How I'm testing and treating SIBO and dysbiosis in 2024

The “kill kill kill” SIBO and dysbiosis treatment paradigm is dead - pun intended - or at least it should be.

I feel like 2023 was truly a watershed year for me in terms of how I view the whole gut health space and SIBO in particular. Many of my clients have already done treatment for SIBO before they see me, and yet were still struggling. Many are also highly reactive to the typical treatment such as rifaxamin or herbal antimicrobials. I always want to know why this is, so that the treatment I give them can be more effective and safer. One of my mottos that I came to the hard way is "don't create new problems trying to fix existing ones".

Along with my 1:1 work with clients, I spent a lot of time doing more in-depth research to challenge my own pre-existing views of SIBO. Having had SIBO myself, I feel like I know the challenges of SIBO intimately and understand the impact it has on my clients. I also know that it’s a condition considered to have a high rate of relapse, so I feel we can all be doing better in treating it. Not using cookie-cutter approaches and always challenging our accepted views when new evidence comes to us is important. Most clients I see also only have a partial diagnosis - I’m always picking up on things that have been missed for whatever reason.

I’ve been heavily influenced by many practitioners and researchers such as Jason Hawrelak, Nirala Jacobi, Steven Sandberg-Lewis, Mark Pimentel, Lucy Mailing, Nikki Di Nezza. I enjoy learning from a wide variety of people - those who are more academically focused, those who are naturopathic clinicians and also medical doctors. I truly believe we can learn from a wide range of people regardless of where they fit in the healthcare world.

Changes in how we view SIBO

One of the biggest shifts has been in moving away from a strict/outdated view that SIBO is an overgrowth - the terminology “SIBO” or “small intestinal bacterial overgrowth” is confusing. Mark Pimentel’s work with his research group has characterised the small intestine microbiome (from 34 minutes) in those with SIBO and it’s clear that it is dysbiotic, with a high level of pro-inflammatory Proteobacteria species present, especially E.coli and Klebsiella. So, it’s not a generalised overgrowth of every species, it’s an overgrowth of particular species and a lack of protective/health-promoting species. Many of the health-promoting species actually produce their own natural antibiotic substances and also provide other benefits that can keep IBS and dysbiosis symptoms at bay.

Having said all that, some people do genuinely have challenges in keeping their bacteria levels in the small intestine under control which can lead to overgrowth. This is often due to motility issues such as migrating motor complex impairment (which may happen due to issues with the nervous system or after food poisoning), connective tissue conditions such as Ehlers Danlos syndrome or PPI use.

It’s crucial to consider that the microbiome is part of a bigger context which is the gut environment itself and - zooming out even further - the organism, that’s you! So, addressing the bigger picture is incredibly important because the microbiome doesn’t exist in a vacuum - there is an essential symbiotic relationship between the microbiome and the person it resides in. The microbiome provides benefits to us and we provide benefits to the species that make up our microbiome.

In this regard, I have been strongly influenced by concepts introduced to me by Lucy Mailing, PhD. Lucy is an independent researcher and consultant who has both the academic background in microbiome science and the lived experience of working on her gut health to significantly improve her eczema. The concept of “oxygen dysbiosis” was relatively new to me, and I spent plenty of time in 2023 doing a deep dive into her free and paid content to understand how this could help me improve my work with clients. This concept presents the idea that many cases of dysbiosis are due to a dysfunction of the overall gut environment following one or more insults such as antibiotics, psychosocial stress, alcohol or poor diet - or a combination of these. The resulting environmental dysfunction is then the key driver behind significant dysbiosis and without strategic interventions aimed at addressing this dysfunction, the dysbiosis - whether SIBO or large intestinal dybiosis - will never be resolved even with dietary changes, antimicrobials and prebiotics. This matches with my observations of people who spend years and years trying to fix their gut health to no avail. I’m also confident it explains the subset of SIBO clients who are ultra-sensitive to pharmaceutical and herbal antimicrobials - not to mention that too many protocols are using overly strong, broad-spectrum treatments such as Flagyl (metronidazole), oregano and potentially berberine. I’ve lost count of the number of clients I’ve had whose pre-existing gut symptoms worsened significantly on these treatments. We have many people lacking appropriate training in herbal medicine who are prescribing these.

