The Probiotic Prescription: Understanding Your Gut Bacteria

Yogurt is one of a number of probiotic-rich foods that help us maintain a healthy microbiome. Pixabay

It is just you and about 100 trillion bacteria?  Prebiotic, probiotic, symbiotic-- what does it all mean—to you and your health? The study of gut bacteria and probiotics are breaking ground. Ravaged by antibiotics, declining in diversity, as unique as your fingerprints, and dynamically changing throughout the cycle of your day, the body’s microbiome – the balance of bacteria -- is an important and cutting-edge health topic.

Known in the past as gut bacteria and gut flora, the microbiota, or microbiome, is a collection of about 1,000 different kinds of bacteria that have immense importance to human health.  They live mainly in the lower gastrointestinal tract.  There are also bacteria on your skin, in your lungs and other parts of the body.  These bacteria are with us even from the beginning: the placenta has a microbiome of its own and it’s thought to have an impact on infant health.

Research continues to point to the importance of microbiota to our health. Microbiota are now considered by some experts to even be an actual organ in the body.

Just some of the functions of a healthy microbiome include:

  • Microbiota help mediate and support balanced and healthy immune system function, and help the intestinal lining defend against pathogens
  • Microbiota assist in digestion, reduce inflammation, and reduce inflammatory response
  • Vitamins, like vitamin B and K, are synthesized in the microbiome
  • Microbiota inhibit and deter growth and overpopulation of harmful bacteria
  • Transplant of microbiota-rich fecal material --known as Fecal Bacteriotherapy or Fecal Microbiota Transplantation -- into patients suffering recurring infections of Clostridium difficile has proven a quick, inexpensive, and highly effective treatment for eliminating this infection and restoring a healthy microbiome

    With such far-reaching health benefits, taking good care of our microbiome should be a top priority. Unfortunately, there are many ways we are interfering with a healthy microbiome, with antibiotic overuse, and diet at the top of the list.


    Antibiotics are antimicrobials.  They work to weaken and kill bacteria in the human body. While they can be life-saving, it’s important to understand that antibiotics do not discriminate between “good” and “bad” bacteria.

    Overuse and overprescription of antibiotics have led to the development of extraordinarily dangerous, antibiotic-resistant bacteria. The Centers for Disease Control and Prevention (CDC) continues to warn about the impact of antibiotic overuse around the world:

    • Antibiotics are no longer as successful against bacteria.
    • Harmful bacteria quickly pass protective genes to other types of bacteria, causing development of “superbugs.”
    • Fatal cases of gonorrhea and diarrhea are caused by drug-resistant superbugs.  Drug-resistant tuberculosis is on the rise.
    • Costs of treating human infection continue to increase as formerly effective types of antibiotics no longer halt dangerous bacteria.
    • Antibiotics are taken every day by patients who may not need them.  A course of antibiotics reduces microbiome diversity and hampers the function of microbiota.
    • Antibiotic residue from drugs fed to food animals may assist the development of dangerous superbugs, and has infiltrated the water supply.

    In a particularly important study, researchers correlated antibiotic use in children, changes in microbiota, and adult disease onset as a result of dysbiosisDysbiosis is an imbalance in the microbiome that some suspect as a basis of development for conditions including irritable bowel syndrome (IBS), autoimmune diseases, colitis, cancer, chronic fatigue syndrome, obesity, and other illnesses.


    You are what you eat.  Really.  What you consume is sorted, digested, and incorporated by your gut.  A varied and nutritious diet is needed for health and physical maintenance. 

    Prebiotics and probiotics are compounds found naturally, and in supplements, that may improve digestive, and all around health. A synbiotic is a food or supplement that contains both a prebiotic and probiotic. 

    Many Americans eat foods and take supplements that contain active bacterial cultures as a way to help digestion, or to rebalance the intestinal system after use of antibiotic drugs. While specific results are not guaranteed, probiotic supplements are generally considered safe and are widely available in the marketplace.

