Chinese medicine & acupuncture for Small Intestinal Bacterial Overgrowth (SIBO)

What is covered in this article?

1. Defining small intestinal bacterial overgrowth (SIBO) and its potential causes
2. Common symptoms
3. Current functional diagnosis and treatment options
4. One of the key Chinese herbal formula’s for treating people with SIBO
5. Chinese medicine dietary and lifestyle considerations to ease symptoms and prevent recurrences
6. A look at Betaine Hydrochloride in restoring stomach function and addressing one of the root causes of SIBO

What is Small Intestinal Bacteria Overgrowth?

Small Intestinal Bacterial Overgrowth (SIBO) refers to an imbalance and overgrowth of bacteria in the small intestine, which is marked by non-specific digestive symptoms. Although their are several proposed causes for this condition, current research indicates that dysfunction to the anatomy and motility of the small intestine are the largest risk factors for developing the condition [1]. Other potential causes include chronic use of antacids, also known as proton pump inhibitors (PPI’s), low stomach acid (hypochlorydria) or bile acids, pancreatic enzyme deficiency, dysfunction of the ileocecal valve, and metabolic or systemic conditions such as type 2 diabetes and hypothyroidism [2].

Previous research has been undertaken to investigate the common bacterial strains causing SIBO. One study based on a culture of jejunal aspirates demonstrated Streptococcus and Staphylococcus species, Klebsiella pneumoniae, E. coli, Pseudomonas aeruginosa, Enterococcus faecalis, and Enterococcus faecium were some of the dominant bacteria amongst patients with SIBO [3].

Common symptoms of SIBO

SIBO often presents with a range of non-specific symptoms, including abdominal bloating and distention, gut pains, frequent burping or flatulence, reflux, nausea, changes to bowel habits and stool, weight loss, vitamin B12 deficiency, increased intestinal permeability (‘leaky gut’) and fatigue [4]. However, the two most common symptoms of SIBO are chronic loose stools and abdominal bloating, which is typically worse after consuming a meal containing carbohydrates or high FODMAP foods (more on this later). Ongoing research has also revealed that there is a likely a connection between SIBO and irritable bowel syndrome (IBS), as up to 78% of IBS sufferers may have underlying gastrointestinal dysbiosis and/or SIBO infection [5].

How is SIBO diagnosed?

The clinical ‘gold standard’ for testing SIBO is a small intestinal culture via endoscopy, however this method of testing is typically not used due to the invasiveness and limitations in obtaining an accurate sample. Instead, a 2-3 hour breath test is often the first line of investigation, as its considered simple, straightforward and non-invasive [4].

To perform a SIBO breath test, a patient will consume a small sugar solution, typically lactulose, which is a non-absorbable sugar in humans. Bacteria present in the gastrointestinal tract will metabolise the lactulose, and in turn produce hydrogen and methane gases as a byproduct. A positive SIBO breath test will result in early peaks in breath methane and hydrogen due to an overgrowth of bacteria in the small intestine, which metabolise the lactulose. Conversely, a negative SIBO test will result in a peak in breath hydrogen and methane at around the 2 to 3 hour mark, indicating normal metabolism of the lactulose by bacteria in the large intestine.

Functional medicine treatment for SIBO

To treat someone with SIBO, it is vital to address the underlying cause, reduce bacterial overgrowth, and treat potential nutritional deficiencies. Dietary measures are often required for chronic cases, including reducing lactose (a milk sugar) and commencing a low sugar/carbohydrate diet [6]. Among the most commonly utilised dietary interventions for SIBO is the low-FODMAP (fermentable oligosaccharide, disaccharide, monosaccharide and polyol) diet, which restricts many foods and should ideally be used short-term to prevent nutritional deficiencies (see Figure.1 below for examples of low-FODMAP foods).

The core idea of a low-FODMAP diet is to restrict the intake of certain carbohydrates which can be fermented and metabolised by bacteria present in the small intestine, thereby reducing symptoms of gas and bloating [7]. A low-FODMAP diet is also secondarily used to starve the the overgrowth of bacteria, making it easy to reduce their numbers whilst in the ‘active phase’ or antimicrobial part of treatment.

Potential concerns of a Low-FODMAP diet:

Although a low-FODMAP diet is commonly used in the treatment of IBS and SIBO, there are some limitations which should be discussed based on a review paper from 2017 [8].