So, my approach now is to address the gut environment dysfunction as a priority while also working more directly on the microbiome. I avoid using the stronger, broad-spectrum antimicrobials in the majority of cases and have a strong focus on nurturing the environment and the individual to restore eubiosis - which is a healthy microbiome. I really feel the oxygen dysbiosis/gut-environment-dysfunction concept is key to recovery for tough cases

Oxygen dysbiosis as a "gut injury"

I've started describing the oxygen dysbiosis scenario as a "gut injury" because I feel it's the best way for people to understand what has happened to them. In most of my client cases, they have an extensive antibiotic history, sometimes dating back to childhood. Clients describe being given antibiotics for "every little sniffle" as children or they were put on antibiotics for 3 years for acne and then had further gut insults such as food poisoning, alcohol overuse, even more antibiotics - eg. if they are "diagnosed" with a Blastocystis hominis "infection" - and ongoing chronic stress.

Viewing the dysbiosis as an injury helps clients to understand it's not just the microbiome itself that is impaired - the overall gut environment is injured. The larger historical context is that the current generations of people are the first ones dealing with antibiotic over-use and resultant gut injuries. Antibiotics have only been in common usage for 50 or so years - a drop in the ocean compared to how long humans have been on Earth! So, we are actively working on a relatively new health/illness phenomenon and still developing and learning the best ways to treat it. There is a lot we do know about how to treat dysbiosis, but we still have a lot to learn. This is why there are still so many mixed opinions out there about how to treat this problem. We know that it can take 20+ years for new knowledge from research studies to filter down to clinical practice. DNA-based stool testing - the best we have available - is also relatively new to the wider public and we are going to get some things wrong with our understanding of the microbiome. Accepting all of this is really important, accepting that we don't have 100% control over every aspect of our health is paramount to maintaining good mental health and being sustainable and consistent with taking positive steps forward.

Now, since we are referring to this as a "gut injury", naturally this means there is rehab involved with various steps. Think of Matilda player Sam Kerr with her devastating ACL injury. It's going to take her 9-12 months of rehab to get back on the field, with improvements along the way. I usually work with clients for around a year or more because this is how long it takes to address the various layers of health that need addressing. We know with SIBO and dysbiosis that many secondary issues arise such as nutrient deficiencies and autoimmunity. The drivers behind the dysfunction also need to be addressed - all of this takes time. Most of my clients feel 30% better within a few months and then significantly improved around 12 months. Avoiding rigid expectations around timeframes is important however, because for most people, different things in their life may come up that temporarily require more attention such as family matters, housing and work for example. In some cases, I work with clients for a longer period and there is often an element of ongoing maintenance that they need to follow to stay on top of their health. The goal is to get people back to significantly better health, while also being realistic about the possibility of some form of long-term management. In all cases, it's important to me to make the treatment manageable at all stages - I have learnt so much in the last 2-3 years especially about paying attention to individual requirements and keeping the communication flowing. However my clients can look after their mental health on this journey is also imperative.

Breath testing and Stool testing

I am slowly moving away from breath testing for a few reasons. One is the cost - I feel it’s a better idea to channel more funds towards treatment or for a stool test which will give greater detail about the type of dysbiosis present. Breath testing can be problematic, which I will explain below. Taking a good case history along with symptom evaluation is usually the best way to assess for SIBO. Having said that, if a client wants testing or maybe their doctor has already ordered it, I will help to order/interpret results.

If breath testing is preferred, then I recommend fructose testing over lactulose. Lactulose speeds up gut transit time, so a rise of over 20ppm in the gas result before the 90 minute mark could actually be reflective of a normal healthy response to lactulose by the bacteria in the large intestine - remember there is supposed to be a much higher number of bacteria in the large intestine. Also, the bacteria in many people’s microbiomes may not consume lactulose, which can lead to a false negative. Jason Hawrelak has spoken at length about the preference for fructose testing.  I don’t recommend glucose testing as most people test negative since glucose testing can only detect SIBO quite high up in the small intestine, which is much less common - I confirmed this with SIBO Test, one of the largest breath test providers in Australia.

In cases of very limited budget, a DIY fructose test can easily be performed at home with an emphasis on symptom observation. Or if a fructose test is not available where you live, but you still want to see the actual hydrogen and methane numbers, you can swap out the lactulose or glucose that comes with your kit for 25g of fructose powder mixed into water - this can be purchased online.

In all cases, I recommend doing the prep diet for 48 hours rather than 24, because many people have slow transit time - even without typical constipation. This is the best way to get a baseline gas level as close to zero as possible, which helps to more clearly show us the gas rise after the baseline measurement.

