improve the gut microbiome naturally

When I have the chance to listen to a full orchestra, I appreciate the fact there are so many musicians playing different instruments—each bringing out particular notes at the right tempo with precise rhythm and intensity, each doing their part to create a full, rich, and multi-layered sound. I think about the human microbiome similarly. On an even grander scale, trillions of bacteria, viruses, fungi, and genetic materials all work together in a multi-layered way to promote health and well-being in your microbiome Just like a conductor’s careful direction, there are ways to improve your gut microbiome naturally with food and dietary supplements. 

A healthy functioning microbiome supports effective digestion, sustains a responsive immune system, informs the maintenance of hormonal balance, impacts fertility for both men and women, and promotes clear thinking and an even-tempered mood. The more it is studied, the more we understand that a well-orchestrated microbiome plays a substantial role preventing both acute and chronic illness and fostering sound physical, cognitive, and emotional health.

Many parts of the body have been studied to reveal their specific microbiome, such as those  found in the digestive system, which is essential to optimal health, but the eyes, lungs, and vaginal, urinary and respiratory tracts also have their own microbiome. In other words, the microbiome is at work throughout our human physiology, communicating and helping conduct essential roles. While we are each made up of trillions of cells, we are also made up of trillions of organisms that define the microbiome. For example, a thriving microbiome is essential for digestion, absorption, and elimination. We also know the microbiome that is not working in concert with circadian rhythms harms  fat metabolism and weight gain. The gut microbiome affects  how you metabolize nutrients and how you use your calories. There has been much discussion about the role of the microbiome in optimizing immunity and keeping our ability to fight  infection alert and responsive. 

Restoring balance in the gut microbiome naturally

The state of dysbiosis, when the various bacteria in the microbiome are no longer living in harmony, includes a myriad of human complaints, including gastric upset,inflammatory bowel disease (IBD), metabolic syndrome, obesity, and even depression. What causes an unhealthy microbiome? A growing body of evidence highlights the impact processed food, over-production of antibiotics and medication and industrial farming has on a healthy microbiome. This collective input damages the diversity of the human microbiome. As an example, research shows that early-in-life use of antibiotics disturbs the microbiome and is associated with the development of asthma in children. In general, antibiotic use is one suspected cause for autoimmune ailments

The Standard American Diet (SAD), defined as  highly processed foods, refined carbohydrates and added sugars, hydrogenated and saturated fats and red meat, interferes with a balanced microbiome (more from our partners at Standard Process on SAD). Another less than healthy habit that affects the microbiome is excessive drinking.


Adding dark greens and artichokes gives your microbiome what it needs to thrive.

Though many people know these choices do not make up a nutritious  diet, change can be difficult due to developed tastes, cultural factors, finances, and access to healthy foods. Naturopathic doctors have extensive training in therapeutic nutrition and can help you get on the right track regarding diet and improving your microbiome. Talk to your doctor about making small changes, such as adding more green vegetables to your diet and backing off on starchy carbohydrates and sugary drinks.

Increasingly, the role of stress, its response, and its impact on the microbiome is being examined, and not surprisingly, intense or ongoing stress harms the health and balance of the microbiome. Being mindful of your microbiome and working to create a robust and diverse internal environment is an area well worth your time and effort. We each can improve our microbiome, which can help prevent and treat chronic ailments, improve overall immune function—helping to side-step more acute ailments—and promote healing of all kinds. 

Daily choices to improve your microbiome

There are many choices you can make to improve your microbiome: 

A healthy diet during preconception and pregnancy helps mom and baby’s health.
  1. Right from the start, the state of both parents’ microbiome (including the father) can influence conception for pregnancy, delivery, and postpartum care. If you are becoming pregnant, choices about lifestyle, food, and proper  supplementation are crucial to establish and maintain both short and long-term maternal and baby health. 
  2. Maternal diet, method of delivery, nursing or feeding, medications prescribed, and bathing approaches all influence the microbiome, which can optimize physical and emotional health in mother and baby, encouraging healthy development of the child.
  3. Beyond that time, for both children and adults, choosing an anti-inflammatory diet is central to one’s microbiome. When available and affordable, choosing organic food helps. Avoid foods you are allergic or sensitive to. If you drink alcohol, do so only in moderation.
  4. Being in contact with the outdoors, nature and dirt helps diversify your microbiome. Even just spending time in green spaces and outside can positively impact the microbiome. Get dirty because an overemphasis on cleanliness may, in fact, not work in your favor. Encourage your child to play outdoors when and where feasible and safe.
  5. Toxic exposure in the environment causes many issues, including adding to the degradation of the microbiome, so working to decrease toxic exposures as much as possible in your food, your home, and your personal care products is a good idea.
  6. Taking a probiotic may well be worthwhile. One of the most common products in the food and supplements area is probiotics defined as “live microorganisms which when administered in adequate amounts confer a health benefit on the host.” Before you choose a probiotic off the shelf, ask a doctor trained in gut health which strain is best for you. If you are undergoing chemotherapy or are immune-compromised, work with a naturopathic doctor to find the right strain. Though they are generally recognized as safe, there is some evidence of potential harm from probiotics of potential harm from probiotics for individuals with health issues, such as systemic infections. 
  7. Choose foods that promote a healthy gut. Many foods contain probiotic organisms like fermented dairy found in yogurt and kefir, soy products like miso and tempeh, honey, fermented drinks like kombucha, and fermented vegetables like sauerkraut and Korean kimchi. Don’t worry about eating enormous quantities of these items; instead, include a few each day as part of your regular diet.

