The functional nutrition approach to healing Small Intestinal Bacterial Overgrowth focuses on identifying and addressing the root causes of symptoms through diet and lifestyle changes. This whole body, root cause approach is individualized based on a comprehensive functional nutrition assessment, individual symptoms, health history, and labs aiming to restore balance to the digestive system.

What is Small Intestinal Bacterial Overgrowth or SIBO?

Small intestinal bacterial overgrowth otherwise known as SIBO is an over population of bacteria in the small intestine that disrupt the gut microbiome resulting in multiple GI symptoms. What is happening behind the scenes is that these gut bacterial microbes are backing up from the large intestine, making a home in the small intestine, and as a result disrupting the entire gut microbiome by not being in the correct place in the body. These are not considered “bad gut bacterial microbes”, they are simply not in their original home where they can function at their best. There are trillions of bacterial microbes in the large intestine (think large intestine equals large amounts of gut bacterial microbes) and only a small amount in the small intestine (think small intestine equals small amounts of gut bacterial microbes). Once the bacterial microbes start populating into the small intestine, the GI symptoms will begin to occur as a result such as gas, bloating, and abdominal distention.

The whole body, root cause approach to Healing SIBO from a functional nutrition perspective:

Overall from a whole body, root cause approach, to heal SIBO we would look at using a therapeutical diet to manage GI symptoms, targeted supplements along with herbal antimicrobials, probiotic strains, and then work to rebalance the gut using the 5R Treatment Protocol. Any potential root causes are identified using the STAIN method specifically looking at stress, toxins (mold, plastics, heavy metals), adverse food reactions, infections, and nutritional imbalances.

During the initial comprehensive functional nutrition assessment, we will look at:

• Past Medical History: initial comprehensive patient questionnaire, symptom questionnaire, root causes: STAIN (stress, toxins, adverse food reactions, infections, nutritional imbalances), history of N/V/D/C, family history of GI disorders, current medications/OTC’s and supplements.
• Anthropometrics: changes in body weight, weight loss, weight gain.
• Nutrition Focused Physical Exam: dark circles under eyes, mouth sores, red, swollen, or coated tongue, skin rashes, hair thinning/hair loss, swollen joints, abdominal distention/bloating.
• Dietary and Food Habits: nutrient density in meals, caloric intake, meal pattern and timing, macronutrient balance, fiber types and sources, processed food and refined sugar intake, alcohol intake, adverse food reactions (food allergies or intolerances), FODMAPs, lactose, fructose, or sucrose intolerance, gluten sensitivity, histamine intolerance, prebiotic sources, probiotic sources, fermented foods, gut microbiome diversity.
• Conventional Labs: Comprehensive metabolic profile (CMP), CBC with differential, fasting insulin & HbA1C, complete iron profile including serum ferritin, serum 25-OH Vitamin D, and serum B12.
• Functional Labs: GI-MAP by diagnostic solutions, OAT test by mosaic diagnostics, or Breath test for small intestinal bacterial overgrowth (SIBO).
• Wearables Data: apple watch for exercise/HRV (heart rate variability), whoop for exercise/HRV, oura ring for sleep tracking.

A personalized functional nutrition care plan will be created for you based on the data from the initial comprehensive functional nutrition assessment that includes personalized diet therapy, targeted supplements, herbal antimicrobials, probiotic strains, as well as lifestyle changes in stress level, sleep quality, and exercise which are important for gut health.

By addressing these underlying causes — through personalized approaches like nutrition, simple lifestyle changes, and targeted supplements — functional nutrition aims to bring the body back into balance and resolve SIBO at its root.

What are common symptoms of Small Intestinal Bacterial Overgrowth?

Symptoms are a sign that something is off internally within one of these systems: Inflammation, Gut Dysbiosis or Gut Imbalance, Impaired Detoxification, Hormonal Imbalance, Mitochondrial Dysfunction, Circadian Rhythm Disturbances, Oxidative Stress, Neuro-disruption, or Immune dysregulation. Symptoms are essentially your body crying out for help in the only way that they know how to communicate. Watery diarrhea, bloating, abdominal pain and distension are the most common clinical manifestations of SIBO. Additionally, malnutrition and vitamin (B12, D, A, and E) as well as minerals (iron and calcium) deficiency may be present.¹ Symptoms associated with SIBO include:

• Bloating (common)
• Abdominal distention (common)
• Abdominal pain (common)
• Burping
• Gas
• Malabsorption of nutrients
• Diarrhea
• Constipation
• Fatigue

What are root causes of Small Intestinal Bacterial Overgrowth?

• Low stomach acid production
• Potential vitamin/mineral deficiencies that could contribute to low stomach acid
• Chronic stress also leading to high cortisol (leading to potential hormonal imbalances)
• Lack of a nutrient-dense diet

Why is stomach acid production important during the process of healing Small Intestinal Bacterial Overgrowth and how will I know if I have low stomach acid production?

