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Are Your Uncomfortable Gut Symptoms Due to SIBO?

Small intestinal bacteria overgrowth (SIBO) is a common but under-diagnosed condition. Historically viewed as a controversial diagnosis due to its wide-ranging clinical presentations and overlap with other conditions, it has recently gained support as a viable explanation for gastrointestinal problems (1). Although antibiotics remain the most common treatment method for SIBO, functional medicine's holistic approach of addressing the root cause and restoring balance to the gastrointestinal tract through individualized approaches like diet modification and root cause identification is gaining popularity.

Are Your Uncomfortable Gut Symptoms Due to SIBO?

What is SIBO?

SIBO is a gastrointestinal disorder characterized by an excess and imbalance of bacteria in the small intestine (1). Unlike the large intestine, the small intestine normally contains few bacteria due to the rapid movement of food and the presence of bile (2). However, if the passage of food and waste products in the small intestine slows, bacterial overgrowth may occur, producing toxins and gas, interfering with the absorption of nutrients, and causing chronic bloating, constipation, diarrhea, and other symptoms (2).

Risk factors and causes of SIBO

It is unknown how prevalent SIBO is because it is thought to be under-diagnosed or attributed to an underlying disease (3). Its presence is extremely common in several predisposing conditions (3). In fact, research would suggest that up to 25% of patients with Crohn's disease also have SIBO (3), and one-fifth of those with celiac disease do as well. Other autoimmune diseases, chronic stress, vagal nerve dysfunction, gastroparesis, diabetes, and other illnesses that slow food movement through the small intestine can also cause SIBO (2).

Notably, SIBO is present in over half of patients with irritable bowel syndrome (IBS) and is associated with symptom exacerbation of this condition (4). However, some trials have reported a significant improvement in IBS after treatment of SIBO (3).

SIBO may also be caused by abdominal surgery complications or structural problems in or around the small intestine (2).

SIBO may be asymptomatic or, in extreme cases, cause malabsorption. Other symptoms may include (2, 3):

• Loss of appetite

• Abdominal pain

• Nausea

• Bloating

• Uncomfortable feeling of fullness after eating

• Chronic diarrhea or constipation

• Rapid, unintentional weight loss

• Malnutrition

It is important to note that the American College of Gastroenterology (ACG) states that no single symptom can be attributed explicitly to SIBO as symptoms often masquerade as other diagnoses (5). The ACG explains that this is due to the varied presentation of patients with SIBO and the number of underlying risk factors that can lead to its development (5). For example, in a patient with chronic pancreatitis, it is hard to determine if diarrhea is caused by an exocrine insufficiency or coexisting SIBO (5). Therefore, the ACG recommends that the symptoms, risk factors, and any history of attempted treatments for underlying conditions all be considered (5).

The potential consequence of untreated SIBO:

If SIBO is left untreated, a variety of medical consequences may occur. The excess bacteria break down bile salts – an essential component needed to digest fats – resulting in the poor absorption of fats, carbohydrates, and proteins. Due to the incomplete absorption of fats, the body cannot fully absorb fat-soluble vitamins A, D, E, and K, leading to vitamin deficiency. The bacteria also use vitamin B-12, which is needed for nervous system functioning and blood cell and DNA production. Vitamin B-12 deficiency can cause fatigue and tingling and numbness in the hands and feet. The continued presence of SIBO may limit calcium absorption, eventually leading to osteoporosis and kidney stones (2).

Diagnosing of SIBO

The diagnostic gold standard for SIBO diagnosis is a small intestine aspirate and fluid culture (1, 2). However, this test, which requires the insertion of a tube down the throat, remains unpopular due to its invasive nature and high cost (1, 2). As a result, glucose and lactose breath testing are more commonly used diagnostic tools. These breath tests, which measure the amount of hydrogen, methane, or hydrogen sulfide gas exhaled by patients after drinking a sugar-based water mixture, are non-invasive and inexpensive (1, 2). However, these tests are not without flaws and limitations. Glucose or lactulose breath testing has been found to produce false negatives in patients with distal SIBO and false positives in patients with a fast gut transit (1).

New techniques are being investigated to overcome the limitations of the currently available diagnostic tools. Metagenomics — the analysis of genetic material — can reconstruct bacterial genomes and study the diversity of the gut microbiome. It can also identify microbial pathways and antibiotic resistance genes. Although it is still in its early stages, recent studies show promise for its use as a diagnostic method (1).