If budget is limited but you can afford some testing, my recommendation is to invest in a high-quality stool test rather than breath testing. The combination of taking a good clinical history and stool testing will make it clear if dysbiosis is present. The stool tests I recommend most often are the ones that combine microbiome reporting with digestive markers because for most of my clients, they really do benefit from investigating both these aspects of gut health. However - and there is always a "however" in gut health - the microbiome in the large intestine is different to that of the small intestine, so a stool test won't be reflective of the species you have in the small intestine. It's still useful though for detecting overall problematic patterns such as excess bacteria in the Proteobacteria phylum, lack of diversity and a lack of butyrate-producing species.

As for follow-up breath testing, I prefer that clients focus on how they feel rather than going back to do more testing. In general, we need to nurture the ability to tap into how we are feeling rather than just look at numbers. Of course, for clients that would really prefer to re-test a breath test, I am happy to support that choice.  For stool tests I do recommend follow-up testing to check in on how the overall microbiome restorative work is progressing since there is more granular detail in a stool test compared to a breath test and we want to check that the diversity is improving alongside reductions in inflammatory bacteria and increases in health-promoting bacteria.

Recommended stool tests

For Australian clients, I recommend Co-Biome from Microba, specifically the option that measures both the microbiome and the digestive markers - Meta Explore GI Plus.

I recently did an Instagram Live talking about why this is my stool test of choice and taking you through my own results. Check it out below:

View this post on Instagram

A post shared by Allison Jones Naturopath (@allisonjones_electricvitality)

For those in the US, a good combination is Thorne/Cosmos ID (Shotgun metagenomics technology) or Biomesight (16S technology) along with Genova GI effects - the two former tests look at the microbiome and the Genova test provides digestive markers. Or, if you’re working with a gastroenterologist, some - not all - of the digestive markers that are on the GI Effects can be ordered by them such as calprotectin and elastase.

In Europe, MyBiome from Synlab uses metagenomics or Biomesight uses 16S, which is a more affordable option.

MyBiome is also available in Colombia and Egypt.

Medivere (Germany) uses 16S and also reports on digestive markers, however it’s unclear as to the accuracy of those markers. We know that some functional labs may have accuracy issues with their digestive health markers - specifically GI Map (which I do not recommend).

Treatment

With the above in mind, below is a summary of how I currently treat clients with SIBO or dysbiosis.

A key understanding from my work with clients is that most people with SIBO also have dysbiosis in the large intestine, so any treatment for SIBO should also address the large intestine. Rifaxamin - the antibiotic of choice for SIBO - is pretty safe, but it doesn’t do anything for the large intestine microbiome because it only acts in the small intestine. Also, the studies looking at rifaxamin for SIBO suggest 50% of people are non-responders and there’s also a high rate of relapse after treatment. Also, rifaxamin does not address SIFO which may be present (fungal overgrowth). Most likely, this is because in the medical setting, the drivers causing the SIBO are almost never addressed - the treatment tends to be very superficial and never individualised.

• It goes without saying that treating the underlying drivers/causes for someone’s SIBO or dysbiosis is essential. Whether it’s poor digestive secretions - which are antimicrobial themselves - a sluggish thyroid, ileocecal valve dysfunction or food poisoning which affects the MMC (migrating motor complex - the cleansing waves that clear out bacteria from the small intestine between meals)
• Incorporating the ideas on how to treat "oxygen dysbiosis" from Lucy Mailing's free and paid content is already proving very effective with my clients
• Treatment is always individualised depending on whether the SIBO is characterised by hydrogen, methane or hydrogen sulfide (or a combination).
• Herbs, probiotics, prebiotics, diet and lifestyle enhancements are still key features of my treatments. Regarding herbs, I am moving away from oregano because there is increasing evidence this is too broad spectrum and can do harm which I have personally seen evidence of on before and after stool testing. The jury is still out at the moment regarding the use of berberine-containing herbs, as some research suggests it can reduce diversity, however the treatment length was longer than what naturopaths would typically use for SIBO and dysbiosis.
• Other additions may include: prokinetics, occasional use of biofilm busters (most herbs used for dysbiosis already have anti-biofilm activity)
• Nervous system support and mental health support is a cornerstone of my work with clients - we know there is a significant bi-directional relationship between the gut and the brain and most people dealing with chronic health challenges have experienced significant effects on their mental health which can influence results.

