I last wrote about testing and treating SIBO and gut microbiome dysbiosis back in 2024, so thought it was high time for an update. A couple of years ago, I learned about the framework/concept of "Oxygen Dysbiosis" from Lucy Mailing, PhD.
Since then, more researchers and practitioners have come to know and understand how this framework is a central factor in chronic gut conditions, including recurrent SIBO along with conditions related to microbiome health such as Crohn's Disease, Ulcerative Colitis, Endometriosis, NAFLD (Fatty Liver) and autoimmune conditions. Unfortunately, most treatment protocols are not factoring in this central factor, so please read on if you deal with recurrent gut issues or other gut-related conditions, as this just might be the most important article you read about it.
This year, I invested in specialised training with my well-respected Naturopath colleague Karly Raven, so that I could further understand this framework and develop a more formalised, strategic treatment approach for clients with stubborn and complex gut and health issues.
With that in mind, I wanted to update the content on my website so that prospective clients can gain an insight into how I work. I know from my own personal experience that it pays to research how practitioners work before investing time, money and emotional energy working together.
SIBO breath testing
One of the most important things to understand about SIBO is that people with SIBO almost always also have large intestine/colonic dysbiosis as well as SIBO. SIBO doesn't occur in a vacuum. In fact, many people working in this field believe that many cases of SIBO originate in the large intestine - dysbiotic bacteria migrate upwards into the small intestine. If motility, the ileocecal valve and/or the migrating motor complex aren't working properly - the bacteria in the small intestine aren't correctly swept out and a buildup occurs.
All pathology tests have their pro's and con's, and so it is with SIBO breath testing.
The tests can be misleading and not always reliable - for example, glucose only detects SIBO quite high up in the small intestine (not common) and lactulose cannot ferment some of the species typically found in SIBO, so it can produce false negative results. Lactulose also speeds up transit time, so it can influence how the results are interpreted.
Based on information from esteemed Naturopath Dr Jason Hawrelak (PhD), fructose is the preferred test I use, however lactulose may be better at picking up IMO (Intestinal Methanogen Overgrowth) than fructose. So it really depends what we suspect and then choosing the appropriate substrate (sugar) to test with.
As such, I am using breath testing less and less as my clinical knowledge and experience advances. I'd much rather that people spend their budget on a high-quality stool test - such as Microba - since the information is much more detailed than what is available from a breath test.
I've come to the conclusion that it's better to use clinical skills and questionnaires to ascertain if SIBO is present. Also - as mentioned previously, most cases of SIBO also have large intestine dysbiosis, which will show up on the stool test. This ties in neatly with treatment - naturopathic and nutritional treatment of SIBO is far superior to medical treatment because naturopathic treatments address dysbiosis in both areas concurrently, whereas medical treatment such as rifaxamin is ONLY able to address small intestine dysbiosis. Medical treatment of dysbiosis also tends to be superficial and many doctors don't really believe in SIBO or dysbiosis as it is.
The main exception to my preference not to use breath testing is where a client has chronic constipation and their stool test isn't indicating an overgrowth of methane-producing species - I've covered this in a video previously. My colleagues and I have observed cases where methanogens are not detected on an individual's stool test, but the breath test shows a high level of methane. So, if only the stool test is used, then the methane dysbiosis will often remain undetected. The stool test is not faulty, it's because the level of methanogens may be below the detectable limit in the faecal sample or most of the methanogens are inhabiting the small intestine rather than the large intestine (and therefore may not be found in the faecal sample).
SIBO and Dysbiosis Treatment
The key point to understand here is that the natural regulatory systems of the gut environment regulation have failed - that is the core tenet of the Oxygen Dysbiosis framework. The dysbiosis will always return if this regulation is not rebuilt from the ground up. Dysbiosis is a result of the dysregulated gut environment, not a root cause.