Probiotic strains matter

Not all probiotic strains do the same thing. It is why a naturopathic doctor can explain to you how specific strains of probiotics lead to particular actions and outcomes. A licensed naturopathic doctor can help you identify which probiotic strains will be best for you. There are guidelines for the industry with regard to labeling and content for probiotics, an essential step toward ensuring safety and efficacy. Probiotics have been shown to impact many common symptoms and illnesses— from bowel diseases and high cholesterol to addressing skin and dental issues.  There is also a growing appreciation of the gut-brain connection and how probiotics, as part of a whole person medical approach, have a positive impact on anxiety and depression. But you must have the right strain for the best benefits. 

The concept of fecal microbiota transfer (FMT) is relatively new and is showing promise. It is when the microbiota, in the form of a specially prepared stool of a healthy person, is placed in another person for therapeutic effect. Beyond the “ick” factor, this approach is FDA approved for the treatment of Clostridium difficile (C. diff.), which is an often difficult-to-treat diarrheal disease most often contracted in the hospital, a nursing home setting, or after a course of antibiotics. There is a growing body of research suggesting FMT may be useful in the treatment of numerous other physical as well as psychological ailments. Time and further research will tell, but the fact FMT is being researched underscores how very much the role of the microbiome and its impact on health and disease is valued. 

You need probiotics and prebiotics

The microbiome needs food to thrive. Elements called prebiotics provide much-needed nourishment for the microbiome and are just as important as probiotics. Prebiotics are fibrous filaments that feed your microbiome. Eating  a diet high in fiber, including vegetables, fruit, whole grains, nuts and seeds, and legumes, is very important. Common foods with the highest prebiotics are artichokes and Jerusalem artichokes, garlic, leeks, onions, dandelion greens, green bananas, and barley. 

Prebiotics are particularly important because they can only be gotten by diet. When prebiotics break down in your gut, it leads to short-chain fatty acids that are important energy sources for one’s intestines, immune system, and cellular health. Some studies even suggest that prebiotics can reduce one’s risk of cancer by improving the immune system. 

Studies show taking probiotics and prebiotics together may well influence hormone production and how neurotransmitters function, impacting  hunger, appetite, satiety, and weight gain and loss. Building a beneficial microbiome is one among many natural medicine approaches to consider if you are trying to reach a healthy-for-you weight. 

As we learn how the microbiome is developed, maintained, and influenced over the course of a lifetime, there is much to learn; however, we know it is working in a broad and orchestrated way. Knowing it exists, avoiding things that impair its function, and tending to its health by improving its diversity and robustness, are all well worth the time and effort. It may well have a far-reaching impact on your health and vitality.


This article is provided by the Institute for Natural Medicine, a non-profit 501(c)(3) organization, partnered with the American Association of Naturopathic Physicians. INM’s mission is to transform healthcare in America by increasing both public awareness of naturopathic medicine and access to naturopathic doctors for patients. INM believes that naturopathic medicine, with its unique principles and practices, has the potential to reverse the tide of chronic illness that overwhelms existing health care systems and to empower people to achieve and maintain their optimal lifelong health. INM strives to achieve this mission through the following  initiatives:

  • Education – Reveal the unique benefits and outcomes of naturopathic medicine
  • Access – Connect patients to licensed naturopathic doctors
  • Research – Expand quality research of this complex and comprehensive system of medicine

Amy Rothenberg ND, DHANP is a contributor to INM and practicing licensed naturopathic doctor in Northampton, Massachusetts. Dr. Rothenberg is the American Association of Naturopathic Physicians 2017 Physician of the Year. Dr. Rothenberg’s writing can be found on NaturalMed.org, Better Nutrition’s Naturopathic Health Hub, Medium, Thrive Global, andThe Huff Post. She is the proud mother of 3 adult children.