    In addition to evidence pointing to the healthy effect of probiotics on the body, including mental health, one study examined the gut-mind connection and found probiotics might even reduce social anxiety in higher risk individuals.

    You can promote gut health by eating whole, healthy foods, following a balanced diet, and staying lean. A 2013 study found greater microbial diversity in the gut flora of people who are lean.

    Reducing overall stress is also an immune system and gut health booster. 

    Try to avoid things that kill beneficial bacteria, like antibiotics.  Antibiotic medications are literal life-savers for those who need them—but if you have a common cold, the flu, or even some sinus infections, for example -- an antibiotic is a waste of money...and your microbiome.


    Be proactive by choosing foods that feed you—and your 100 trillion friends.  Consider the following:

    • Prebiotic:  Once they reach your gut, probiotics need a snack. Prebiotics are fermentable fibers that feed probiotic bacteria.  Upon arrival, prebiotics pair up with probiotics to help the microbiota support its host—you.  Foods rich in prebiotics include artichokes, plums, apples, tomatoes, leeks, onion, garlic, bananas, honey, whole grains like oats, wheat, rye, and bran. Also, look for foods with fibrous stems, like broccoli stalks. (Remember to steam or lightly cook, to minimize the goitrogenic potential.)

      When scanning labels, look for inulin. Found in more than 30,000 plants, inulin is a natural plant fiber and prebiotic that is often used as a food additive to increase fiber and function.
    • Probiotic:  Probiotics are living microorganisms that can offer a health benefit when supplied in appropriate amounts. Many products now claim to deliver live cultures—even frozen yogurt.  Most probiotic containing foods are fermented products, and include yogurt, a fermented milk drink called kefir, a fermented soybean product called tempeh, and some soft cheeses. Saving the best for last, yes, it is true, dark chocolate has probiotic properties.
    • Fermented foods:  Yogurt is produced via a fermentation process.  Other fermented foods are produced by combining vegetables and species of Lactobacillus, which increases vitamin levels and improves digestibility.  Used historically before pasteurization and invention of refrigeration, fermentation can preserve vegetables like peppers, cabbage, garlic, onions, olives, cucumbers, carrots, and turnips.  Also, consider other fermented products like kombucha, kimchi, sauerkraut, and miso.
    • Synbiotic:  Foods and products that pair a pre- and probiotic are called synbiotic.  Tasty synbiotic pairs include yogurt and a banana, yogurt and grains, kombucha with chia seeds, feta cheese with onions, or beans and pickles.  Use your imagination—and your taste buds—to come up with combinations that work for you.


    While prebiotic and probiotics are plentiful in a variety of foods, it may not be easy to get enough of these foods in your daily diet. In that case, you may want a probiotic supplement. (You can learn more about probiotics in Dr. Cathy Wong's article, Acidophilus and Probiotics.

    Keep in mind that you want to get good quality supplements, which isn’t always easy. Also, be careful about unwanted fillers and other ingredients. (For example, recently, a group of scientists found gluten in probiotic supplements labeled “gluten-free.”)

    Some quick tips to help you keep your microbiome healthy include:

    • Talk to your healthcare provider before you take probiotic supplements, especially if you have an underlying illness or condition.
    • Your microbiome is unique, and there is no best type of microbiome, except the one that is diverse and healthy.
    • Look for the Live & Active Cultures seal from the National Yogurt Association (NYA).
    • Frozen yogurt may—or may not—have live cultures depending on processing.

    For thyroid patients, studies pose links between gut health and autoimmunity, and specifically, thyroid disease. Research continues to explore the links between microbiome imbalances, leaky gut syndrome/intestinal permeability, and thyroid disease.

    Bacteria are our friends—except when they are not.  Healthy respect for the active, important role played by microbiota is important. Pre- and probiotics, in food and supplements, help us maintain a healthy relationship with our environment—inside and out. 

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