Natural SIBO Treatment Protocols That Actually Work

SIBO is infamously difficult to kill and even more difficult to keep that way. This is because attacking a small intestinal bacterial overgrowth with anything less than a really comprehensive natural treatment protocol, that is more than just diet or antibiotics, is essential for long-term healing. Natural SIBO treatment protocols that rely on single herbal products just don’t seem to cut it. And secondly, because SIBO is often the consequence of some other dysfunction or imbalance within the body, if this is not resolved following SIBO eradication, it can increase your risk of relapse and the need for further SIBO treatment. Layer over the top of these challenges the huge variety of symptoms seen amongst SIBO sufferers, which means that intervention needs to be tailored specifically to the individual, and you start to understand why natural SIBO treatment really is the domain of practitioners specialising in this condition.

With that in mind, I wrote this blog post series to help you understand the latest research and intervention options available. The science of natural SIBO treatment is ever-changing as new research sheds light on the most effective options we have around. This basically means that what we do today is completely different to what I was doing (and what you might read on old blog posts and forums) to treat SIBO two years ago. So, where to start with the most cutting edge, all natural SIBO treatment and herbal options? I’ve divided this ‘treatment’ post up into the four phases I use with my SIBO clients.

Here is a summary of what we are going to cover in Part 3:
> How to make changes to your diet that reduce your SIBO symptoms fast
> The three most effective ways to remove a SIBO overgrowth
> Natural herbal SIBO treatment considerations
> Why supporting digestion and detoxification while eradicating SIBO is essential
> When to introduce probiotics for SIBO and how to avoid aggravating your symptoms
> The importance of addressing the root cause of SIBO and why relapse is so common

Refresh on SIBO symptoms and SIBO testing

SIBO Symptoms

If you’re looking for a recap on the basics of SIBO, read this post: Is SIBO The Hidden Cause of Your IBS?
> What is SIBO and how it can ruin your health
> Why it’s important to know which ‘type’ of SIBO you have
> Symptoms to look out for and why SIBO is often the cause of IBS
> The most common underlying root causes of SIBO?

SIBO Testing

If you’re looking for a recap on SIBO testing, read this post: The Science (and Art) of SIBO Testing
> The ‘gold-standard’ SIBO test you need to ask your practitioner about
> Why a negative test result doesn’t always mean you don’t have SIBO
> Why SIBO testing and SIBO retesting is so important
> Other GI testing you should consider



If you have raging SIBO symptoms and/or have just received a positive SIBO diagnosis, the very first thing you want to do is get your symptoms under control. The fastest way to do this is through diet. And while diet is a great short-term symptom management tool, it’s important to keep in mind that diet alone will not heal a bacterial overgrowth in the small intestine. Starving the bacteria of their fuel source helps, but if you continue with such a restricted diet for a long period of time, you also risk starving the bacteria in your large intestine (your microbiome) that play a vital role in your health and with keeping SIBO at bay (1, 2).

Feed the bacteria or starve them?

Let’s get into some of the dietary options you might have heard about so you can understand how they work. There are two distinct theories about how to approach SIBO treatment so I will mention them both. The first is to actually eat fermentable carbohydrates during treatment to feed the overgrown bacteria, meaning you will likely be highly symptomatic - bloating, gas, constipation, diarrhoea, etc, will be running rampant through your day. This is based on the assumption that happy and well-fed bacteria are more sensitive to antibiotics and are easier to kill, and that when starved, bacteria go into a sort of ‘survival mode’ where they do not replicate and are therefore harder to penetrate with antimicrobials (3). This approach may work better if you are opting for a short-course of antibiotics (7-14 days), but will be less relevant on 30-60 days of natural antimicrobials - after all, the bacteria can only hide or hibernate for so long. And as we have said, eating lots of fermentable carbohydrates can really aggravate your symptoms and make life more difficult than it needs to be.


My approach to SIBO diets

For this reason and because my clients tend to prefer using natural antimicrobials to antibiotics, I like to adhere to the second theory. My clinical approach to diet in both this initial phase, and during phase two, is to focus on reducing symptoms caused by the bacterial overgrowth. We do this by reducing the main food source that the overgrowth feeds on - fermentable carbohydrates.