1. A low-FODMAP plan has not been adequately tested against other diets, such as a gluten-free diet which is also moderately reduces high FODMAP foods. Therefore other dietary measures could be just as effective but less restrictive. However at this stage, there is currently not enough evidence to support the use of other diets for the treatment of SIBO.
2. A low-FODMAP diet may increase the rates of eating disorders in certain individuals.
3. When used long-term, a low-FODMAP diet can lead to several nutritional inadequacies, compounding nutritional deficiencies already present for people with chronic SIBO.
4. Lastly, many FODMAP foods are metabolised and fermented by the beneficial bacteria present in the large intestine. Therefore, restricting FODMAP foods long-term can lead to a decrease in the numbers of beneficial bacteria, which are essential for modulating the immune system, producing certain vitamins (vitamin B1 and K2), short-chain fatty acids such a butyrate, and preventing overgrowth of harmful bacteria in the gut.

Figure 1: Examples of high-FODMAP foods

With concern to some of these limitations, it is imperative that a low-FODMAP diet is used short-term during the active treatment phase, which is typically between 4-6 weeks for most cases. However, in a clinical setting adjustments to one’s diet is specific and depends on individual circumstances, severity of the condition, other co-morbidities, and medications.

Antibiotic treatment for SIBO:

Antibiotics such as Rifaximin, Tetracycline, Neomycin, Metronidazole and Clindamycin are the most frequently used for gastrointestinal related infections. Among these, Rifaximin appears to be the most safe and effective antibiotic in the treatment of SIBO, with a success rate of around 67.7% according to some studies. However, other studies have indicated varying success rates [9].

Although Rifaximin is a broad-spectrum antibiotic, it is often the preferred antibiotic of choice as it targets both anaerobic and aerobic bacteria. Additionally, Rifaximin has shown minimal absorption into the blood stream, prevents bacterial translocation and adherence to the gastrointestinal tract wall, demonstrates moderate anti-inflammatory effects, and appears to exert minimal damage to the microbiome present in the large intestine [10].

Although Rifaximin is generally considered a safe and well tolerated treatment option, it will only reduce the present bacterial overgrowth in the small intestine and not address the underlying cause or prevent SIBO relapses. In the cases of SIBO relapses, repeated antibiotic use can lead to antibiotic resistant bacterial strains which are becoming an ongoing global health threat. Epidemiological studies have demonstrated a clear link between chronic antibiotic use and the dissemination of antibiotic resistant bacteria, which is an ongoing global threat to healthcare [11].

Antimicrobial herbs:

Previous research has explored the efficacy of antimicrobial herbal therapies in treating Small Intestinal Bacterial Overgrowth (SIBO). Notably, a 2017 study compared the use of specific herbal antimicrobials to the antibiotic Rifaximin, evaluating their potential as effective alternatives in managing SIBO. The specific herbal antimicrobials used in the study included oregano oil, wormwood, and berberine—the latter being a bioactive plant compound commonly extracted from Coptis chinensis (Huang Lian), a Chinese herb known for its potent antimicrobial and anti-inflammatory properties.

The study found that a combination of antimicrobial herbs may be as effective, or even more effective, than Rifaximin in the treatment of SIBO. However, several limitations should be noted, including the timing of the intervention, a lower-than-standard dose of Rifaximin, lack of dietary control, and the inclusion of multiple herbs, which made it difficult to determine the individual effect of each one [12]. Despite these limitations, the results suggest that antimicrobial herbs could offer a viable treatment option for SIBO and merit further investigation in well-controlled clinical trials.

Figure 2: Berberine Complex

Key Chinese herbal formula & SIBO

Several key classical Chinese herbal formulas can be considered in the treatment of someone with SIBO, depending on the individual’s symptoms, pulse, and tongue diagnosis. Among them, the herbal formula Ban Xia Xie Xin Tang stands out for its well-documented use across a range of gut related conditions [13, 14, 15]. Traditionally used to harmonise the Stomach and Intestines, this formula addresses hallmark digestive symptoms such as abdominal bloating and fullness, irregular bowel movements (either diarrhoea or constipation), acid reflux, nausea, flatulence, and abdominal discomfort—many of which closely mirror the clinical picture of SIBO.

Ban Xia Xie Xin Tang contains the herbs Huang Lian (Coptis chinensis) and Huang Qin (Scutellaria baicalensis), both of which are used in Chinese medicine to clear heat, eliminate dampness, and resolve toxicity. Both herbs also contain the active compound berberine, which has been shown in research to exert strong antibacterial effects against a range of pathogens, including antibiotic-resistant strains such as Methicillin-resistant Staphylococcus aureus (MRSA) [16]. In addition to its antimicrobial properties, studies have indicated that berberine may enhance host immune function, supporting the body’s natural ability to fight infections [17]. This combination of traditional use and modern pharmacological activity makes Ban Xia Xie Xin Tang a particularly relevant formula in the treatment of SIBO-like presentations.