Conventional medicine treatment of SIBO

Treating the underlying cause, nutritional support, and treating the overgrowth are the three pillars of SIBO treatment (6).

Antibiotic therapy remains the most common treatment, and a short course of antibiotics can significantly reduce the number of abnormal bacteria and reverse the mucosal inflammation caused by the bacterial overgrowth (2, 6). Rifaximin is the preferred antibiotic to treat SIBO as it has a reduced toxicity profile, is used in IBS treatment, and has been more effective in eradicating the bacteria than other antibiotics (1). It is worth noting that rifaximin is expensive - $1247 for a short course - and not routinely covered by many commercial health plans in the United States (4). It is also not without its risks, including developing antibiotic-resistant organisms and infections like Clostridium difficile colitis (1).

Additionally, the return of excess bacteria is likely if the underlying disease is not treated. One trial found the average symptom improvement duration was only 22 days, which translates to a need for at least 12 courses of antibiotics a year to provide consistent symptom relief (6).

Antibiotics are expensive, may cause side effects or complications - like resistance - and may require multiple courses (6). Although they are a proven method of treatment relief, 40% of patients with SIBO-like symptoms may continue to feel sick despite antibiotic treatment (1). Patients who do not find success with antibiotics should be evaluated for other diagnoses like disaccharide deficiency, food intolerance, and motility disorders or consider other treatment methods (1).

Functional medicine treatment

Functional medicine focuses on identifying the root cause and building a treatment plan based on the findings, an important step in a condition often caused by underlying diseases.

Although more research is needed to support the efficacy of some alternative therapies, they remain a viable option on their own or in combination with traditional treatments (1). These options may include probiotics, herbal supplements, dietary changes, and nutritional support.


Probiotics are live microorganisms that can reduce SIBO symptoms when taken in sufficient quantities. Probiotics modulate gut microbiota, sustain the intestinal epithelium's integrity, up-regulate anti-inflammatory cytokines and growth factors, and produce fatty acids and regular endocrine and neurological functions. Probiotics may also boost the effectiveness of antibiotics; in a recent study, patients treated with rifaximin plus probiotics showed greater symptom improvement than those treated with antibiotics alone (1). However, a different study showed that probiotics might intensify SIBO symptoms like gas, bloating, and brain fogginess (7). In this study, halting probiotics intake while continuing antibiotic treatment resolved brain fogginess and other associated symptoms, suggesting not all probiotics are equally effective and should be used with caution in patients with SIBO (1, 7). Additionally, a recent study showed that probiotic users were significantly more likely to have methane positive breath tests than non-users, suggesting that probiotic use can predispose individuals to methane variant bacteria overgrowth, commonly associated with constipation (1). More large-scale studies are needed to better understand the use of probiotics for SIBO treatment (1).

Herbal Supplements

Herbal supplements intended for SIBO relief have become increasingly popular as patients look for an alternative to antibiotics (1). A 2014 study found that herbal supplements are as effective as antibiotic therapy with rifaximin (4). Some of the herbal therapies tested in the study include oil of oregano, berberine extract and thymus vulgaris, wormwood, lemon balm, red thyme, and Indian Barberry root, all of which have antimicrobial and other beneficial properties.

The study found 46% of herbal users had negative breath tests during the four-week follow-up versus 34% of rifaximin users. Additionally, the study stated that patients resistant to rifaximin could be given the choice of herbal therapy as a rescue therapy (4). Herbal treatments appear to be less likely to cause infections like Clostridium difficile colitis compared to antibiotics and may be less harsh on the gut microbiome (4). It is worth noting that there is limited data on herbal supplements for SIBO, and the products available significantly differ in quality and efficacy (1).


Dietary changes may help relieve SIBO symptoms like bloating, flatulence, and abdominal pain (1). Adopting a low FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet is common, despite most of the evidence on its efficacy being based on IBS (1). FODMAP stands for a list of sugars that can be fermented in the gut and which bacteria in the small intestine thrive on (1). Limiting FODMAP foods can deprive the bacteria of the nutrients needed for growth and proliferation. Despite its effectiveness, FODMAP diets can be challenging without professional advice on trigger identification and the process of eliminating and reintroducing food.

An elemental diet — a form of liquid meal replacement that contains micronutrients — has been suggested to relieve SIBO symptoms (1). A retrospective study that looked at the potential benefits of such a diet for patients with SIBO found patients treated with an elemental diet for 14 days had an overall symptomatic response rate of 85%. However, this diet is expensive and should not be used as a long-term treatment of SIBO as the underlying cause of the bacterial overgrowth may remain (1).