This means that most carbs in your diet are going to cause some level of bloating, gas, diarrhoea or constipation, etc, if you have SIBO. These include:
> Starch - grains, beans, high starch vegetables
> Resistant starch - whole grains, seeds, legumes
> Soluble fibre - grains, beans, nuts, seeds, vegetables, fruit
> Sugar - fruit, dairy, sweeteners
> Prebiotics - beans, vegetables, roots, herbs, prebiotic supplements

Proteins and fats are your friend at this point and make up the majority of the diet designed to limit SIBO symptoms. Two diet options that are low in fermentable carbohydrates that I like to use with my clients are SCD/low-FODMAP and AIP/low-FODMAP. For those who are very sensitive to oxalates, histamines, amines, salicylates, sulphur or other food components, or who have food sensitivities, I will layer this over the top.

Diet is very individual and you can achieve dramatic improvements in symptoms in a short time-period if you figure out what works best for you. I should also make a note here that this type of diet seems to work equally well for the hydrogen-producing bacteria type of SIBO as it does for the methane-producing archaea type of SIBO. This is because as you starve off the hydrogen-producing bacteria by limiting carbs, you are also limiting the hydrogen gas used as fuel by the archaea to produce methane.


Tips to reduce inflammation and promote gut healing

Another thing to note about the diets I choose to work with is that by limiting carbohydrates, we are also limiting inflammation-causing anti-nutrients that are commonly found in grains, legumes, nuts and seeds. While normally tolerated, these foods can be problematic for anyone with a compromised digestive system. By avoiding them in the short-term, we are also helping to reduce gut inflammation. Here are a few tips I give my clients starting Phase 1:
> Aim for 70% cooked and 30% raw foods. Cooking vegetables and fruit will lower the fibre and resistant starch content making them less likely to cause you symptoms.
> Ensure fruit is ripe, as under-ripe fruit is high in resistant starch which can cause symptoms.
> Limit snacking between meals (4-5 hours) to give the migrating motor complex (MMC) a chance to move bacteria and food remnants from the small intestine to the large intestine ready for excretion from the body.
> There are other food sources such as alcohol, caffeine and artificial sweeteners that can compromise healing by providing fuel for the bacterial overgrowth. This is why I ask my clients to limit them during SIBO treatment.
> Fermented foods; at this stage of healing, I ask my clients to avoid all of the beneficial fermented foods like sauerkraut, kombucha, kefir, etc, as they are the perfect fuel for bacteria and will generally aggravate symptoms.



With diet keeping symptoms under control, the next step is to remove the overgrowth. There are three main options here; natural antimicrobials, antibiotics and the elemental diet. Because of SIBO’s notorious stubbornness, for many clients their treatment will involve a combination of two or even three of these approaches over successive protocols. Each has its strengths and weaknesses and are more or less suited to different clients - there is no one ‘magic protocol’ for all SIBO cases. With that in mind, I’ll discuss each one in the order they are most commonly used. 

Natural herbal antibiotics for SIBO - my preferred SIBO treatment approach

My preferred approach involves all-natural eradication protocols using natural herbal antimicrobials for SIBO. Not only do I find them less aggressive, they have also been shown to be at least as effective as antibiotics in clinical trials (4). Two important principles to keep in mind with antimicrobials are: 1) Combine to kill - there are varying types of bacteria and archaea that can cause SIBO and not all antimicrobials can kill off all types. The best way to overcome this is through the use of blends and combinations for maximum effectiveness. 2) Rotate to avoid resistance - bacteria are smart and will adapt quite quickly. While not as common as antibiotic resistance, the effectiveness of a given herb tends to diminish with successive rounds.

Most protocols last around 30-60 days per cycle and vary by the type of SIBO you have. As a general rule, I like to use berberine, neem and oil of oregano for hydrogen-dominant SIBO and allicin, oil of oregano and neem for methane-dominant SIBO. Other great herbs to consider are cinnamon, thyme and pomegranate which also works really well for those with Candida or Blastocystis hominis. You can access some great blends such as Candibactin AR and BR and Biocidin that have multiple herbs in them. I like to use these when a client has parasites, bacteria or yeast in their large intestine, in addition to SIBO.

