How to Improve Your 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, Better Nutrition’s Naturopathic Health Hub, Medium, Thrive Global, andThe Huff Post. She is the proud mother of 3 adult children.

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.

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Deb Hubers

Debra Hubers is a serial entrepreneur and has started seven businesses; ranging from an advanced genomics to an employer health care purchasing cooperative. Deb has over 35 years of experience in healthcare finance, education, technology, and pharmacogenomics.

Ms. Hubers has dedicated her career to measuring and improving healthcare outcomes. Her expertise is leveraging technology to deliver personalized, preventative medicine. Ms. Hubers co-founded La Vita Compounding Pharmacy in 2007. Collaborating with her business partner, physicians and strategic partners, Deb has grown La Vita to be one of the most respected and sought-after personalized medicine providers on the west coast. She is also Co-Founder of EpigeneticsRx, a leading provider of precise, personalized, prevention which positively impacts genetic expression.

Alex Keller, ND

Dr. Alex Keller, ND, AFMCP is a graduate of the University of Ottawa with an Honours Bachelor in Health Sciences and Psychology. Although originally intending to attend conventional medical school, following a three-month volunteer internship at a rural Kenyan hospital where he observed how doctors used local food to treat patients, he shifted his career goals and pursued a degree in naturopathic medicine at the Canadian College of Naturopathic Medicine in Toronto.

After one year of practicing with the esteemed Dr. Chris Pickrell, ND, RH in a community acupuncture setting, in 2015 he and his wife Dr. Jenn Keller, ND moved to rural Ottawa, Canada where they started an organic farm and retreat center. In the same year, Alex and his athletic therapist sister Jess Keller combined their practices to form Keller Active Health, an integrative physical therapy clinic.

Ever curious and passionate about the education of evidence-based natural medicine, in 2017, Dr. Keller joined a fledgling Ottawa-based health tech startup named Fullscript. He serves as its Medical Director and oversees the development of medical education content for practitioners across North America.

Prior to medicine, Alex worked in the renewable energy sector, where he developed a deep passion for sustainable agriculture and environmental stewardship. This connection between medicine and agriculture now drives Alex to focus much of his energy on bringing awareness to the quality and sourcing standards in the supplement and organic agriculture supply chains.

Today, he splits his professional time practicing as a clinician, working for Fullscript, and expanding the farming operation while chasing his kids with Jenn and occasionally running ultra-marathon trail races. He is also currently completing an Executive MBA through the Quantic School of Business & Technology with a focus on supply chain innovation.

Pamela Snider, ND

Pamela Snider, ND, is Executive and Senior Editor for the Foundations of Naturopathic Medicine Project, producing a first of its kind international textbook of Naturopathic medicine through a series of international retreats and symposia. A nationally recognized integrative health and policy leader, she is active in both national and regional integrative health initiatives. Dr. Snider serves on the Board of Directors, was founding Executive Director and co-founder of the Academic Consortium for Integrative Health (ACIH/ACCAHCa consortium of the councils of schools, accrediting agencies and certifying bodies of the licensed, traditional and emerging integrative health professions, and is currently Vice Chair and co-founder of the Integrative Health Policy Consortium (IHPC).  Dr. Snider served as a founding Board Member of the Academy of Integrative Health & Medicine from 2014-2016. Her public policy work includes completing a two year appointment to the DHHS Center For Medicaid and Medicare Services (CMS) Medicare Coverage Advisory Committee (MCAC); serving as a Steering Committee Member for  the HRSA funded American College of Preventive Medicine NCCIM Integrative Medicine in Preventive Medicine Residency program, co-directing in USPHS Region X the Building Bridges Between Provider Communities Group, an exploration of interdisciplinary collaboration and common ground between public health and CAM; serving for 22 years on Washington State’s Health Professional Loan Repayment and Scholarship Program Advisory Committee (HPLRSP); providing technical assistance to and developing key language for the enabling legislation for NIH Center for Complementary and Alternative Medicine (NCCIH/NCCAM); and staffing Joseph Pizzorno ND during his appointment as Commissioner on the White House Commission on CAM Policy.

From 1994-2003, Dr. Snider served as Associate Dean for Public and Professional Affairs and Naturopathic Medicine at Bastyr University, dividing her work between academic and public affairs activities, including chairing the Naturopathic Medicine Program Curriculum Review Committee.  Dr. Snider has been teaching, publishing and lecturing widely on Naturopathic philosophy, theory integrative health, public policy, and other topics for over 30 years. Currently, an Associate Professor at National University of Natural Medicine (NUNM) in Portland, OR, Dr. Snider also continues at Bastyr University in her 22nd year as a faculty member teaching naturopathic medicine history, clinical theory, and global context. Among her Naturopathic medicine professional roles she serves on the Institute for Natural Medicine’s Leadership Council.  In 1989, she co-led the naturopathic profession with Dr. Jared Zeff, in developing a unifying definition of naturopathic medicine and its principles of practice adopted unanimously by the American Association of Naturopathic Physicians (AANP) House of Delegates. She was a co-investigator in the 2004 NIH NCCAM research study, the North American Naturopathic Medical Research Agenda and CAM Advisor in NIHCCAM’s Financing Integrative Health Care (University of Washington).  Her areas of experience include healthcare education; naturopathic and interdisciplinary clinical theory, curriculum development; clinical practice; government and legislative affairs, public policy, interdisciplinary collaboration, and community organizing.  Dr. Snider has received the Ontario Naturopathic Physician of the Year Award, the Physician of the Year Award from the AANP, the President’s Outstanding Vision Award and Distinguished Alumnus Award at Bastyr University, AANP’s President’s Award, an honorary Doctorate of Naturopathic Philosophy from the Canadian College of Naturopathic Medicine (CCNM), the William A Mitchell Vis Award from the AANP and The Gathering – NMSA’s Beacon Award. She received her ND degree in 1982 from Bastyr University of Natural Health Sciences and is a licensed naturopathic physician in the State of Washington. She lives with her husband and children at their homestead in North Bend Washington, in the beautiful mountain to sea landscape and home of The Revival – Restore the Vis, an annual student-led community gathering.

