Close this search box.

Improve the Gut Microbiome Naturally with Naturopathic Medicine

In this article:

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, the microbiome is made up of trillions of bacteria, viruses, and fungi along with genetic materials that all work together in a multi-layered way to promote health and well-being. Just like a conductor’s careful direction, there are ways to add just the right elements to improve the gut microbiome naturally with food and dietary supplements. 

Improve the Gut Microbiome Naturally
The microbiome is at work tin the gut and hroughout our human body, communicating and helping conduct essential roles.

A healthy functioning microbiome supports digestion, sustains a responsive immune system, maintains hormonal balance, impacts fertility for both men and women, and supports 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 in the prevention of both acute and chronic illness and in fostering sound physical, cognitive, and emotional health.

Many parts of the body have their own specific microbiome. We think of only the digestive system, which is most essential, but the the eyes, lungs, and vaginal, urinary and respiratory tracts all have their own microbiome. In other words, the microbiome is at work throughout our human body, 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 has a negative impact on fat metabolism and weight gain. The gut microbiome has an effect on 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 for fighting infection alert and responsive. 

What is dysbiosis in the gut microbiome? 

The state of dysbiosis  includes a myriad of human complaints including gastric upset. inflammatory bowel disease, metabolic syndrome, obesity, and even depression. What causes an unhealthy microbiome? There is a growing body of evidence highlighting the impact of processed food, over-prescription of antibiotics and pharmaceuticals, and industrial farming. This collective input has a grave influence on the extent and diversity of the human microbiome. By way of example, research has shown early-in-life use of antibiotics, which can disturb the microbiome, is associated with the development of asthma in children, and in general, antibiotic use is one causative factor for autoimmune ailments

More broadly, the Standard American Diet (SAD) interferes with a balanced microbiome. You can probably guess by the name, but SAD is defined as  highly processed foods, refined carbohydrates and added sugars, hydrogenated and saturated fats and red meat (more from our partners at Standard Process on SAD). another ess than healthy habit that affects the microbiome is excessive drinking. Though many people know these choices do not make up a healthy 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. 

Increasingly, the role of stress, its response, and its impact on the microbiome are being examined, and not surprisingly, intense or ongoing stress has a negative impact on 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 have the capacity to improve our microbiome, which in turn can help prevent and treat chronic ailments, improve overall immune function—helping to side-step more acute ailments—and promote healing of all kinds. 

How can you improve your gut microbiome naturally? 

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

  1. Right from the start, the microbiome influences and is influenced in pre-conception for each parent,  during pregnancy, delivery, and postpartum care. If you are considering having a child or become pregnant, choices about lifestyle, food and pertinent supplementation are very important 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 in turn 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, with nature, and with dirt help 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 our 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, in your home, and in your personal care products is a good idea.
  6. Taking a probiotic may well be worthwhile. Probiotics are “live microorganisms which when administered in adequate amounts confer a health benefit on the host.” They are found in certain foods (see below)and in dietary supplements. But before you choose just any probiotic off the shelf, ask a doctor who is trained in gut health about a strain that is best for you. Though they are generally recognized as safe, there is some evidence of potential harm from probiotics for certain individuals with health issues. If you are undergoing chemotherapy or are immune compromised contact a naturopathic doctor first.
  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.

Why you should see a doctor about gut health

Gut health and dysbiosis is one oof the top reasons patients see a doctor. A licensed naturopathic doctor is trained in natural treatments for a healthy gut. They will explain how specific strains of probiotics lead to specific actions. An ND can help you identify which, if any, probiotic strains will be best for you. They can also explain the guidelines for the industry with regard to labeling and how many active strains are in probiotics, an important step toward ensuring safety and efficacy. Probiotics have been shown to have an impact on 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 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. 

What foods are high in prebiotics? 

Improve the Gut Microbiome Naturally
Artichokes contain both 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. This is why eating a diet high in fiber, including vegetables, fruit, whole grains, nuts and seeds, and legumes is important. Common foods with the highest amounts of prebiotics are artichokes (they contain probiotics too) 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 that taking probiotics and prebiotics together may well influence hormone production and how neurotransmitters function, which impacts 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.

For more on improving your gut microbiome, take a look at these articles:

Listen to Your Gut: Naturopathic Solutions for a Healthy Microbiome

What is the Gut-brain Axis and How are the Gut and Immune System Connected?, from our partners at Omni Biotic

How do Naturopathic Doctors Treat Digestive Complaints?

Patient Testimonials on seeing a Naturopathic Doctor for Gut Health:

Laura Hill Temmerman, Know and Trust Your Gut

Joel Sprechman, One Great Gut

Experience the benefits of personalized natural healthcare with a trusted, licensed naturopathic doctor in your area.
Find a Naturopathic Doctor
Experience the benefits of personalized natural healthcare with a trusted, licensed naturopathic doctor in your area.
Find an ND

This article is provided by

The Institute for Natural Medicine, a non-profit 501(c)(3) organization. INM’s mission is to transform health care in the United States by increasing public awareness of natural medicine and access to naturopathic doctors. Naturopathic medicine, with its person-centered principles and practices, has the potential to reverse the tide of chronic illness overwhelming healthcare systems and to empower people to achieve and maintain optimal lifelong health. INM strives to fulfil this mission through the following initiatives:

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

About The Author(s)

Guest Author

Amy Rothenberg ND, DHANP

Dr. Rothenberg 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, Better Nutrition’s Naturopathic Health Hub, Medium, Thrive Global, and The Huff Post. She is the proud mother of 3 adult children.

Explore Gastrointestinal Health Articles


INM – NMC profession-wide survey assesses common priorities to drive fundraising.

Results: 1) States licensing 2) Public Awareness 3) Residency Access. INM’s priority areas (access, education, research) and initiatives are defined to match survey results.

Get Involved!