You need adequate amounts of stomach acid for optimal digestion and absorption of nutrients. It helps break down the food that you consume daily into nutrients that energize every cell in your body. Often times with SIBO, stomach acid production is low leading to poor digestion, impaired process of absorbing nutrients leading to specific nutritional (vitamin/mineral) deficiencies which cause the above symptoms:

• Bloating (common)
• Abdominal distention (common)
• Abdominal pain (common)
• Burping
• Gas
• Malabsorption of nutrients
• Diarrhea
• Constipation
• Fatigue

There is a quick and easy test that you can do at-home to find out if you have low-stomach acid production which involves two ingredients: baking soda and water.

Baking soda and water self-test: if you have plenty of stomach acid you will notice burping or belching within the first five minutes because you start producing carbon dioxide gas which will cause you to burp.

Instructions: Place 1/4 teaspoon of baking soda into a 4 ounce glass of water. Make sure to drink this on an empty stomach. It is best taken first thing in the morning or make sure to wait at least three hours after eating a meal so that you are performing the test on an empty stomach. Notice what happens within the first five minutes of ingestion. If you have adequate stomach acid, you will start burping. This happens due to the combination of hydrochloric acid in the stomach (HCI) and sodium bicarbonate (baking soda) that will result in CO2 (carbon dioxide) gases leading to burping.

How can i test for Small Intestinal Bacterial Overgrowth using functional lab testing?

The most accurate method of testing as of now for small intestinal bacterial overgrowth is breath testing which essentially measures three different types of fermented gases: hydrogen, methane, and hydrogen sulfide.

It’s important to follow breath test instructions for the most accurate results since results are affected by many factors such as medications, diet, chewing gum, smoking, exercise, and any medical procedures such as a colonoscopy.

This isn’t an entirely accurate test as someone without SIBO can test positive for SIBO using breath testing. There is still more research that needs to be done as the human body is an intricately designed and complex system. You do not need to purchase a $300 lab test in order to heal SIBO. If the symptoms are present and you are diagnosed by a physician, using a food as medicine approach may be a very effective method in healing SIBO.

My storefront is linked here to order functional labs for gut microbiome imbalances, hormonal imbalances, or vitamin/mineral deficiencies. If you need help creating a personalized functional nutrition care plan based on the interpretation of the labs, you can work with us here.

Functional lab testing would be a good idea if you really wanted to hone in on the specifics of gut microbiome imbalances, hormonal imbalances, vitamin/mineral deficiencies.

Are there any therapeutic diets used in healing Small Intestinal Bacterial Overgrowth from a root cause approach?

Since there is always research still emerging, it’s hard to choose one specific diet for a client with SIBO. It is often a process of trial and error. A therapeutic elimination diet is the go-to for symptom relief while also re-balancing the gut microbiome. Looking at it from the STAIN framework — Stress, Toxins, Adverse Food Reactions, Infections, and Nutritional Imbalances — we aim to identify the root causes and design a personalized nutrition care plan based on your unique biochemical individuality. Biochemical individuality is the concept that each of us has a different nutrition blueprint to achieve optimal wellness. We each have our own, unique genetic expression and that is shown in a personalized nutrition care plan made just for you.

These are short-term therapeutic diets that are not meant for you to stay on the rest of your life. We are aiming to first heal and repair the gut, slowly re-introduce new foods, identify any trigger foods, and then work to rebalance the gut using the 5R Treatment Protocol linked here.

Tip: Keep a food journal so that pre and post meals you can become more in tune with your body and see how certain meals make you feel. Continuously check in with yourself to see how you are feeling, this is the type of subjective information that only you can know for yourself and make sure to share this information with the dietitian that you are working with!

Ask yourself: Do I feel bloated or gassy after eating this specific meal? It’s helpful to have a dietitian that is able to look at your food journals so that they can decipher what specific ingredient or a combination of ingredients that may be causing these symptoms. Having a food journal is also helpful to look for any potential food reactions that may be related to SIBO for example foods high in histamine, oxalates, & salicylates.

Are there any supplements, probiotic strains, botanicals, or herbal Antimicrobials that are helpful in healing Small Intestinal Bacterial Overgrowth?

The research currently shows that focusing on specific strains of probiotics (beneficial bacteria) can be useful during SIBO treatment to help reinforce the wall of the intestine and help repair MMC (migrating motor complex) activity. It may decontaminate SIBO, decrease H2 (hydrogen) concentration, and relieve abdominal pain. Remember supplements are there to “supplement” or to help the main treatment which is using a food as medicine approach to healing.

