This post is the second article in a three-part series on Small Intestine Bacterial Overgrowth, with a focus on SIBO natural treatments, antibiotics, herbal supplements, and lifestyle changes. You can read Part 3 on SIBO diet, ongoing healing, and recovery. You can also revisit Part 1 on SIBO symptoms and testing. For a more complete and updated resource, see my book SIBO Made Simple.
When I finished my SIBO treatment, I was convinced the bacteria were still there.
After nearly six weeks of herbal antibiotics, my digestive system still felt unsettled. My stomach continued to bloat, my digestion felt slow, and I was burping during meals no matter how many FODMAPs were on my plate. Although the symptoms I described in Part 1 of this series had improved slightly, their persistence made me worry that my attempt to clear the bacterial overgrowth had not worked.
This kind of SIBO-related anxiety seems very common among people dealing with the condition. It makes sense. SIBO treatment can be confusing, the available options vary widely, and it often takes more than one attempt for a practitioner to find the right protocol for an individual. Even when treatment works, SIBO can be chronic and may relapse if the root cause is not addressed.
Thankfully, I received news that helped deflate both my stress and the lingering balloon-like feeling in my abdomen: after two months of treatment and waiting, I was officially SIBO free.
If you want more background on what SIBO is and how I navigated diagnosis, return to Part 1 of this series, or read the full story with practical guidance in my book, SIBO Made Simple. If you are wondering whether your symptoms may be related to Candida vs. SIBO, I also have a dedicated post on that topic.
While I waited for my results, which arrived three weeks after I completed my herbal antibiotic protocol, I prepared myself for the possibility that I would need another round of treatment. I researched other SIBO treatment options, compared antibiotics with herbal antimicrobials, and considered whether I would ever feel desperate enough to try the elemental diet.
This post comes from that deep dive. Below, I explain the three main phases of SIBO treatment, the primary approaches used to reduce bacterial overgrowth, and the supplements and lifestyle strategies often recommended to support digestion, motility, symptom management, and long-term recovery.
One part of a SIBO treatment plan that is not discussed enough is optimism. Stress can worsen many chronic health conditions, even though chronic health issues are naturally stressful. As difficult as it may be, try to stay positive and remember that healing usually takes time, patience, and adjustment.
My motivation throughout the process was knowing that my experience might help someone else feel less lost. You do not need to be a blogger or writer to find value in that silver lining. Many people who have been through SIBO keep notes, track symptoms, and create spreadsheets to better understand what helps them.
I am grateful that I can now direct people to SIBO Made Simple, which gathers these resources in one place. It is the kind of practical guide I wish I had when I was first trying to understand SIBO treatment.
Remember that dealing with SIBO is a wellness project in itself. There may be trial and error along the way. But every step can teach you more about your body and help you make better decisions moving forward.
With health and hedonism,
Phoebe
THE 3 PHASES OF SIBO TREATMENT
Although more doctors are learning how to approach SIBO testing, treatment often focuses too heavily on the kill phase. Clearing bacterial overgrowth is important, but lasting improvement usually requires a broader plan that also supports gut healing and relapse prevention.
Here is a simple way to understand the timeline:
1. The Kill Phase (2 to 4 weeks)
This phase lasts as long as the prescribed medication protocol, which may include an antibiotic such as Rifaximin or a herbal antimicrobial protocol. There is debate about whether a low FODMAP diet is helpful during the kill phase. For people with severe symptoms, beginning a lower FODMAP elimination approach may reduce discomfort and support the next phase of healing. However, some practitioners caution against being so restrictive that bacteria lose their food source entirely and become less active.
2. The Healing Phase (2 to 3 months)
Many practitioners recommend that you retest for SIBO about two weeks after completing antibiotics or herbal antimicrobials. Some people skip retesting if symptoms have improved and the test is too expensive. Others wait for a negative result before moving into gut-healing strategies, dietary modifications, and the slow reintroduction of higher FODMAP foods.
3. The Recovery Phase (ongoing)
SIBO can be a chronic condition. If it returns, it does not always mean the treatment failed. It may mean that the underlying cause has not been fully addressed. This is where lifestyle habits, meal timing, stress management, digestive support, and motility-focused supplements or medications may become important, especially for people who struggle with constipation or sluggish digestion.
This article focuses mostly on the kill phase, but some lifestyle recommendations also apply to healing and recovery. Those topics are explored more fully in the final part of this series.
For many people, the hardest part is knowing what to do after medication. The space between a SIBO diet and long-term gut healing can feel overwhelming. Helping bridge that gap with recipes and a clear roadmap is one of the main reasons I wrote SIBO Made Simple.
THE BEST ANTIBIOTICS AND HERBAL TREATMENTS FOR SIBO
The main SIBO treatment options during the kill phase fall into three categories: pharmaceutical antibiotics, herbal antibiotics, and the elemental diet. Except for the elemental diet, which is a more complete and restrictive protocol, treatment is often supported with diet, lifestyle changes, and targeted supplements.
Your practitioner should also consider whether your SIBO is hydrogen-dominant, methane-dominant, or related to other gas patterns. Symptoms often provide clues: methane is commonly associated with constipation, while hydrogen is often associated with diarrhea. However, this is not always the case, so it is important to discuss testing and symptoms with your healthcare provider before choosing a protocol.
1. Antibiotics (about 2 weeks)
Several pharmaceutical antibiotics are commonly used for SIBO, including Neomycin, Metronidazole, and Rifaximin. Neomycin is often discussed in relation to methane-dominant cases. Rifaximin, also known by the brand name Xifaxan, has a strong reputation because it primarily works in the gut and is often described as having “eubiotic” effects.
