• Scott Sohn, MS, RDN, LD

The Gut Microbiome: A hidden life-force within us.

Updated: Apr 11, 2019

Did you know that we share our bodies with approximately 100 trillion other organisms? In fact, there are 10 times as many microbial cells as human cells living on or inside our bodies! These organisms are collectively referred to as our microbiome. The microbiome has three distinct functions; metabolic, protective, and trophic. Metabolic functions include the fermentation of dietary carbohydrates and fiber into amino acids and short chain fatty acids (SCFAs), the production of vitamins B and K and the metabolism of bile acids. The microbiome also exerts protective functions by creating a barrier within the gut that crowds out disease causing pathogens and provides a protective mucus lining. The trophic functions of the microbiome are becoming more evident and are shedding light on the emerging importance of the gut-brain axis. The microbiome is shown to affect our brain biochemistry, our response to stress, our mood, behavior and our food cravings. Most importantly, the early colonization of gut bacteria during infancy has been linked to brain development.

Some bacteria are classified as commensal, which means they are simply along for the ride. They exist within our guts and derive nutritional benefit without harming us.

Others are considered symbiotic and their activities are mutually beneficial to us.

A third type are pathogenic. Pathogenic bacteria are opportunistic microbes that can create disease within our bodies when left unchecked.

The types and balance of bacteria that reside in the gut have an important impact on our health. This collection of living organisms is like a genetic fingerprint, unique to each of us. Our microbiomes are associated with a number of factors including our food choices, our immunity, obesity prevalence, and even our behavior. Recent research has linked the gut microbiome to nearly every process within the human body.

Immunity: The collection of bacteria (microbiota) in our microbiome perform a variety of functions that are vital to our health and even survival. Approximately 70% of our immune cells are located within our gut. Our microbiome establishes the parameters by which our bodies judge whether something is friend or foe, maintaining balance and keeping harmful pathogens from taking hold.

Nutrient Digestion & Absorption: Our gut microbiome plays a key role in the breakdown and absorption of nutrients from the foods we eat. The metabolic activities of our gut bacteria through fermentation also produce important substances that we need, such as short chained fatty acids (SCFAs), along with vitamins B and K. SCFAs produced in the gut provide an energy substrate for colon cells and may reduce inflammation associated with inflammatory bowel disease. B vitamins such as folate, thiamine, biotin, riboflavin and pantothenic acid are essential for human metabolism while vitamin K plays a key role in blood clotting mechanisms and bone mineralization processes.

Disease Prevention: A balanced gut microbiome helps promote health and prevent disease by neutralizing some of the toxic by-products of digestion, reducing harmful substances (such as toxins and carcinogens), and discouraging 'bad' bacteria and yeasts from taking over. Imbalances in the microbiome have been linked to immune dysfunction, GI disorders, psychological problems, yeast overgrowth, and a wide variety of pervasive health issues. A healthy microbiome proliferates and prevents disease causing pathogens from establishing a foot hold. Healthy bacteria crowd out bad bacteria and form a protective barrier which promotes homeostasis within the body. Balancing the microbiome has been shown to alleviate certain allergy symptoms, while mitigating the symptoms of lactose intolerance and inflammatory bowel disease.

HIV Management: Those with HIV disease are particularly susceptible to gut problems due to side effects from medications. Many people with HIV complain about symptoms such as diarrhea, nausea, bloating and fatigue. Balancing the microbiome through diet is shown to be effective at alleviating many of the symptoms associated with HIV and antiretroviral treatment.

You are what you eat! The good news is that we can cultivate a healthier gut microbiome by changing what we eat. When it comes to food choices and gut health, the key players are prebiotics and probiotics. Probiotics refer to the good bacteria found in certain foods, while prebiotics are indigestible fibers, naturally found in fruits, vegetables and other plants, which serve as fuel for probiotics and help them grow.

Fermentation is the process of converting carbohydrates (sugars) to alcohol or organic acids using microorganisms—yeasts or bacteria — under anaerobic (without oxygen) conditions, producing the good bacteria our gut needs to stay healthy. To add more good bacteria to your diet, try fermented dairy products such as yogurt, kefir and aged cheeses as well as non-dairy fermented foods such as kimchi, sauerkraut, pickles, miso, tempeh, natto, and kombucha tea. Cultured non-dairy yogurts made from soy, almond and coconut milks are good substitutes for dairy sensitive individuals. Don’t forget to include prebiotic-rich foods such as asparagus, berries, legumes, bananas, garlic and onions to promote probiotic growth! Adding prebiotics and probiotics to your diet can result in significant health benefits.

The gut microbiome and its impact on human health is a hot topic today. New research continues to emerge revealing the complex relationship that exists between our gut bacteria and multiple processes within our bodies. We are continuing to learn more about the various roles that microbes play within our bodies, and their impact on health and disease. What we do know is that maintaining a healthy, balanced microbiome has multiple health benefits, which can be realized in a relatively short period of time. Get started today by following these simple steps.

Follow these five simple steps to begin re-balancing your gut flora

  • Eat more plants! Beans, nuts, seeds, whole grains, fruits, and vegetables are naturally rich in fiber, providing fuel for “good bacteria.”

  • Limit sugar, processed foods, and saturated fats, which are found mainly in animal products, and provide fuel for “bad” bacteria.

  • Try Fermented Foods – these are great source of helpful bacteria.

  • Lower Stress. Exercise, meditation, massage and yoga are some good options.

  • Prioritize Sleep! Aim for 7 to 8 hours of sleep each night; decrease caffeine and alcohol intake, especially in the evening; limit screen time; and establish a relaxing bedtime routine.

Try this recipe for a tasty dose of both prebiotics AND probiotics.

Recipe: Spiced Waldorf Salad

From the Greater Atlanta Dietetic Association (GADA) Cookbook


· 3 large apples, chopped

· 2 stalks celery, chopped

· ¼ cup dried cranberries

· ¼ cup pecans, finely chopped

· ½ tsp. cinnamon, ground

· 1/8 tsp. ginger, ground

· Light sprinkle of ground cloves

· 6 oz. low fat vanilla yogurt

Directions: In a medium bowl, add chopped apples, celery, cranberries, pecans and spices. Spoon yogurt into apple mixture and stir gently to mix all ingredients. Serve over lettuce, if desired.

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