The role of diet in SIBO treatment

I mostly view diet for SIBO as one of inclusion rather than exclusion where possible. Taking into account every individual’s personal background, their type of dysbiosis and other factors, I will decide alongside them what dietary approach is best. If a client comes to me with a background of disordered eating, limited ability to prepare food or high stress levels associated with their diet - for example from following restrictive diets trying to fix their health - I am very cautious about using a SIBO diet or low FODMAP diet. In all cases, these diets should be used cautiously and for a set period of time with food re-introduction a key part of the plan. In all cases, I provide clients with the required resources and support they need to follow the dietary advice I give them.

SIBO diets or the low FODMAP diet are often very helpful for rapid symptom reduction which can give people breathing space from their symptoms and confidence to keep the momentum going. But following these diets should not come at the expense of someone’s mental or physical health - we know the microbiome can be negatively affected the longer someone is on the low FODMAP diet. The exclusion aspect of diets will not cure SIBO or dysbiosis, it’s purely for symptom relief - which is often incredibly helpful if it's managed well. A low FODMAP diet done well, with a well-managed re-introduction phase ends up helping people re-introduce more foods successfully and sooner. Esteemed practitioners like Dr Jason Hawrelak and Dr Mark Pimentel don’t often use a low FODMAP diet - Dr Pimentel for example has argued in the past that keeping the bacteria “well fed” on a regular diet makes it easier to kill them. I hope you can understand from this paragraph that the choice of diet is very individual and dependent on various factors.

Taking the view that SIBO is a form of dysbiosis has reinforced for me the importance of supporting the growth of the more beneficial bacteria. It’s these bacteria that produce beneficial metabolites such as IPA and short chain fatty acids - such as butyrate - and provide key benefits for our health. A key part of this approach is to use microbiome-friendly foods. 

The challenge is that the higher FODMAP foods that people often react to are actually the foods that benefit the microbiome! With this in mind, food re-introductions are important because most people will not react negatively to ALL the FODMAPS and the amount of a food is a key indicator of whether it will be tolerated or not. 

We know that the longer a restrictive diet such as low FODMAP is followed, the greater the negative impact on the microbiome - not to mention the potential effects on mental health.This is why regular consultations are so important, to ensure the right steps are taken at the right time and oversight is maintained. For some clients, they have other food intolerances besides the FODMAPs, so if they are to minimise FODMAPs in addition to their specific food intolerances, it’s a recipe for despair.

I am moving away from using the Elemental Diet in most cases as I find it can worsen symptoms in sensitive clients - IBS-D and IBS-M mostly - and should only be used for those whose health is relatively robust and who can also lighten up their schedule for the duration. Also, there is still work that needs to be done to restore the microbiome afterwards anyway so it’s not a magic fix. Having said that, if someone's methane levels are quite high - it means there is a ton of hydrogen production in the background - and the Elemental Diet may be helpful in more quickly knocking down the level of gas. Another possibility is to do a semi- or partial Elemental Diet, where the ED formula is consumed along with low fermentation and/or pro-microbiome foods.

A non-diet approach that is often very helpful is the Nerva hypnotherapy app which has been shown to be as effective as the low FODMAP diet. In some cases, in person gut-directed hypnotherapy is more powerful.

*For those who don’t experience much symptom relief from a SIBO or low FODMAP diet, usually there are other food intolerances at play or factors such as fat malabsorption. Sometimes we don’t know everything that’s going on immediately and it can take a bit of trial and error for the answers to arise.

Biggest mistakes I see being made with SIBO treatment

• Rushing the overall process - jumping in with antimicrobials first before considering the overall gut environment and the factors that have created the dysbiosis. Working on the relationship to symptoms and nurturing healthy coping mechanisms can really help avoid the rush.
• Placing too much emphasis on “kill, kill, kill” without enough on feeding the microbiome - this includes using really strong herbal antimicrobials
• Not addressing the overall gut environment
• Neglecting the nervous system and emotional health - I've never come across anyone whose mental and emotional health hasn't been somewhat affected by their digestive health challenges and we know how important the gut-brain axis is for good health.

Do you need help with natural treatment for SIBO?

If you have IBS and/or SIBO, I'd love to help you recover your health. Find out how you can work with me.

I have completed training with SIBO Doctor - Nirala Jacobi - and have completed courses presented by Jason Hawrelak. I also keep up to date with the latest research in SIBO, IBS and dysbiosis.