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How to Rebalance the Gut Microbiome: A Functional Medicine Protocol

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How to Rebalance the Gut Microbiome: A Functional Medicine Protocol

We live in a world inhabited by microbes. The gut microbiome is a complex and diverse ecosystem of approximately 100 trillion different microorganisms that inhabit the human gastrointestinal tract. A well-balanced gut microbial population works in concert to maintain homeostasis and protect against pathogenic organisms. The gut microbiota plays a crucial role in our digestion, mood, immune health, energy, hormone balance, and chronic illnesses.

Root cause medicine has unearthed the interconnectedness between the gut microbiome and various physiological functions and systems within our body. An imbalance or disruption in our gut microbial community is referred to as microbial dysbiosis.

Rebalancing the gut microbiome with functional medicine is key to optimizing overall health. This approach focuses on microbial diversity and symbiosis between the human and their gut microbiome.


What is the Gut Microbiome?

The gut microbiome comprises a variety of bacteria, viruses, fungi, and parasites that predominantly reside in the large intestine (colon). Bacteria are the dominant microorganisms that compose the gut microbiota. A healthy gut microbiome is essential in maintaining our overall health and well-being.

A harmonious gut microbiome aids digestion and nutrient absorption, regulates the immune system, prevents the colonization of harmful pathogens, maintains an intact gastrointestinal lining, prevents the entry of harmful substances directly into the bloodstream, and is key to our body's overall metabolic, mental, and neurological health.

Various factors such as mode of delivery at birth (vaginal vs. caesarian), host genetics, stress, exposure to toxins, food insensitivities, lack of exercise, poor sleep hygiene, unhealthy dietary habits, infections, and the use of antibiotics can lead to microbial dysbiosis and compromise gut health.

Signs and Symptoms of Gut Microbiome Imbalance

An imbalance in the gut microbiome can manifest in various ways. Some potential symptoms of gut microbiome imbalance are as follows:

  • Digestive Distress – gas/bloating, persistent abdominal discomfort/pain, diarrhea, constipation, heartburn, increased food sensitivities
  • Mental Health Issues – brain fog, difficulty concentrating, anxiety, and depression
  • Immune System Dysfunction – frequent infections, exacerbation of autoimmune conditions (e.g., Multiple Sclerosis), skin irritations (e.g., Hives, Eczema)
  • Systemic Symptoms – chronic fatigue, weight changes

A healthy gut microbiome is crucial for our overall health. Long-term health consequences of dysbiosis in the gut may lead to:

  • Digestive Disorders – Leaky Gut Syndrome, IBD, Small Intestinal Bacterial Overgrowth (SIBO)
  • Metabolic Dysfunctions – Insulin Resistance, Obesity, and High Cholesterol
  • Cardiovascular Conditions – Coronary Artery Disease (CAD)
  • Histamine Intolerances – Allergies, Asthma, and Skin Conditions
  • Neurological Disorders – Alzheimer’s Disease and Parkinson's Disease

Functional Medicine Assessment of Gut Health

A functional medicine assessment of gut health aims to take a systems-oriented approach and evaluates an individual’s dietary habits, lifestyle factors, and includes a comprehensive medical history. This framework to diagnose an unhealthy gut is augmented with the following diagnostic tools for gut microbiome:

Gut Microbiome Analysis through a GI-MAP by Diagnostic Solutions is used to assess the diversity and balance of the gut microbiome. This test is a comprehensive stool analysis that quantifies clinically relevant gut microbiota through DNA using qPCR technology and can assess bacterial dysbiosis, candida overgrowth, and the presence of parasites. Additionally, a Comprehensive Stool Analysis by Doctor’s Data may also be used and is another great option.

The presence of Zonulin may indicate damage to the tight junctions that keep our gut lining intact. Advanced Gut Permeability Testing via GI-MAP + Zonulin by Diagnostic Solutions in a stool sample can offer valuable insights into the presence of Leaky Gut Syndrome as an underlying cause of gastrointestinal dysfunction.

A SIBO Breath Test by Gemelli Biotech measures the presence and amount of hydrogen, methane, and hydrogen sulfide gas produced by the bacteria in the small intestine. This diagnostic tool helps functional medicine practitioners identify Small Intestinal Bowel Overgrowth (SIBO).

Nutrient Status is a key aspect of gut health, and poor nutrient absorption can lead to gut issues. Blood tests may be conducted to check for deficiencies. The Cellular Micronutrient Assay by Cell Science Systems and the Micronutrient Test by SpectraCell Laboratories are great examples of this types of testing.

