How To Protect Your Body’s Microbiome

In November 2022, the FDA approved its first fecal microbiota product, Rebyota. Rebyota is clinically indicated for preventing the recurrence of a GI condition known as C. difficile by restoring the natural flora and bacteria in the gut.

Key takeaways:
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    The body’s microbiome is a community of microorganisms that assist the body with maintaining its health and regular functions.
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    There are many microbiomes in the body, many of which interact with each other, but each has its own purpose.
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    Prebiotics, probiotics, and postbiotics all work together to allow healthy bacteria to thrive in the body.
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    There are many lifestyle choices that will improve not only general health, but also naturally boost the body's microbiomes.

The FDA approval of Rebyota is another acknowledgment of just how important the microbiome is becoming in healthcare and disease prevention. Although science continues to advance, some actions can be taken now to protect the body's microbiome.

What is a microbiome?

In general, a microbiome is a community of microorganisms consisting of bacteria, protozoa, fungi, and/or viruses. There are estimated to be trillions of microorganisms in the human body, which creates a relationship that both the microorganisms and the human body benefit from.

  • Microorganisms help with digestion.
  • They assist with protecting the skin barrier.
  • They play a key role in infection prevention.
  • Microorganisms help increase immunity.
  • They create substances that the body cannot produce on its own, like certain vitamins.

There has been recent scientific evidence that the health of the gut microbiome impacts the nervous system. The phenomenon is called the “gut-brain axis.” A 2014 study refers to this as “a communication system that integrates neural, hormonal, and immunological signaling between the gut and the brain,” which offers microorganisms a mechanism to access the brain. Remember the last time you were nervous and felt your stomach turn? This is due to the influence that the gut and brain have on one another.

Microorganisms have been shown to react to stress, which can temporarily or permanently alter the microbiome composition and metabolism. In an ideal environment, the microbiome and the human body benefit from one another. However, when that biome is altered, “bad bacteria” take over and produce toxins. These substances may cause infection, irritation, or discomfort.

Microbiomes that exist in the body

Science is now beginning to recognize all of the following as viable microbiomes in the body:

  • Gut microbiome.
  • Skin microbiome.
  • Vaginal microbiome.
  • Oral microbiome.
  • Nasal microbiome.

When each of these environments is balanced, it helps the body carry out necessary functions and protect the body from illness. Although contracting a sickness won’t likely be from one single factor, here are a few conditions that are linked with unbalanced microbiomes:

  • Eczema.
  • Irritable bowel syndrome.
  • Inflammatory bowel disease.
  • Small intestinal bacterial overgrowth (SIBO).
  • Obesity.
  • Type 2 diabetes.
  • Asthma.
  • Rhinitis (chronic stuffy nose).
  • Gingivitis (gum disease).
  • Vaginal yeast infection.
  • Anxiety and depression.

Prebiotics, probiotics, and postbiotics

Enter prebiotics, probiotics, and postbiotics. These are all used to maintain harmony in the body’s microbiomes. Even though they sound similar, they play slightly different roles in microbial maintenance.

Dr. Mahmud Kara, MD describes the differences in terms of your body as a vehicle:


These are like the fuel for a car. Prebiotics are the compounds that create food for probiotics to live off of.


These are like the car’s engine. Probiotics are the actual organisms that provide benefits to the body.


These are like the car’s wheels. Postbiotics come from the substances that probiotics create. Those substances contain nutrients and vitamins that are beneficial to the body.

Dr. Kara recommends the following foods that are rich in pre, pro, and postbiotics:

  • Artichokes;
  • Cabbage;
  • Grapefruit;
  • Chickpeas;
  • Oats.
  • Yogurt;
  • Kefir;
  • Sauerkraut;
  • Kimchi;
  • Pickles.
  • Miso;
  • Flaxseed;
  • Garlic;
  • Cottage cheese;
  • Kombucha.

Maintaining and improving your microbiome

Eating the above foods is beneficial for all microbiomes, but other than eating a specific diet, what else can be done to protect the microbiomes?

Because the microbiomes thrive off of beneficial bacteria, a key in biome maintenance is ensuring that there are beneficial bacteria and that not too many bacteria are killed off. When too many beneficial bacteria are absent, it leaves room for non-beneficial bacteria to thrive.

There are circumstances that assist with maintaining and regulating a healthy microbiome. This includes individuals who:

  • Were born via vaginal delivery.
  • Sleep 7-9 hours nightly.
  • Exercise 3-5 times a week.
  • Eat a probiotic-rich diet and eat fermented foods regularly.
  • Avoid heavy consumption of alcohol.
  • Avoid antibiotics use when not medically necessary.
  • Avoid smoking.
  • Floss their teeth daily.
  • Avoid antibacterial hand soap or alcohol-based mouthwash unless prescribed.
  • Avoid washing the vagina with soap.
  • Wash hands with soap and water, rather than hand sanitizer when possible.
  • Reduce stress levels as much as possible.

The future of microbiome research

Science on microbiome sequencing, supplementation, and general health is still ongoing. In the future, testing that relays the makeup of our individual microbiomes may become widely available as part of personalized disease treatment and prevention.

Until then, it’s best to use healthy microbiome practices by taking good care of your general health, eating a balanced diet, and speaking with your medical provider about proper preventative care.


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