A Guide To SIBO And Healing Your Dysbiotic Gut
SIBO stands for small intestinal bacterial overgrowth. The small intestine is the main site where digestion and absorption of nutrients occur. Poor intestinal motility caused by SIBO disrupts a healthy number of bacteria in the gut and can lead to nutritional deficiencies and many inflammatory gut-related issues.
To really understand SIBO, you need to know how gastrointestinal motility affects gut bacteria and how bacterial growth abnormalities impact your health.
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Understanding SIBO
Your “gut” is comprised of the small and large intestines. Gut bacteria are essential players in this system, aiding in digestion, preventing gut-related medical conditions, and even stabilizing mental health due to the gut-brain axis. These bacteria come from various sources:
- Ingestion: Bacteria enter the digestive system through the food and drink you consume. These bacteria can be beneficial, aiding in digestion to maximize nutritional absorption and maintaining an overall healthy gut environment.
- Natural flora: The body’s natural flora, including bacteria in the mouth and upper digestive tract, also end up in the gut. After stomach acid digests food into what’s called “chyme,” it moves from the stomach to the small bowels, carrying these bacteria with it.
When you’re not eating (while sleeping and in between meals), your migrating motor complex (MMC) pushes gut bacteria from the small intestines into the large intestines, where most of the gut bacteria should live. But sometimes, this process can fail, causing symptoms of SIBO.
In cases of motility disorders, bacteria that are meant to migrate down instead grow up into the small intestines, where it doesn’t belong.
This excess bacteria eats up nutrients meant to be absorbed through the intestinal lining into your bloodstream, causing vitamin deficiency. It even ferments food in the small intestine, leading to uncomfortable SIBO symptoms such as flatulence.
Another process that makes it likely for a person to develop SIBO is poor gastric acid secretion. This can happen due to aging, overuse of proton pump inhibitors (PPIs; typically used to combat acid reflux), or H. pylori infection. Normal gastric acid production suppresses bacterial growth by design, so when this isn’t happening, it allows for overgrowth of bacteria in the small intestine.
Diagnosis and treatment are imperative as SIBO is often considered a risk factor for the more serious leaky gut syndrome, which is linked to many chronic and autoimmune conditions such as inflammatory bowel disease.
Symptoms
SIBO is associated with gut-related symptoms that are frustrating but often considered “normal” at first glance by mainstream medicine since they can be very common. SIBO symptoms include:
- Constipation
- Diarrhea
- Cramping
- Gas
- Nausea
- Bloating
- Acid reflux, heartburn, GERD
Severe cases of SIBO can also lead to irritable bowel syndrome (IBS).
Other than the uncomfortable symptoms listed above, one of the biggest concerns of SIBO is malnutrition. Since SIBO inhibits the absorption of vitamins, fat, carbohydrates, and protein from foods, nutrient deficiency is often a major problem in those with SIBO.
Iron, calcium, vitamin D, vitamin A, and vitamin B12 deficiencies are some of the most common in SIBO patients. These nutrients are needed to prevent fatigue, weakness, brain fog, imbalanced hormones, poor immune function, and more.
If you have SIBO symptoms, I implore you to seek diagnosis and begin SIBO treatment to overcome these deficiencies and get your gut health back on track.
Get To The Root Cause
Functional medicine is all about getting to the root cause of your condition. When you discuss a treatment plan with your healthcare professional, please advocate that your root cause be identified first.
Certain conditions have been linked to a predisposition for SIBO, including:
- Pancreatitis (1)
- Diabetes (2)
- Scleroderma (3)
- Abdominal surgery, especially gastric bypass and other surgeries that create a “blind loop” in the gut (4)
- Celiac disease (5)
- Rosacea (6)
- Dysmotility (7)
- Diverticulosis (8)
- Inflammatory bowel disease (IBD), especially Crohn’s disease (9)
- Advanced liver disease, including cirrhosis of the liver
- Gastroparesis
Because your gut controls 80% of your immune system and can regulate your mood and genetic expression, we’re just beginning to see the far-reaching associations between SIBO and seemingly unrelated conditions like those listed above. (10)
Aging has also been shown to contribute to the prevalence of SIBO since your digestive tract slows down as you get older.
In rare cases, people are born with abnormal passages between parts of their bowels. This is called a fistula, and it may also increase the risk of SIBO. However, as this is an anatomical problem, it can only be reversed by surgery. A similar issue known as strictures may develop after GI surgery, in which scar tissue develops from one side of the intestine to the other to inhibit digestion.
By uncovering your root cause and incorporating some of these functional medicine tools, you can be well on your way to overcoming SIBO.
