As a Naturopath and Nutritionist, natural treatment of SIBO is one of the key areas I work with clients on. SIBO is one of the conditions I see most regularly and I have the appropriate training to treat it.
Although SIBO (Small Intestinal Bacterial Overgrowth) is one of the main causes of IBS (Irritable Bowel Syndrome), it remains largely unknown to the frontline workers in the medical profession. This means people with SIBO are often left undiagnosed and untreated.
I have completed advanced SIBO training with SIBODoctor.com - The Practitioner Mastery Program - and have also completed courses presented by microbiome expert Jason Hawrelak, PhD.
Read on for an overview of how I diagnose and treat SIBO.
What is SIBO?
SIBO (Small Intestinal Bacterial Overgrowth) is basically a condition involving inappropriate bacterial overgrowth in the small intestine. It’s not an infection and doesn’t involve pathogens – it involves bacteria that are supposed to be in the human digestive tract. This region of the body is supposed to contain a much smaller number of bacteria than the large intestine, which is where most of the study has been done on the gut microbiome. There are specific protective mechanisms in our anatomy and physiology – such as the Migrating Motor Complex that acts as a sweep - which prevent this overgrowth and they are disrupted in SIBO.
There are many different risk factors for SIBO such as gastroenteritis which damages the Migrating Motor Complex, altered anatomical features (eg. ileocecal valve dysfunction, endometriosis), and physiological disturbances such as low levels of digestive secretions - stomach acid, pancreatic enzymes and/or bile. Medications can also trigger SIBO – I have seen many cases of SIBO that were caused by the overuse of Proton Pump Inhibitors for GERD and gastritis.
Different types of SIBO exist and some people can have more than one. Hydrogen SIBO, Methane SIBO and Hydrogen Sulfide SIBO are the three currently known types - unfortunately, testing for the latter is not widely available for most people. All of these types of SIBO have a common feature of elevated hydrogen production which can effectively fuel the other two types, due to conversion of hydrogen to methane or hydrogen sulfide. This is dependent on exactly which species have overgrown.
SIBO often co-occurs with SIFO, which is Small Intestinal Fungal Overgrowth. It presents with many of the same symptoms as SIBO and is currently best assessed with a Great Plains Lab Organic Acids test which reports on fungal markers found in the urine. SIFO can occur if an individual has had multiple rounds of antibiotics any time in the past, or if their immune function is impaired, which is quite a common scenario.
Each case of SIBO is different because there are so many variables that influence digestive function. Typical symptoms of SIBO can include: bloating, belching, diarrhoea, constipation, reflux and abdominal pain. It’s believed that SIBO is one of the main causes of IBS (Irritable Bowel Syndrome). These symptoms can change day to day in one individual with SIBO. The symptoms are caused by the overgrowth of bacteria fermenting particular foods in to the gases.
Since the gut is so central to our overall health – owing to its role in nutrient absorption and immune function - SIBO has also been linked to many non-digestive conditions and symptoms such as acne rosacea, fibromyalgia, chronic prostatitis and autoimmune diseases.
SIBO can also cause other negative health effects such as nutrient deficiencies - since the bacteria can consume/steal them from us before digestion -, fat malabsorption which can affect bone density, microvilli damage – causing problems digesting certain foods and also histamine intolerance.
SIBO research has grown exponentially in the last five years, but it’s important to acknowledge that we are really somewhere near the start of our journey into understanding and treating SIBO. Having said that, there is a lot that we DO know. SIBO is a very treatable condition when done right.
SIBO is considered a relapsing condition and this is why it’s crucial to confirm what factors have led an individual to develop SIBO, because this informs both individualised treatment and also long term strategies for keeping it under control.
How is SIBO best diagnosed?
Breath test is the most accessible testing available, because a small intestinal aspiration is rarely done in a clinical setting and requires a day procedure in a hospital or clinic. Breath testing is non-invasive, relatively affordable and can be done at home.