Susan Haeger

Susan Haeger is Founder/Principal of Transformative Health Solutions Inc. She has applied her twenty plus years in executive leadership to help shape and drive adoption of progressive health policy for whole person healthcare. She was a section contributor to the 2021 INM/AANP published professional white paper, Naturopathic Physicians as Whole Health Specialists: The Future is Whole Person Health Care that provides supporting evidence for the profession’s significant and unique contributions to preventive, whole person care and models of integrative clinical practice.

Bruce Barlean

Bruce Barlean is an owner and founder of Barlean’s, a global dietary supplement manufacturer located in the Pacific Northwest in Ferndale, WA. Bruce has been actively involved in the Natural Products industry since 1989 and is passionate about making a difference in the world and positively impacting the lives of others.

Bruce believes that people can make a difference in the world through ordinary purchases. He is committed to improving the quality of life for every person on the planet by making the best products and by using the profits to support outreach programs. Bruce summarizes it simply, “We make good stuff to do good stuff”.

In the late 1980’s Bruce became passionate about how health could be dramatically improved with Flax Oil Supplementation. Bruce along with his entrepreneurial parents saw the potential to improve the lives of many people and in 1989 they began selling Flax Oil under the Barlean’s name. From 1989 – 2000 the business grew an average of 40% year over year. While most companies saw a decline in business in the 2001 recession, Barlean’s continued to grow and soon became America’s #1 selling flaxseed oil and continues to be to the present. The brand has since expanded to include additional oils, green food concentrates and other premium supplements. Bruce continues to drive innovation and over the years his products and company have won countless awards including: Eight consecutive Vity Awards for #1 EFA, Six consecutive Vity Awards for #1 Greens Food Supplement, Natural Choice Award for Best Specialty Supplement, Best Product of the Year, Best New Product, Gold Medal Taster’s Choice Award, Gold Medal American Masters of Taste Award, #1 Health Food Store Brand for Consumer Satisfaction by Consumer Lab, and Manufacturer of the Year.

In 2013 as the company was on the eve of celebrating the 25th year in business Bruce and his parents decided to take their desire to help people to a new level that they call Pathway to a Better Life – which is now seen in the Barlean’s logo. Bruce and his parents had always been generous in their giving and support of charities, but as part of the Pathway to a Better Life they decided to increased partnership with charitable organizations such as: Vitamin Angels, Compassion International, KidsTown International, Autism Hope Alliance, Engedi Refuge, Project 92, and others. And because so many people are unable to meet basic nutritional needs, Bruce created a comprehensive Omega-3 and multivitamin formula that he distributes free-of-charge to local food banks. In addition, Bruce decided the company would supply food banks with organic coconut oil to provide people with a health alternative to standard cooking oils.

Always generous with his time Bruce has served as a youth leader for his local church for several years and continues to mentor youth. He has been on several not for profit boards including; Whatcom County Pregnancy Center (2003-2006), Natural Products Association (dates?), and the Institute for Natural Medicine Leadership Council (presently).

The Barlean family have been avid supporters of Bastyr University since the 1990’s and in 2013 were given Bastyr’s most prestigious honor, the Mission Award, which recognizes their leadership over time in improving the health and well-being of the human community.

Bruce currently resides in Ferndale, WA with his wife Lisa and their two dogs: Heinz & Shadow. When he’s not helping others he can be found fishing (catch & release).

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Michelle Simon

Michelle Simon, PHD, ND

President & CEO

As president and CEO of INM, Dr. Simon brings her passion for working with organizations dedicated to improving the quality and delivery of healthcare. This desire stems from her years of practice as a licensed naturopathic physician. In addition to holding a Naturopathic Doctorate from Bastyr University she also holds a PhD in Biomedical Engineering from the University of North Carolina at Chapel Hill.

She has served on boards for the American Association of Naturopathic Physicians (AANP), the Naturopathic Physicians Research Institute (NPRI), and several advisory boards. Dr. Simon served nine years on the Washington State Health Technology Clinical Committee, as Ambassador to the Academy of Integrative Health and Medicine (AIHM) and was recognized as 2018 AANP Physician of the Year. Dr. Simon shares with her husband a passion for adventure travel, preferably by boat or motorcycle. She also enjoys teaching a women’s off-road motorcycling class.