Science of Food: Beneficial bacteria in your gut (column)

Lisa Julian
Science of Food
There is a complex environment of diverse bacteria that is present in our guts, unique to each individual.
Courtesy Getty Images | Science Photo Library RF

We have only just begun to learn about how the diverse community of bacteria living inside our bodies plays a role in our overall health. We know now that our digestive tract is home to trillions of bacteria and other microorganisms (i.e. our gut flora or gut microbiota) that are communicating and living synergistically with us. These microbes influence the metabolism of foods, absorption of nutrients, production of hormones and neurotransmitters, and have a huge impact on the proper functioning of our immune system. There is so much new information emerging, so to keep within my word limit I will focus this article on the connection of our guts with our immune systems.

A large proportion of your immune system is actually in your intestines, and the gut microbiota living there play a role in either maintaining a strong and healthy immune system or impeding it. Your immune system is made up of many different components, what I refer to as a “molecular army,” that includes specific tissues in the body, specific molecules like antibodies and cytokines, and different types of red and white blood cells like macrophages, that are triggered or released in an immune response. These different immune responses are activated to protect your body from invaders like viruses, bacteria, cancer cells and foreign particles, which are activated when the body receives a signal that an invader is present.

A specific tissue that lines the intestines called the gut-associated lymph tissue stores 70 percent to 80 percent of the body’s immune cells, clearly making the digestive tract an important part of the immune system as a whole. How do the bacteria actually affect the immune system? After we eat food, it travels down the digestive tract where the bacteria are present. They break down and metabolize the food into smaller pieces, eventually to the molecular level, that can serve as signals in the body, signaling to the immune system to turn on or off certain processes.

For example, researchers have discovered that some gut bacteria ferment dietary fiber into important compounds called short-chain fatty acids, or SCFAs, that serve as a signal to benefit the host by inhibiting inflammatory pathways in the immune response. Inflammation is one of the primary mechanisms that are activated in response to infection. While we want the body to use inflammation to win battles with pathogens, we also want it to turn off after the immune systems has done its job, which can often be problematic.

If your body does not contain types of bacteria, then some SCFAs won’t be produced and the signal to turn off inflammation may not be generated. Chronic inflammation can serve as a driver for many diseases, even cancer, so not surprisingly many gastrointestinal disorders result in auto-immune and inflammatory diseases like IBS (irritable bowel syndrome), Celiac disease and gluten sensitivity, ulcerative colitis and colon cancer.

How can we strengthen our immune systems? Nourish the bacteria in your gut. The number of bacteria living in the human gut outnumbers our own cells by a ratio of nearly 10:1, so it is of utmost importance to create a healthy environment in your gut that will nourish the good bacteria living there and reduce the unwanted bacteria that can cause problems. “Probiotic foods” that contain live bacteria like low-sugar yogurt, fermented foods and whole fruits and vegetables in general, can help to increase the good bacteria living in your gut. However, it is your whole diet that matters, especially the “prebiotic foods” that contain fiber and nutrients that feed the good bacteria (such as dark leafy greens, onions, garlic, whole grains, broccoli, nuts and bananas) and that keep things moving through the gastrointestinal tract to prevent the buildup of toxins.

We want to keep the good bacteria in our guts and reduce the bad. Refined sugars and certain fats found in processed foods do the opposite and will favor the growth of unwanted bacteria, so eliminate these and base your diet on whole foods rich in fruits, vegetables, whole grains and foods containing omega-3 fats to help build a healthy gut.

Antibiotics are also to be avoided unless absolutely necessary. Antibiotics will often wipe out both the good bacteria and the bad bacteria, interfering with proper immune function and making the body vulnerable as it can take time to re-establish one’s normal gut flora after an antibiotic load. Glyphosate or RoundUp, the most widely used herbicide in the world, is an antibiotic and its harmful effects on the gut microbiome are one reason why this chemical is so toxic to human health and may be an underlying cause of gut problems that we are seeing today. Other pesticides can do the same, so eat organic food when possible and avoid eating meats raised with antibiotics.

There is a complex environment of diverse bacteria that is present in our guts, unique to each individual, to help metabolize food in order to create certain chemical byproducts that serve as signals to the immune system. It is the right balance of on/off signals that is required for gut health and a proper functioning immune system. Because the food we eat affects this balance, we must consider our everyday diet as an important aspect in our understanding of human health.

Keeping a healthy gut flora starts with the foods we eat on a daily basis that will literally either feed the good bacteria or feed the bad. Taking a probiotic in the form of a pill is misleadingly ineffective; it’s the whole diet, again unique to the individual, that will create the right environment to foster a healthy gut flora. Although modern science does not quite yet understand all the pieces involved in this complex relationship, we do know that a healthy gut, including the trillions of bacteria living there, supports a healthy immune system.

Lisa Julian Ph.D. has a passion for organic chemistry the “molecules of life,” and its application to food and health. She’s the owner of Elevated Yoga & Holistic Health in Frisco and teaches Science and Nutrition at CU Denver and CMC. She can be reached at 970-401-2071 or For more information about services offered at her studio, visit

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