Both types of test can actually miss a diagnosis (so, a false negative). For example, with the breath testing for example, not all bacterial species typically found in SIBO can ferment the test substance (eg. lactulose or glucose). Also, there is currently only one publicly available breath testing option that measures hydrogen sulphide gas, which is considered the third type of SIBO (although a flatline level throughout the test *may* be an indication along with symptoms).
The aspiration is dependent on a culture-based method, to detect the different species present. Unfortunately, many species cannot be cultured easily in the lab. That’s one reason why PCR/DNA based stool testing is also recommended over any that uses the outdated culture method.
This all means that SIBO can also be diagnosed on a clinical basis – that is, based on symptoms and history. Even if it turns out SIBO isn't present, the naturopathic treatment will positively influence the large intestine microbiome anyway and is largely minimal risk.
For breath testing, I always recommend testing for 3 sugars – lactulose, glucose and fructose because invariably, most people will not test positive for all sugars. So, just testing lactulose for example may miss cases where the person would be positive for glucose or fructose. While that can be a bit tedious, it’s well worth it to get an accurate assessment of whether SIBO is present.
There is a special preparation period for the test involving diet and cessation of particular supplements. Also, each test sugar needs to be done on a separate day to prevent any overlap (ie. residual levels of the previous testing substance).
I also routinely run stool testing alongside breath testing because I’ve found most people with SIBO also have dysbiosis in the large intestine and the symptoms almost always cross over. Depending on the individual case, I will either order Genova GI Effects or Diagnostic Solutions GI Map. What I love about the GI Effects test is that it is so thorough when looking at digestive function, along with reporting on the microbiome. The GI Map is better I think at detecting parasites and H. pylori, along with reporting on specific bacteria that can trigger autoimmune conditions.
Other indicators you may have SIBO
Blood tests and stool tests can sometimes also provide clues as to whether someone has SIBO – eg. low levels of B12 or iron, elevated folate without supplementation, low levels of pancreatic elastase, elevated faecal fat (fat malabsorption), elevated levels of bacteria or short chain fatty acids on stool tests. Unexplained inflammation in the small intestine is also another possible suggestion of SIBO due to the inflammatory metabolites produced by - or contained in - some types of bacteria such as LPS (lipopolysaccharide) or endotoxin.
I’ve seen many people who tested positive for SIBO on the breath testing and also had extremely high levels of numerous bacterial species on their stool test, indicating slowed motility through the entire digestive tract. Even a high level of beneficial bacteria can be a problem because it throws everything out of balance.
A process of differential diagnosis is also important because when an individual presents with symptoms of IBS, there are around 30+ conditions or underlying causes that can cause the symptoms, not just SIBO. So you may suspect you have SIBO, when in fact it is something else.
Test result interpretation
Based on the results, I refer to the US consensus guidelines on breath tests to make a diagnosis, keeping in mind the possibility of false negatives.
My preferred labs are Aero Diagnostics and SIBOtest.com as they both adhere to stringent guidelines relating to test preparation, checking the sample for validity and have 20 minute intervals for measuring each gas. Many other labs don’t have the same level of quality. They also use clinically relevant interpretation guidelines, whereas other labs are using older information which may lead to false negative results. If you have access, the Trio Smart Breath test using both lactulose and glucose - measures all 3 gases - hydrogen, methane and hydrogen sulfide. If choosing this option, I also recommend a fructose breath test alongside it to minimise the possibility of a false negative diagnosis.
Additionally, if the SIBO was triggered by gastroenteritis, having a test for anti-vinculin and anti-CdtB antibodies - the IBS Smart test - is essential because it will tell you if you need to be on regular SIBO antimicrobial treatment every year and whether prokinetics are needed long term.
What factors influence your individualised treatment?
The exact treatment depends on a variety of factors such as:
- Root cause/s of SIBO, such as history of food poisoning, inadequate digestive secretions, hypothyroidism, ileocecal valve issues
- Symptoms being experienced – not every case of SIBO is the same. Symptomatic treatment is important to give you, the individual, some quick relief while working on reducing the bacterial load
- Which gases are involved – although there are similarities, treatment of hydrogen SIBO and methane SIBO are not completely the same. Also, if I suspect hydrogen sulphide SIBO is present, that also needs to be treated somewhat differently again. Having said that, all of these types of SIBO have a base of elevated hydrogen levels.