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Testing And Diagnosis
To know for sure if you have SIBO, you’ll need to see your healthcare provider for an official diagnosis. SIBO can be diagnosed through a hydrogen breath test, which measures the presence and amount of hydrogen and methane gas produced by the wayward bacteria in the small intestine.
To complete the test, you drink a solution containing sugar, such as lactulose (most commonly used in SIBO tests), glucose, or xylose. If the bacteria is present, it will feed off the sugar and release hydrogen or methane gas, which is how the test works to identify SIBO.
Other tests a doctor may perform include a small intestine aspirate and fluid culture, where the provider will do an endoscopy to retrieve a sample of the contents of your small intestine. This is more invasive, so I typically don’t recommend it because hydrogen breath tests are just as effective.
My Functional Medicine Treatment Plan
Conventional medicine typically treats SIBO with a course of antibiotics like rifaximin or metronidazole. While antibiotics do help kill the bad bacteria, they also end up killing the good bacteria necessary to keep SIBO from returning.
In fact, studies have shown that many patients have to be on antibiotics long-term since they contribute to SIBO recurrence and increased gut symptoms. (11) If you want to avoid the vicious antibiotic cycle, read on to learn how I treat SIBO in functional medicine.
1. Uncover Any Underlying Causes
The first step to sustainable healing for SIBO is to identify the root cause of why it occurred in the first place. Work with a functional medicine practitioner who can run labs and compile a comprehensive health history to uncover the cause of SIBO and devise a plan of action for healing. I discuss the most common underlying causes of SIBO further below.
2. Avoid High-FODMAP And Lactose-Containing Foods
FODMAPs stands for “Fermentable Oligo-, Di-, Monosaccharides, And Polyols,” which are specific carbohydrates that feed gut bacteria and encourage them to proliferate. Some foods that are high in FODMAPS include onions, cabbage, beans, apples, and rye.
Monash University, a leader in research on this topic, has a great app to help you stick to low FODMAPs.
Lactose is also a trigger for SIBO in many patients, so it’s a good idea to cut milk products from your diet, at least until you can identify if this worsens your condition.
3. Take Probiotics
Probiotics containing a combination of Bifidobacteria, Enterococcus, and Lactobacillus have been shown to affect irritable bowel syndrome positively, and may aid in rebalancing your microbiome population. (12)
While they can be great in other situations, avoid probiotics that contain prebiotics, which can feed the bacterial overgrowth present in SIBO. You can also incorporate more probiotic-rich foods into your diet, such as sauerkraut, kimchi, yogurt, and kefir.
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4. Try Herbal Remedies
Research has shown that herbal remedies can be just as effective, if not more so, in treating SIBO, especially considering they only target the bad bacteria, thus limiting the recurrence rate. (13) Some herbal remedies to consider include oregano oil, skullcap, lemon balm, licorice root, and berberine extract.
5. Intermittent Fasting
An intermittent fasting protocol, where the patient limits food intake for a short period of time to starve out the bacterial overgrowth, can be an effective attack on SIBO. Constantly eating also doesn’t give your migratory motor complex the chance it needs to kick in. Allowing more time between meals is an easy way to encourage the MMC to work more efficiently.
6. Other Supplements
In addition to probiotics that can be used to support a healthy microbiome environment, other supplements can also be used to help correct nutrient deficiencies caused by SIBO-induced malabsorption. A few of these include:
- Vitamin B12
- Vitamin D
- Iron
- Zinc
Digestive enzymes are also a great option if you struggle with SIBO as they help to reduce symptoms like bloating, gas, and abdominal pain, can help improve nutrient absorption, as well as help digestion of problematic foods like FODMAPs.
If you’re not sure where to start, I wrote a comprehensive supplement guide with recommended dosages and more information on what to look for when choosing supplements.
FAQs
Each person’s body responds a bit differently to dietary patterns in SIBO, but the most common ways to eat to address SIBO are:
- A low-FODMAP diet to avoid carbohydrates most likely to feed bad gut bacteria
- A dairy-free diet to cut lactose from the diet
- In extreme cases, an elemental diet may be prescribed (this is a very short-term, liquid-only diet designed to give you the nutrients you need without feeding gut bacteria with any form of carbohydrate)
If you don’t treat and reverse SIBO, several long-term health issues may result:
- Your gut won’t be able to absorb the macronutrients it needs (fats, carbs, and proteins) to survive. This usually leads to inflammation of the gut lining and leaky gut, followed by eventual malnutrition, unintentional weight loss, and more frequent diarrhea.
- You’ll struggle to absorb the fat-soluble vitamins you consume (A, D, E, and K). Deficiencies in these all lead to very serious consequences over time.