If low stomach acid and digestive enzyme production due to maldigestion, you can supplement or use natural prokinetic agents to help reduce bacteria overgrowth and prevent SIBO from recurring. You may use herbal antimicrobials if symptoms don’t improve such as oregano, berberine, or neem in order to reduce unwanted bacteria in the GI tract. Supplementation with a mixture of plant extracts (oregano, berberine, wormwood, yarrow, thyme, ginger, licorice, etc.) has been described as being equally effective as rifaximin for the treatment of SIBO.²

Make sure to order from a high quality and third party tested brand instead of purchasing from Amazon where practically anyone can sell anything without any rigorous testing. To make it easier for you, you may order from my supplement dispensary below through Fullscript’s catalog where each brand and product meets strict top quality standards. You can learn more about third party testing here.

My supplement dispensary is linked here (with a 30% off discount!) and you do not need to be a client to place an order.

What are some diet and lifestyle tips that can help me during the process of healing Small Intestinal Bacterial Overgrowth?

Look at sleep, diet, exercise, and stress management.

Here are some helpful tips for you to begin the process of healing SIBO:

• Chewing food thoroughly and mindfully.
• Intermittent fasting potentially (only if cortisol levels are already balanced otherwise IF is a stressor and will elevate cortisol)
• Pre-meal deep breathing to encourage MMC (migrating motor complex) function.
• Having proper mealtimes where you are sitting down (not standing up!) and making sure to properly and mindfully chew your food. By carving out a special time to eat, you are telling your body to relax into the parasympathetic state (rest and digest state) which is essential for optimal digestion. Allow your body to slow down, make sure that you are in a seated position, rest, remove any distractions, and simply enjoy your meals for better digestion.
• Removing the use of straws while drinking.
• Reduce chronic stressors in your life! Chronic stress is a root cause of SIBO and vagus nerve dysregulation has been linked to bacterial overgrowth. The vagus nerve is the link between the gut and the brain & they interact/influence each other! Some tools to help with stress: yoga, meditation, breathwork, prayer, low intensity cardio.
• Adequate hydration: adding a couple drops of apple cider vinegar or digestive bitters into your water bottle and drinking before meals (not during meals which will mess with stomach acid production) to increase stomach acid production.
• Proper sleep: having a good sleep routine will help with getting a good nights rest leading to better gut health.
• Using a tongue scraper in the morning before or after you brush your teeth.
• Try eating with your hands in order to eat less portion sizes, to get more in touch with the texture of your food, and to eat more mindfully and slower. The skin microbiome on your fingers will positively affect your gut microbiome. (make sure that you have clean hands and use your right hand preferably)
• Using a bidet

Gentle reminder: It’s important to be patient during this process of healing which may take some time but will ultimately be worth it in the long run. You got this.

Note: Don’t stress yourself with an all or nothing mentality where you feel like you have to implement everything on this list all at once. Sometimes in order to reach the end goal, you need to take baby steps at first and build these habits bit by bit.

How can I heal Small Intestinal Bacterial Overgrowth with the help of a functional nutrition dietitian?

Each person is unique and this is recognized in a personalized functional nutrition assessment and intervention plan that engages and empowers the patient in this process to restore optimal function, manage symptoms and promote overall health and well-being.

Functional nutrition addresses the whole person, not just an isolated set of symptoms. We look at it from a root-cause perspective and create a focus on prevention through nutrition, therapeutic diets, targeted supplementation, exercise, interpretation of conventional and/or functional lab testing, botanicals, detoxification protocols, and stress management tools.

Overall from a whole body, root cause approach, to heal SIBO we would look at using diet therapy, work to restore proper motility in the small intestine, look for any potential vitamin/mineral deficiencies that could contribute to low stomach acid, specific probiotic strains, herbal antimicrobials, natural prokinetic agents, digestive support, as well as lifestyle modifications (sleep, stress, and exercise) to heal SIBO from a root cause standpoint and to prevent it from reoccurring. Finally, we would work to rebalance the gut using the 5R Treatment Protocol linked here.

By addressing the underlying causes of SIBO — through personalized approaches like evidence-based nutrition, simple lifestyle changes, and targeted supplements — functional nutrition aims to bring the body back into balance and resolve SIBO at its root.

References:

1. Losurdo G, Salvatore D’Abramo F, Indellicati G, Lillo C, Ierardi E, Di Leo A. The Influence of Small Intestinal Bacterial Overgrowth in Digestive and Extra-Intestinal Disorders. Int J Mol Sci. 2020 May 16;21(10):3531. doi: 10.3390/ijms21103531. PMID: 32429454; PMCID: PMC7279035. ↩︎
2. Chedid V., Dhalla S., Clarke J.O., Roland B.C., Dunbar K.B., Koh J., Justino E., Tomakin E., Mullin G.E. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob. Adv. Health Med. 2014;3:16–24. doi: 10.7453/gahmj.2014.019. ↩︎