Another benefit of using antimicrobials means we can use blends that address other issues indirectly, such as SIFO (Small Intestinal Fungal Overgrowth), a very common comorbidity for SIBO sufferers, affecting around half of SIBO cases (5).


Where do conventional antibiotics for SIBO fit in?

Antibiotic SIBO treatment protocols have evolved substantially over the last decade and now offer a genuine second line treatment or alternative to natural antimicrobials. A move away from broad-spectrum antibiotics to variations that are non-absorbable and small intestine-specific have increased effectiveness and reduced systemic side effects, such as urinary tract infections.

Rifaximin (Xifaxan) is currently the most commonly used antibiotic for SIBO treatment and has reported success rates of around 50% for those with hydrogen-dominant SIBO (6). While less effective for methane-dominant SIBO, one study has reported success rates as high as 85% using a combination of Rifaximin and another antibiotic called Neomycin (7). Relapse rates of around 50% at nine months (8) mean that even after initially successful treatment, it’s important to be vigilant with symptoms, heal the gut and focus on fixing the underlying root cause (phases 3 and 4). Because of issues with resistance after repeated rounds (9) and for those not able to clear SIBO with antibiotics, natural antimicrobials have reported clearance rates over 50% in those who fail on Rifaximin (4).


SIBO Elemental Diet - when all else fails

For clients who have completed multiple rounds of antimicrobials (or antibiotics) without success, the SIBO Elemental Diet is another standalone option available with strong clinical evidence (10). It basically involves drinking powdered, predigested nutrients that are mixed with water and removing all solid foods from your diet for 2-3 weeks. Because the nutrients in this form are absorbed so rapidly, the bacteria do not have a chance to feed on them and use them as fuel. The idea is to completely starve the bacteria of nutrients in a more extreme way to an SCD + low-FODMAP style diet.

I like to use the SIBO elemental diet as a last-resort option as avoiding real food isn’t exactly natural and often more than two weeks is required. It can be challenging due to the horrid taste, as well as SIBO die off symptoms potentially being more severe than when you are treating using herbal antibiotics.

The product I currently use is Physicians’ Elemental Diet by Integrative Therapeutics, which contains a balanced blend of macronutrients, essential vitamins, minerals, and electrolytes to act as a sole source of nutritional intake for a two to three week period. However, given that each large bag only provides 3-4 days worth of meals (depending on your caloric needs), it can get quite expensive if you aren’t getting it at wholesale prices through your practitioner.


Treating SIBO Biofilm 

An estimated 75% of bacterial infections, and possibly higher in archaeal and fungal infections, involve biofilms (11, 12, 13). Biofilms are colonies of microorganisms that are protected by an extracellular matrix - which we think of simplistically as a protective home for the infection to live in. This protective home makes the infection up to 1000 times more resistant to antibiotic therapies and therefore, more difficult to kill (11, 14). This is why a comprehensive treatment protocol should include the use of a SIBO biofilm disruptor.

Busting up the biofilm whilst using antimicrobials can be achieved by incorporating specific herbal products. I like to use a blend called Biofilm Defence by Kirkman Labs or InterPhase Plus by Klaire Labs as both are well tolerated by my clients and contain the right enzymes that break down biofilms.



Digestion support considerations

Whilst taking antimicrobials during this phase, it is also important to support digestion and absorption of the nutrients you eat. We do this because an overgrowth in the small intestine will block the intestinal lining where absorption of the nutrients in the foods we eat happens (15). This means taking supplements like digestive enzymes that help you break down and absorb the foods you eat; stomach acid support from betaine HCL to help with killing off any bad bacteria that is contaminating the foods you eat; and nutritional support in the form of anti-inflammatory fish oil capsules, hydrolysed fish protein for easily absorbed amino acids and multi-minerals supplements if needed.