By acknowledging the interconnectedness of various factors contributing to our overall gut health, functional medicine aims to identify the root cause in a more holistic and personalized approach.


Nutritional Strategies to Rebalance the Gut Microbiome

Michael Pollen quoted in his book Food Rules, “Eat food. Not too much. Mostly plants.” is a good rule of thumb to begin with.

Gaining favorable exposure to high-fiber foods that provide a source of prebiotics to the gut microflora should be part of the dietary strategies for gut health. Prebiotics occur naturally in foods such as leeks, asparagus, chicory, Jerusalem artichokes, garlic, onions, wheat, oats, and soybeans (1)

Vegetables and fruits have been identified to have polyphenol compounds that alter the gut microbiota, resulting in a greater abundance of beneficial microbes (2). Introduce a new fruit or vegetable into your diet every week; variety is the spice of life. The high-resistance, complex carbohydrates in fruits and vegetables could exert prebiotic activity and increase microbial diversity in the gut (2).

Reducing exposure to highly processed foods, especially those with a high sugar content, can vastly improve the health of your gut.

Increase the intake of low-sugar, fermented foods such as unsweetened yogurt, kefir, kimchi, sauerkraut, natto, and miso in your daily diet (3). The live active probiotic cultures in fermented food promote the restructuring of the gut microbiota. Microbial metabolites and bioactives produced from fermented food supplementation play an important role in the microbiota-gut-brain axis and are known to have mental health benefits (3).

Individuals have unique host physiology and microbiota signatures. Due to variations in microbiome composition and abundance of specific microbial species, personalized nutritional interventions must be emphasized. It is imperative to note that there is no one-size-fits-all diet to rebalance the gut microbiome. 

The Role of Probiotics and Prebiotics

Probiotics are live strains of strictly selected microorganisms that, when administered in adequate amounts, confer a health benefit on the host (4). Reinoculating the gut microbiome through probiotic supplementation is especially important after antibiotic therapy. Introducing beneficial bacterial strains through probiotic supplementation inhibits the infiltration and growth of pathogenic bacteria via their competition for space and resources and helps restore the gut’s microbial balance (4). The following table provides guidelines on the specific selection criteria for probiotic strains, notably Lactobacillus and Bifidobacterium, to be included in human nutrition (1).

Additionally, probiotics are suggested to have both nutritional and beneficial immunomodulatory effects in patients with inflammatory bowel disease (IBD) (4).

Prebiotics for microbiome support are high-fiber, non-digestible foods that resist digestion in the small intestine, undergo fermentation by the gut microflora in the large intestine, and selectively stimulate the favorable growth of gut microbiota. Prebiotics improve gut barrier function and host immunity, reduce potentially pathogenic bacteria, and enhance small-chain fatty acid (SCFA) production (6).

Lifestyle Modifications for Gut Health

As discussed previously, various factors, including diet, stress, environmental toxins, and sleep hygiene, can all influence the health of our gut microbiome. As such, adopting lifestyle changes for gut health and the diversity of our microbiota is crucial.

Be proactive in identifying the food your body loves and the food your body hates. The P88-DIY Dietary Antigen Test panel by Precision Point and IgG Food Explorer panel by Diagnostic Solutions are great diagnostic tools to identify any hidden food intolerances. Remove potential irritants from your diet, slowly reintroduce one at a time, and monitor the body’s reactions that may point to gut microbial dysbiosis.

Chronic stress suppresses the immune system and reduces blood and oxygen flow to the intestines, wreaking havoc on our microbiota-gut-brain axis. Stress-reducing activities such as meditation, mindfulness practices, and low-intensity yoga to manage chronic stress can positively affect the gut microbiome.

Sleep fragmentation and short sleep duration are associated with gut dysbiosis. Conversely, sleep loss may be mediated by overgrowth of specific gut bacteria (5). Establishing a high-quality sleep routine and aiming to get 7-9 hours of sleep each night can promote gut health and overall well-being.

The gastrointestinal lining is highly susceptible to disruption from exposure to toxins. It is vital to avoid smoking and excessive alcohol consumption, as well as limit the overuse of antibiotics and long-term use of Non-Steroidal Anti-Inflammatory Drugs (NSAIDs).