Figure 3: Herbs contained in Ban Xia Xie Xin Tang

Other herbs contained in Ban Xia Xie Xin Tang include Gan Jiang (Rhizoma Zingiberis/ginger) and Jiang Ban Xia (Rhizoma Pinelliae), which are used in Chinese medicine to harmonise the stomach, resolve phlegm and mucus, and alleviate nausea. Research indicates that ginger can increase HCL production, as well as gut motility, gastric emptying time, and relieve digestive symptoms such as nausea or vomiting [18, 19]. Based on this research, ginger should be considered when addressing some of the underlying causes of SIBO, such as delayed gastrointestinal tract motility and low stomach acid production.

The last remaining herbs in Ban Xia Xie Xin Tang are Zhi Gan Cao (Radix Glycyrrhizae), Da Zao (fructus jujubae) and Ren Shen (Radix Ginseng). These herbs are used in Chinese medicine to replenishing Qi and Blood, restore Yang to increase energy levels, and relieve heat and toxicity. Research has also demonstrated that Zhi Gao Cao exerts antimicrobial, anti-inflammatory and immunoregulatory effects in the body [20].

Chinese medicine dietary considerations:

Regarding Chinese medicine interventions, it is essential to address the key lifestyle or dietary factors which contribute to the susceptibility to developing SIBO. The following suggestions can be used to assist both the acute and recovery phase of treatment, but please note that these are only general guidelines and often dietary advise is tailored to the individual and their presentation.

1. Consume only cooked and easy to digest foods and avoid cold or raw foods such as salads, smoothies, juices and ice-cold beverages.
2. During the initial stages of treatment, avoid the consumption of fruit, wheat-grains and sugary foods as these directly contribute to Dampness and Spleen weakness according to Chinese medicine. Low sugar containing fruits such as blueberries may be tolerated in small quantities.
3. Avoid consuming fluids 30mins prior and 30mins after a main meal to ensure the digestive fire is strong. If fluids are required to take medications/supplements during a meal, take small slow sips of warm water.
4. Mix 1 tsp of apple cider vinegar (ACV) with 1 tsp of water (1:1 ratio) and consume this when eating a main meal. ACV helps to stimulate stomach acid production. However, it is best to avoid ACV if you suspect you have histamine intolerance. You can read more about histamine intolerance here. Generally considered a safe alternative to ACV is supplementing Betaine Hydrochloride + pepsin, which aids in stomach acid production and protein digestion (more on this in the next section).
5. Avoid snacking between main meals, which allows intestinal Qi to move food contents throughout the intestine, preventing food stagnation. This is akin to our modern understanding of the migrating motor complex or intestinal peristalsis, which is a key factor to preventing SIBO.
6. Take note of any suspected foods which potentially trigger gas, bloating, gut pains, loose stools, and consider eliminating these within the active phase of treatment.
7. Chew all foods thoroughly and in a relaxed state.

Betaine Hydrochloride for SIBO

Hypochlorhydria, or low stomach acid, is a well-recognised contributing factor in developing SIBO, particularly in older adults or individuals with a history of long-term proton pump inhibitor (anti-reflux medication) use. Adequate levels of hydrochloric acid (HCl) in the stomach are essential for sterilising ingested food, breaking down proteins, activating digestive enzymes, and maintaining the acidic environment which prevents bacterial overgrowth in the small intestine. To help restore stomach acid levels, research has explored the therapeutic use of Betaine Hydrochloride (HCl) combined with pepsin, a key enzyme involved in protein digestion. This combination aims to support optimal gastric acidity during meals, particularly when consuming protein-rich foods.

A common clinical approach to assessing suspected hypochlorhydria involves a titration protocol. This typically begins by taking one capsule of Betaine-HCl with a protein-containing meal and gradually increasing the dosage with subsequent meals until a mild sensation of warmth, burning, or reflux is felt in the stomach area. This response is considered the threshold indicating the individual’s maximum tolerated dose has been met. If these symptoms occur after just one capsule, it generally suggests that stomach acid production is within a normal range and supplementation is unnecessary [19, 21]. This protocol is often used under the guidance of a practitioner to support digestive function, particularly in individuals presenting with symptoms suggestive of low stomach acid, such as bloating, poor appetite, nutritional deficiencies like iron and B12, and reflux after meals.

Caution: If experiencing any acute flare of gastritis or eosophagitis, then HCL should not be taken until these gut inflammatory disorders have been addressed. This is why its imperative to work with a qualified health professional who can guide and individualise the treatment according to specific needs.

Closing Thoughts:

SIBO is a complex and multifaceted condition which requires addressing diet and lifestyle, actively decreasing bacterial overgrowth, and removing key drivers. A combination of western functional medicine and Chinese medicine may offer the solution to navigating and treating this difficult condition. If you have been struggling with SIBO or any other niggling digestive disorder, seek the advise of a trusted health professional who can get to the bottom of your symptoms and help you regain a sense of inner health and wellbeing!

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