract,” she says.

Aim for 25-35 grams of fiber a day, and consume alcohol in moderation (one drink a day for women), and exercise regularly, says Cimperman. These will obviously improve your overall health and reduce your risk for disease, with the added benefit of modifying your gut microbiome.

“When you improve the microbiome, you will have [fewer] cravings,” says Dr. Kellman.


If there’s too much unhealthy gut bacteria, a microbiome issue can develop because the gut microbiome is imbalanced. According to Nielsen, signs may not be readily apparent and may include:

  • Skin conditions
  • Hard to explain weight gain, particularly around the middle
  • Insulin resistance
  • Non-allergy food reactions
  • Constipation
  • Autoimmunity
  • Mood/energy alterations

Many times when patients visit Dr. Kellman, they don’t know they have a microbiome issue. The average length of time before realizing they do could be months or years. He diagnoses with symptoms, a breath test called a Quintron Test, and sometimes a stool sample.

Ultimately, when it comes to gut microbiome, “It’s important for one to take a proactive approach to one’s health,” says Dr. Kellman. “Healing is the most important healthy aging process one can do.”

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