Integrative Therapies and Complementary Approaches

Complementary approaches to microbiome rebalancing, such as Traditional Chinese Medicine (TCM), including herbal medicine and acupuncture, are gaining modernization. Studies have shown the metabolites of herbal medicine to be associated with improving the composition of gut microbiota, consequently ameliorating its dysfunction as well as associated pathological conditions (7). Acupuncture is a safe and effective therapeutic intervention for patients with refractory Crohn’s Disease. It demonstrated an increase in intestinal anti-inflammatory bacteria and SCFAs-producing bacteria, enhancing intestinal barrier function and inhibiting proinflammatory cytokines (8).

Mind-body techniques, including mindfulness, meditation, tai chi, and yoga, have significant benefits in stress management and can positively impact the gut-brain axis. Incorporating stress-reducing activities into our daily lives can contribute to a healthier gut and provide a new gateway to approach mental health.

A collaborative approach between conventional treatments and integrative therapies for gut health fosters a synergistic impact on the overall well-being of those struggling with microbial dysbiosis.

Monitoring and Adjusting the Protocol

Human beings and their gut microbiota are highly dynamic organisms – they both exhibit variability in genetics and lifestyles. Therefore, there is no standardized, universal intervention to rebalance the gut microbiome.

Observing how an individual’s body responds to dietary changes, lifestyle modifications, and pre-and probiotic supplementation can provide valuable insights into constructing a targeted gut rebalancing protocol.

Functional medicine practitioners often fine-tune the gut health protocol based on progress and identifying plateaus. Routinely adjusting the gut health protocol supported by gut microbiome testing, food sensitivity testing, and other diagnostic tools ensures a more efficacious and personalized approach.


Key Takeaways: How to Rebalance the Gut Microbiome

Unfortunately, what happens in the gut does not stay in the gut and affects our overall well-being. Fortunately, functional medicine offers a comprehensive approach to rebalancing the gut microbiome by fostering a diverse and resilient microbial community.

It begins with optimizing our diet with whole foods, vibrant fruits, and vegetables rich in polyphenols and prioritizing high-fiber and probiotic-rich foods to nourish our gut microbiome.

Implementing stress management techniques, prioritizing high-quality sleep, and minimizing exposure to toxins all contribute to a well-balanced gut microbiome.

Functional medicine practitioners are well-versed in using specialized gut microbiome testing to ascertain the underlying cause of an unhealthy gut. This enables them to tailor treatment plans based on an individual’s unique health history.

Good health starts with gut health!

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article

  1. Markowiak, P., & Śliżewska, K. (2017). Effects of Probiotics, Prebiotics, and Synbiotics on Human Health. Nutrients, 9(9), 1021.
  2. Rinninella, Cintoni, Raoul, Lopetuso, Scaldaferri, Pulcini, Miggiano, Gasbarrini, & Mele. (2019). Food Components and Dietary Habits: Keys for a Healthy Gut Microbiota Composition. Nutrients, 11(10), 2393.
  3. Balasubramanian, R., Schneider, E., Eoin Gunnigle, Cotter, P. D., & Cryan, J. F. (2024). Fermented Foods: Harnessing Their Potential to Modulate The Microbiota-Gut-Brain Axis for Mental Health. PubMed, 105562–105562.
  4. Kim, S.-K., Guevarra, R. B., Kim, Y.-T., Kwon, J., Kim, H., Cho, J. H., Kim, H. B., & Lee, J.-H. (2019). Role of Probiotics in Human Gut Microbiome-Associated Diseases. Journal of Microbiology and Biotechnology, 29(9), 1335–1340.
  5. Matenchuk, B. A., Mandhane, P. J., & Kozyrskyj, A. L. (2020). Sleep, Circadian Rhythm, and Gut Microbiota. Sleep Medicine Reviews, 53(1), 101340.
  6. Slavin, J. (2013). Fiber and Prebiotics: Mechanisms and Health Benefits. Nutrients, 5(4), 1417–1435.
  7. Xu, J., Chen, H.-B., & Li, S.-L. (2017). Understanding the Molecular Mechanisms of the Interplay Between Herbal Medicines and Gut Microbiota. Medicinal Research Reviews, 37(5), 1140–1185.
  8. Bao, C., Wu, L., Wang, D., Chen, L., Jin, X., Shi, Y., Li, G., Zhang, J., Zeng, X., Chen, J., Liu, H., & Wu, H. (2022). Acupuncture improves the symptoms, intestinal microbiota, and inflammation of patients with mild to moderate Crohn’s disease: A randomized controlled trial. EClinicalMedicine, 45(1), 101300. 
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