Overview of how I treat SIBO – what tools I use
I’ve completed courses from the SIBO Doctor (Nirala Jacobi) and also Jason Hawrelak, PhD.
My treatment strategy is based on their respective naturopathic approaches. The main goal is to eliminate or greatly reduce the SIBO without inflicting harm on the large intestine microbiome, and while also preventing relapse. SIBO is unfortunately a condition that does involve a high rate of relapse – usually because the underlying causes haven’t been adequately assessed and addressed.
I use a combination approach using the following tools:
- herbal antimicrobials, including garlic, cinnamon, berberine-containing herbs, pomegranate husk, oregano oil (sparingly), black seed oil
- other herbal medicines as needed – prokinetics, laxatives, carminatives for example
- biofilm treatment – this is used for those who have had SIBO a long time and have failed previous treatment
- prebiotics – I prefer to use PHGG (Partially Hydrolysed Guar Gum) because it has been found in research to improve the effectiveness of rifaxamin in SIBO treatment and is also excellent for the large intestine microbiome. In some cases, GOS can also be well tolerated at later stages
- targeted probiotics – while using probiotics in a condition of bacterial overgrowth may seem counter-intuitive, there is no evidence they make SIBO worse and some particular strains have effects that are beneficial for SIBO, such as for motility enhancement, constipation, reduction of methane gas, abdominal hypersensitivity, and leaky gut
- individualised diet – the ideal diet for treating SIBO is similar to the low FODMAP diet, however it goes further to remove foods that can cause fermentation that are still included on the low FODMAP diet. If you’re interested in why the low FODMAP diet often fails – I have an article all about that. There are various options for this diet including the standard SIBO diet, a low histamine variation and also a vegetarian option. There is also the option of the Elemental Diet which can eradicate SIBO in 2-3 weeks, although I usually reserve this for people who have relapsed or not seen results with the standard SIBO treatment. This is because the Elemental Diet can be psychologically taxing, can flare candida and isn’t suitable for people who are quite unwell or low in vitality. A SIBO or Low FODMAP diet shouldn’t be a long term thing, it can cause negative effects on the large intestinal microbiome the longer it is eaten.
- self-treatment to ease symptoms, including abdominal massage, breathwork
- other tools as needed to address underlying causes – eg. digestive enzymes, Betaine HCl, herbal bitters, bile support
- Vagus nerve treatments
- Referrals to physical therapists as needed – eg. abdominal massage to reduce pain, visceral manipulation for ileocecal valve issues or scar tissue
I also support clients who decide to go down the antibiotic (Rifaxamin) or Elemental Diet route because there is so much in the naturopathic toolbox that increases the efficacy of these treatment approaches.
What to expect
Treatment normally lasts for 8-12 weeks, with maintenance afterwards to prevent relapse. For those with higher gas levels, the treatment may take longer. Old habits are usually re-assessed and long term strategies are used to prevent relapse. Most people don’t need to stay on the restricted SIBO diet, they can usually re-introduce different foods.
Realistically, it can take a good 3-6 months to clear SIBO and find sustainable relief. So, don’t expect to have a few appointments and be cured!
During treatment, there can be a change in digestive function due to the change in diet and also from die-off of the bacteria, which release endotoxins which can overwhelm the liver.
In some cases, a repeat round of antimicrobials is required, especially if there’s a high level of methane - because this means both hydrogen and methane are an issue and therefore treatment will take longer.
Some people will need to undertake a course of antimicrobials twice a year if they have autoimmune damage to the Migrating Motor Complex (caused by gastroenteritis).
Remember – SIBO can be effectively treated but only if done correctly by treating the individual holistically and having a healthy mindset to deal with setbacks.
Let's work together
If you have IBS and/or SIBO, I'd love to help you recover your health. Find out how you can work with me. You can also read all about my personal experience of SIBO and the Elemental Diet.