- You may develop vitamin B12 deficiency, leading to nervous system symptoms like fatigue, weakness, or tingling and numbness in the hands and feet. Ultimately, this damage may be irreversible, especially if it leads to confusion and more severe symptoms.
- Your bones may get weaker over time, increasing your risk for osteoporosis.
- Because you won’t absorb calcium well, you may also develop kidney stones.
Because SIBO can be caused by a number of health conditions, the first course of medication you may be prescribed by a doctor is likely to be for the underlying condition. Once the root condition has been addressed, you may then be prescribed an antibiotic (sometimes, for a very long time) to clear out the bacterial overgrowth. Common ones include:
- Rifaximin (generally preferred, as it’s unlikely to lead to antibiotic resistance)
- Metronidazole (by itself, or combined with other antibiotics like trimethoprin or cephalexin)
- Ciprofloxacin
- Norfloxacin
- Amoxicillin/clavulanate
- Neomycin
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- Signoretti, M., Stigliano, S., Valente, R., Piciucchi, M., Delle Fave, G., & Capurso, G. (2014). Small intestinal bacterial overgrowth in patients with chronic pancreatitis. Journal of Clinical Gastroenterology, 48, S52-S55.
- Yan, L. H., Mu, B., Pan, D., Shi, Y. N., Yuan, J. H., Guan, Y., ... & Guo, L. (2020). Association between small intestinal bacterial overgrowth and beta-cell function of type 2 diabetes. Journal of International Medical Research, 48(7), 0300060520937866.
- Polkowska-Pruszyńska, B., Gerkowicz, A., Szczepanik-Kułak, P., & Krasowska, D. (2019). Small intestinal bacterial overgrowth in systemic sclerosis: a review of the literature. Archives of dermatological research, 311, 1-8.
- Petrone, P., Sarkisyan, G., Coloma, E., Akopian, G., Ortega, A., & Kaufman, H. S. (2011). Small intestinal bacterial overgrowth in patients with lower gastrointestinal symptoms and a history of previous abdominal surgery. Archives of Surgery, 146(4), 444-447.
- Charlesworth, R. P., & Winter, G. (2020). Small intestinal bacterial overgrowth and Celiac disease–coincidence or causation?. Expert Review of Gastroenterology & Hepatology, 14(5), 305-306.
- Parodi, A., Paolino, S., Greco, A., Drago, F., Mansi, C., Rebora, A., ... & Savarino, V. (2008). Small intestinal bacterial overgrowth in rosacea: clinical effectiveness of its eradication. Clinical Gastroenterology and Hepatology, 6(7), 759-764.
- Jacobs, C., Coss Adame, E., Attaluri, A., Valestin, J., & Rao, S. S. C. (2013). Dysmotility and proton pump inhibitor use are independent risk factors for small intestinal bacterial and/or fungal overgrowth. Alimentary pharmacology & therapeutics, 37(11), 1103-1111.
- Tursi, A., Brandimarte, G., Giorgetti, G. M., & Elisei, W. (2005). Assessment of small intestinal bacterial overgrowth in uncomplicated acute diverticulitis of the colon. World Journal of Gastroenterology: WJG, 11(18), 2773.
- Wanzl, J., Gröhl, K., Kafel, A., Nagl, S., Muzalyova, A., Gölder, S. K., ... & Schnoy, E. (2023). Impact of Small Intestinal Bacterial Overgrowth in Patients with Inflammatory Bowel Disease and Other Gastrointestinal Disorders—A Retrospective Analysis in a Tertiary Single Center and Review of the Literature. Journal of Clinical Medicine, 12(3), 935.
- Furness, J. B., Kunze, W. A., & Clerc, N. (1999). II. The intestine as a sensory organ: neural, endocrine, and immune responses. American Journal of Physiology-Gastrointestinal and Liver Physiology, 277(5), G922-G928.
- Lauritano, E. C., Gabrielli, M., Scarpellini, E., Lupascu, A., Novi, M., Sottili, S., ... & Gasbarrini, A. (2008). Small intestinal bacterial overgrowth recurrence after antibiotic therapy. Official journal of the American College of Gastroenterology| ACG, 103(8), 2031-2035.
- Fan, Y. J., Chen, S. J., Yu, Y. C., Si, J. M., & Liu, B. (2006). A probiotic treatment containing Lactobacillus, Bifidobacterium and Enterococcus improves IBS symptoms in an open label trial. Journal of Zhejiang University Science B, 7, 987-991.
Chedid, V., Dhalla, S., Clarke, J. O., Roland, B. C., Dunbar, K. B., Koh, J., ... & Mullin, G. E. (2014). Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Global advances in health and medicine, 3(3), 16-24.
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BY DR. WILL COLE
Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum and the brand new book Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.
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