Detoxing is a MUST

The next thing we need to focus on in this phase is supporting the body with detoxification. During die-off of the bacterial overgrowth, there is a buildup of toxins in the body that needs to be removed. This places excess stress on the liver, our main detoxification organ, so I have my clients support their liver using a herbal blend supplement. I also ask them to use a charcoal and bentonite clay product for a few days each fortnight, when they are actively killing off the overgrowth, to help with removal of the toxins and debris from the gastrointestinal tract. We’ve written a whole blog post on Die-Off Symptoms and Managing Detox HERE.


Constipation and toxicity

Constipation, which is a very debilitating symptom for those with methane-producing archaea, must be dealt with as an absolute priority (16). If there is especially-toxic bacteria and archaea-filled waste being stored in the colon for extended periods of time, the body can reabsorb these toxins. This is particularly important for those who experience more severe SIBO die off symptoms. We must keep the colon clear so I encourage clients to take magnesium and vitamin C daily, as well as complete a vitamin C flush weekly. If you want more information about how to clear constipation, please CLICK HERE to receive my FREE Constipation Clear-out eguide.

Finally, at the end of each round of antimicrobials or after completing the elemental diet, it is essential that we re-test.



With the SIBO overgrowth eradicated, the focus shifts to repopulating the gut with the right balance of flora and healing the gut lining to support long term health and prevent a relapse.

Probiotics for SIBO - yes or no?

Unfortunately, it’s much more complicated than that. It’s about what type of SIBO you have, with your symptoms and client history, which strains of probiotics you have tried, how much and at what point in your SIBO treatment to introduce them. It is one of the many reasons that DIY treatment and off-the-shelf protocols don’t often work for SIBO sufferers… there are just too many variables and a constant need to review and refine treatment.

While not all clinicians agree, the science published so far is pretty clear; probiotic supplements are an effective SIBO treatment both as a stand alone (17) and as a follow-up to SIBO herbal antibiotics (6). The three most beneficial strains of SIBO probiotics to look out for are bifidus infantis, bifidus lactis, and lactobacillus plantarum. These can be taken individually, or in combination. As with all supplements, titrate (introduce) them slowly and build up to a level that you tolerate. More is not always best when re-populating the small intestine.

An alternative school of thought is a concern with adding bacteria in the form of SIBO probiotic supplements to an overgrowth of bacteria that’s already there. And there are some clients whose symptoms are obviously aggravated by SIBO probiotic supplements. For these clients, it can be a bit of (frustrating) trial and error - you may need to try different strains or combinations to find the one that works for you. But in my experience, probiotics are not a make or break part of natural SIBO treatment and for clients who do not tolerate probiotic supplements during eradication, I usually focus on introducing them in this phase.

After SIBO treatment is finished, we titrate the above mentioned strains in supplement form at a very gradual pace. This often means breaking open a capsule and sprinkling out a small amount before building up to more standard dosages.

A note of caution: it’s probably best to avoid your general store bought probiotics for SIBO as many of them contain ingredients that will aggravate your symptoms, including; D-lactate-forming species like Lactobacillus acidophilus, or tapioca and potato starch, maltodextrin, lactose, inulin, pectin as well as other prebiotics that may cause issues.

Probiotic rich foods are another way to help repopulate the gut and improve the balance of flora in the small intestine. As with probiotic supplements, I tend to move slowly with these foods and only after successful eradication in phase two. I like to start clients on small amounts of coconut kefir, before building up to fermented vegetables like sauerkraut, if tolerated. Food like kimchi, miso and kombucha are a few examples of fermented foods that I use with my clients, and that are gaining popularity in the health community.


Are prebiotics the new probiotics for SIBO?

The story with prebiotics is pretty similar to that of probiotics for SIBO. Prebiotics are actually the fuel that feeds bacteria. This means if you still have an overgrowth, it will fuel it, which is why they often aggravate symptoms if eaten during treatment. Raw chicory root, Jerusalem artichoke, dandelion greens, leeks, garlic and onion are all examples of prebiotic-rich foods.

However, once the overgrowth has been eradicated, feeding the good guys and encouraging the right balance of flora is an important part of the long-term healing journey. There is obviously a delicate balance here and prebiotics are something that needs to be introduced slowly.