Treatment is therefore all about the environment and the health of the colonocytes, which governs their ability to utilise butyrate. Supporting the colonocytes so they can utilise butyrate again is essential. Note, this is not about a butyrate production issue - rather, this is due to the colonocytes' mitochondria not working properly, for various reasons. Taking a butyrate supplement often doesn't work because the colonocytes cannot do anything with it. This failure leads to a buildup of oxygen in the environment, which then creates the right conditions for dysbiotic bacteria to take hold - these dysbiotic bacteria are usually in the Proteobacteria and Bacteroidetes families. Bacteria in these families are also the type typically detected in SIBO. Our colonic environment should have very low levels of oxygen, as opposed to other areas of the body. The colonocytes are responsible for consuming this oxygen, among many other roles.
Since they are too broad-spectrum and harsh, I do not use oregano oil, Grapefruit Seed Extract (GSE) and I minimise use of berberine-containing herbs - occasionally, there may be exceptions to the latter. Instead, I use more selective antimicrobials. Otherwise, you may as well be using pharmaceutical antibiotics in terms of causing damage to your microbiome and gut environment. Remember, just because something is "natural" doesn't make it safe. Antimicrobials are also not always appropriate to use straight away in the treatment process, even if they are the more selective type such as pomegranate.
I was previously in support of clients who wanted to use rifaxamin for SIBO treatment, however I now don't recommend it since dysbiosis is almost always present in both small and large intestines. Rifaxamin only works in the small intestine, it will not help the large intestine dysbiosis. Just another reason that well-designed Naturopathic treatment for dysbiosis is the superior choice to pharmeuticals.
I'm also a big believer in using free and low-cost interventions- don't sleep on these! I know that supplements are highly marketed and may be considered sexy or trendy, but many people make great strides with their health by investing their time and energy into the foundations such as nutrition, sleep, purpose, time in nature, community and connections.
As mentioned in the previous section of this article, Naturopathic treatment has a unique, unmatched benefit in that when we are treating SIBO, we are also treating the dysbiosis in the colon - as long as the Oxygen Dysbiosis framework is centred in the treatment. Another thing to keep in mind is that our treatments inherently benefit multiple body systems or processes, unlike most pharmaceuticals. For example, the herb Magnolia is indicated for slow motility and it's also wonderful for the nervous system. So, one herb can address multiple treatment objectives at once.
Treatment therefore centres around the following foundational steps:
- Re-building the gut environment - so the gut can regulate itself to prevent recurrence
- Nervous system work
- Improving motility
- Reducing inflammation and food reactions
- Improving general health with foundational steps
Where does diet fit in?
Diet is a super interesting consideration in all things SIBO and dybsiosis.
There are a number of diets marketed to people with SIBO, dysbiosis and IBS. You've most likely heard of the low FODMAP diet - there's also the SIBO diet, Fast Tract, carnivore and keto diets that are used for these conditions. It's essential to understand that these diets are helpful for symptom relief, but that's all - they won't cure your condition and you do need to be mindful when considering starting one or staying on one.
The key thing to remember with these diets is that they are all restrictive and there should always be a time limit for how long an individual follows them. We know from research that a low FODMAP diet can reduce microbiome diversity over time. If I have a client on the low FODMAP diet, I always ensure we include microbiome-nourishing foods that fit within that dietary framework.
Research also indicates that gut-hypnotherapy interventions including the Nerva app are just as effective as the low FODMAP diet.
When I'm working with a client with a history of disordered eating or who is feeling burnt out from restrictive diets, I always help them find a middle ground with the dietary approach. Finding a diet that reduces symptoms but isn't too restrictive is the best option in this situation. Or, doing away with a special diet altogether is sometimes the right approach.
Testing
The only stool test methodology I recommend is shotgun metagenomic as it gives the most detail in the results and is also the most accurate technology, versus PCR or 16S. For Australian and UK clients, I use Microba and for the US either Tiny Health or Nirvana Biome. In some cases, I may use the Genova Microbiomix test. For breath testing, I use SIBO Test in Australia and Aerodiagnostics for US clients. For clients in other countries, I work with my client to choose the most accurate test they can access.
Work with Me
SIBO and dysbiosis can wreak havoc on your health. Work with me - I'd love to help you on your journey back to the life you love.
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