Due to intestinal inflammation caused by SIBO, lactose and fructose intolerance may develop. Therefore, adopting a lactose and fructose-free diet may be beneficial (6).


Nutritional support, especially in patients with weight loss or vitamin and mineral deficiencies, is an essential component of SIBO treatment (6). Vitamin B12 injections, oral fat-soluble vitamins, and calcium and iron supplements may be used (3, 6).

Lifestyle and prevention

SIBO prevalence increases with age and the risk increases by 50% in people over 75 (3). One study found 33% of disabled older adults and 15.6% of older, non-hospitalized adults had SIBO (6). Medications that slow GI motility, the onset of new diseases, dietary changes, and changes in gut immune function likely play a role in older adults developing SIBO (6).

A 2018 study found that obese patients were 11 times more likely to have SIBO than non-obese patients, but more research is needed to understand the link (8).

Prevention of SIBO may not always be possible due to the underlying causes. However, there are ways to manage gut health (9).

• Diet: eating a wide range of food can help boost gut flora diversity, reducing the possibility of dysbiosis – the microbiome becoming imbalanced. Fruits, vegetables, and whole grains are recommended (9).

• Stop smoking: nicotine products can change the composition of the gut flora, which may cause dysbiosis (9).

• Prokinetics are a drug that promotes digestive motility and may reduce the risk of SIBO. A 2018 study found that patients who took prokinetics and proton pump inhibitors (PPI) were less likely to develop SIBO than those who only took PPI (10).

• Treating hypochlorhydria, or low stomach acid, may reduce the risk of developing SIBO (9).

• Managing other conditions associated with SIBO may help relieve their impact on the digestive system (9).

Small intestinal bacteria overgrowth presents like many other gastrointestinal disorders: bloating, flatulence, constipation, and diarrhea. In fact, it is not uncommon for SIBO to be caused by underlying gut conditions. Therefore, physicians must consider the patient's symptoms, history, and risk factors to determine a diagnosis. While conventional medicine's go-to treatment of antibiotics is effective, it comes with a hefty price tag, potential side effects, and the risk of developing antibiotic-resistant bacteria. Functional medicine methods, which look at diet changes and other alternatives, may be a better fit. Focusing on healthy eating and lifestyle habits benefits everyone's gut, not just those with SIBO. We would be privileged to help you discover what is causing your symptoms, develop a plan to treat the root causes, and come alongside you to implement healthier eating patterns and lifestyle habits to improve your health.


Jonathan Vellinga, M.D.

Jonathan Vellinga, MD is an Internal Medicine practitioner with a broad interest in medicine. He graduated Summa cum laude from Weber State University in Clinical Laboratory Sciences and completed his medical degree from the Medical College of Wisconsin.​

Upon graduation from medical school, he completed his Internal Medicine residency at the University of Michigan. Dr. Vellinga is board-certified with the American Board of Internal Medicine and a member of the Institute for Functional Medicine.




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  4. Chedid, V., Dhalla, S., Clarke, J. O., Roland, B. C., Dunbar, K. B., Koh, J., Justino, E., Tomakin, E., & 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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  7. Rao, Satish S. C. MD, PhD, FRCP (LON)1; Rehman, Abdul MD1; Yu, Siegfried MD1; de Andino, Nicole Martinez ARNP1 Brain fogginess, gas and bloating: a link between SIBO, probiotics and metabolic acidosis, Clinical and Translational Gastroenterology: June 2018 - Volume 9 - Issue 6 - p e162 doi: 10.1038/s41424-018-0030-7

  8. Roland BC, Lee D, Miller LS, Vegesna A, Yolken R, Severance E, Prandovszky E, Zheng XE, Mullin GE. Obesity increases the risk of small intestinal bacterial overgrowth (SIBO). Neurogastroenterol Motil. 2018 Mar;30(3). doi: 10.1111/nmo.13199. Epub 2017 Sep 21. PMID: 28940740.

  9. MedicalNewsToday. (2021, November 25). What to know about SIBO and its treatment.

  10. Revaiah, P. C., Kochhar, R., Rana, S. V., Berry, N., Ashat, M., Dhaka, N., Rami Reddy, Y., & Sinha, S. K. (2018). Risk of small intestinal bacterial overgrowth in patients receiving proton pump inhibitors versus proton pump inhibitors plus prokinetics. JGH open : an open access journal of gastroenterology and hepatology, 2(2), 47–53.


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