As with many complicated conditions, there is also a subset of clients who seem to thrive on prebiotics during and after natural SIBO treatment, something that is not yet well understood but will hopefully become clearer over time. It just highlights the point that what works for some people, will make things worse for others (and visa versa).


The importance of healing the gut lining after natural SIBO treatment

Another important role of probiotics in this phase is with healing a leaky gut, which has most likely developed as a result of SIBO (18). By replenishing the beneficial bacteria in the small intestine, probiotics can reduce overgrown or harmful bacteria, inhibit yeast overgrowth, improve motility and reduce inflammation, all of which are important for gut healing (19). Restoring the health of the small intestine and the gut lining is critical to reducing the risk of a SIBO relapse.

While there are additional supplement and diet recommendations available for healing a leaky gut, there is a lot of overlap between SIBO and leaky gut protocols. Most clients see significant improvement simply by removing the SIBO, along with the continuation of a maintenance diet and supplement protocol for up to 6 months post SIBO treatment.



Now we have a plan sorted for probiotics and healing leaky gut, we can start to address the possible root causes of your SIBO so it doesn’t come back again. Sadly, SIBO is strongly associated with chronic relapse (15), largely because 1) killing off the overgrown bacteria (or archaea) can be difficult; and 2) killing the bacteria itself doesn’t necessarily fix the root cause of why you have the SIBO to begin with. Whether that is a poorly functioning migrating motor complex (most common), a structural issue like adhesions or an open ileocecal valve, a functional issue like hypochlorhydria, immunodeficiency, altered bile flow or enzyme production, root causes need to be investigated and addressed.


Healing the migrating motor complex

The most common cause of SIBO is an impaired migrating motor complex (MMC), as discussed in part 1 of this blog series. The migrating motor complex is a wave of movement, that happens every 90 to 120 minutes in the stomach and small intestine, moving bacteria and undigested material down into the large intestine during fasting at night and between meals (20). Sadly, bacteria can overgrow again within two weeks of finishing treatment if the migrating motor complex is not working effectively. As such, a post-treatment natural prokinetic needs to be used to stimulate the migrating motor complex and keep things moving (21).

Prokinetics are typically started after the completion of antimicrobials and when the retest result is clear. The purpose of using a natural prokinetic for SIBO is to reset the migrating motor complex. Failure to use an effective natural prokinetic is one of the most common reasons for relapse amongst SIBO sufferers. Additionally, it is important that you stay on a prokinetic for a minimum of 6 months after SIBO treatment, even if symptoms have completely resolved. There are a few great options for natural prokinetics, including Iberogast, Motilpro and ginger.


Other structural and functional healing

Beyond the migrating motor complex, there are a vast array of potential underlying root causes of recurring SIBO overgrowths, specific to each individual. Depending on your medical history, comorbidities and current lifestyle, your practitioner should be able to work through solutions to any remaining imbalances that could increase your risk of relapse. They include boosting stomach acid production, avoiding excessive exercise, reducing stress and addressing structural issues like ileocecal valve dysfunction and adhesions.


Maintenance - SIBO relapse prevention

With SIBO relapse rates commonly reported up to a year after eradication, the maintenance phase should last between 6 - 12 months after completing natural herbal antibiotics for SIBO and a retest without any elevations in hydrogen or methane gas.

If you find that you’re symptoms continue or return, you might need to retest or consider testing for and address parasites, bacteria or yeast in the large intestine, SIFO, or ongoing inflammation from food sensitivities. Remember, symptoms are a sign that there is an underlying imbalance in systems of the body that need to be healed (not ignored).


Natural SIBO treatment protocol summary

The science of herbal natural SIBO treatment and testing are continuing to progress as evidence is constantly being added to the growing body of research. This means that what we do today to heal SIBO will probably be different to what we are doing in five years time.

I honestly hope that this three-part series has helped you understand SIBO a little better, and has given you the confidence to seek out testing if you feel like it might be something that is affecting you. Healing SIBO is a journey. If you are ready to begin yours, please head to the Work With Me page to learn more about how I work online with clients in many countries to treat SIBO and other root causes of IBS symptoms.


  1. Heiman, M. L., & Greenway, F. L. (2016). A healthy gastrointestinal microbiome is dependent on dietary diversity. Molecular Metabolism, 5(5), 317–320

  2. Halmos E., et al. (2015). Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut, 64(1), 93-100

  3. Bryk, R., et al. (2008). Selective Killing of Nonreplicating Mycobacteria. Cell Host & Microbe, 3(3), 137–145

  4. Chedid, V., et al. (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

  5. Jacobs, C., et al. (2013). Dysmotility and proton pump inhibitor use are independent risk factors for small intestinal bacterial and/or fungal overgrowth. Aliment Pharmacol Ther, 37(11), 1103-11

  6. Peralta, S., et al. (2009). Small intestine bacterial overgrowth and irritable bowel syndrome-related symptoms: Experience with Rifaximin. World Journal of Gastroenterology : WJG, 15(21), 2628–2631

  7. Low, K., et al. (2010). A combination of rifaximin and neomycin is most effective in treating irritable bowel syndrome patients with methane on lactulose breath test. J Clin Gastroenterol, 44(8), 547-50

  8. Lauritano, E., et al. (2008). Small intestinal bacterial overgrowth recurrence after antibiotic therapy. Am J Gastroenterol, 103(8), 2031-5

  9. Basseri, R. J., Weitsman, S., Barlow, G. M., & Pimentel, M. (2011). Antibiotics for the Treatment of Irritable Bowel Syndrome. Gastroenterology & Hepatology, 7(7), 455–493

  10. Pimentel, M., et al. (2004). A 14-day elemental diet is highly effective in normalizing the lactulose breath test. Dig Dis Sci, 49(1), 73-7

  11. Potera, C. (2010). ANTIBIOTIC RESISTANCE: Biofilm Dispersing Agent Rejuvenates Older Antibiotics. Environmental Health Perspectives, 118(7), A288

  12. Taff, H., et al. (2013). Mechanisms of Candida biofilm drug resistance. Future Microbiol, 8(10), 1325-37

  13. Bang, C., et al. (2014). Biofilm formation of mucosa-associated methanoarchaeal strains. Frontiers in Microbiology, 5, 353

  14. Ramage, G., Saville, S., Thomas, D., & López-Ribot, J. (2005). Candida Biofilms: an Update . Eukaryotic Cell, 4(4), 633–638

  15. Bures, J., et al. (2010). Small intestinal bacterial overgrowth syndrome. World Journal of Gastroenterology : WJG, 16(24), 2978–2990

  16. Triantafyllou, K., Chang, C., Pimentel, M. (2013). Methanogens, methane and gastrointestinal motility. J Neurogastroenterol Motil, 20(1), 31-40

  17. Soifer, L., Peralta, D., Dima, G., Besasso, H. (2010). Comparative clinical efficacy of a probiotic vs. an antibiotic in the treatment of patients with intestinal bacterial overgrowth and chronic abdominal functional distension: a pilot study. Acta Gastroenterol Latinoam, 40(4), 323-7

  18. Riordan, S. (1997). Luminal bacteria and small-intestinal permeability. Scand J Gastroenterol, 32(6), 556-63

  19. Aragon, G., Graham, D., Borum, M., & Doman, B. (2010). Probiotic Therapy for Irritable Bowel Syndrome. Gastroenterology & Hepatology, 6(1), 39–44

  20. Dukowicz, A. C., Lacy, B. E., & Levine, G. M. (2007). Small Intestinal Bacterial Overgrowth: A Comprehensive Review. Gastroenterology & Hepatology, 3(2), 112–122

  21. Pimentel, M., et al. (2009). Low-Dose Nocturnal Tegaserod or Erythromycin Delays Symptom Recurrence After Treatment of Irritable Bowel Syndrome Based on Presumed Bacterial Overgrowth. Gastroenterology & Hepatology, 5(6), 435–442

About author: Bella Lindemann, FDN-P

Bella Lindemann is the founder and lead practitioner of The Functional Gut Health Clinic. With her science degree, functional nutrition certification and extensive experience, she is a recognised expert in gut health and the science of SIBO. Having worked with hundreds of SIBO cases, including her own, she is passionate about helping her clients address this imbalance and take back control of their digestive symptoms.