Studies suggest that Rifaximin may have relatively mild side effects and minimal impact on beneficial bacteria in the colon compared with broader-spectrum antibiotics. For people who are nervous about antibiotics, this is one reason it is often considered.
The concern with repeated antibiotic use is the potential for resistance. For some people, one course may be useful, but repeated cycles should be carefully discussed with a practitioner, especially when other options may be appropriate.
2. Herbal Antibiotics (4 to 6 weeks)
Many people choose herbal antimicrobials not only because they seem more natural, but because certain herbal protocols have been studied and shown to be comparable to pharmaceutical options in some cases.
The downside is that herbal protocols usually require more pills over a longer period of time and may still cause digestive side effects. Natural does not always mean gentle for every body. During my own protocol, I experienced discomfort and worsening constipation at times.
The upside is that some herbal products are available without a prescription, which may make them more accessible for people who are not working with an integrative practitioner. That said, it is still wise to involve a qualified healthcare professional whenever possible.
Two commonly discussed herbal protocols include:
- Metagenics Candibactin-AR + Candibactin-BR
- Biotics FC Cidal + Dysbiocide
A common dosing approach is 2 capsules, twice daily, for 4 weeks, though protocols vary. I personally used the Biotics system for six weeks.
These formulas combine herbs that are commonly used for antimicrobial support, including berberine-containing herbs, ginger, and oregano. Some people prefer a pre-formulated product, while others work with a practitioner to combine individual herbs. Dr. Allison Siebecker has discussed using 1 to 3 herbs in combination for 4 weeks, following product label dosing and clinical guidance.
- Allicin: Derived from garlic, allicin does not contain the same FODMAP components found in the whole clove. It is often discussed for methane-dominant SIBO and may be used alone or alongside other herbs.
- Berberine Complex: Berberine-containing herbs include goldenseal, Oregon grape, barberry, and related botanicals. They are often used in combination with oregano oil and neem.
- Neem Plus: Neem comes from a tropical evergreen tree and is often used as part of herbal antimicrobial protocols.
- Oil of Oregano: Oregano oil is commonly used for antimicrobial support. During my protocol, I sometimes added a small amount to water or took it in capsule form.
3. The Elemental Diet (about 2 weeks)
If other approaches fail, some practitioners consider the elemental diet. It is usually viewed as a last resort because it requires replacing meals with a medical formula for about 14 days. The goal is to provide absorbable nutrients while limiting fuel for bacteria in the small intestine.
Elemental formulas contain nutrients in a form that can be absorbed early in the digestive process. This means they may not reach the area where unwanted bacteria are present in the same way whole foods do.
The protocol is often suggested for 14 days, followed by retesting. Some people request rapid results so they can decide quickly whether to continue for an additional week if the test remains positive.
Antibiotics and herbal antimicrobials are generally not used at the same time as the elemental diet unless a practitioner advises otherwise, because the purpose of the diet is to starve the bacteria by removing their usual food sources.
For more information, recommended formulas and important tips on this protocol, click here.
THE BEST STRATEGIES FOR MANAGING MOTILITY AND SUPPORTING DIGESTION
Antibiotics and herbal antimicrobials can both be used as kill-phase strategies. What often makes the difference long term is how well you support digestion, motility, and the underlying factors that allowed SIBO to develop.
As discussed in lesson 1, one important contributor to SIBO is a slowed or impaired Migrating Motor Complex, often called the MMC. The MMC helps sweep the small intestine between meals. When it does not work properly, bacteria may be more likely to linger and overgrow.
Here are a few simple habits that may support digestion and motility:
- Try meal spacing: leave at least 3 to 4 hours between meals and avoid constant snacking.
- Drink plenty of water.
- Sip bone broth before bed if it agrees with you.
- Eat slowly and chew your food thoroughly.
- Add lemon juice to water before meals if tolerated, as some people find it supports digestion.
Sometimes diet and habits are not enough to stimulate motility, which is where prescription prokinetics and non-prescription supplements may be considered. This list is not meant to be an “everything at once” plan. Instead, think of these as options to discuss with your practitioner or use selectively based on symptoms.
- Digestive Enzymes: Digestive enzymes may help break food down more efficiently so it is less likely to sit in the gut and feed bacteria. I used capsules with lunch and dinner and skipped them at breakfast. You can read more about digestive enzymes for IBS.
- Prescription Prokinetics: These medications stimulate the MMC and may be used after the kill phase to help prevent relapse. Many doctors prefer to start them after antibiotics or herbal antimicrobials are complete. Common options discussed in SIBO care include Low Dose Naltrexone and Low-dose Erythromycin. Your doctor should determine whether these are appropriate and how they should be dosed.
- Non-Prescription Motility Supplements/Prokinetics: These options may support bowel regularity and motility, especially if constipation worsens during treatment. Start with one approach and adjust carefully.
- Motilpro: A ginger-based product often used for motility support.
- Smooth Move Tea: A strong herbal laxative tea that some people use occasionally when constipated.
- Psyllium Husk: A prebiotic fiber that may help support more regular bowel movements, though tolerance varies.
- Natural Calm: A magnesium-based product often used for relaxation and bowel regularity. Magnesium pills may also be used at night.
- Supplements for Reducing SIBO Symptoms: Bloating, gas, and digestive distress may not disappear immediately. In some cases, symptoms can temporarily worsen during kill-phase treatment.
- Iberogast: Often used before or with meals to help with bloating and digestive discomfort.
- GingerMax: A ginger supplement that may support digestion when taken with meals.
- Enteric Coated Peppermint Oil: Peppermint oil may help reduce bloating, gas, and other symptoms of digestive upset for some people.
- Supplements for Breaking Up Biofilm: Biofilm support is sometimes added to kill-phase treatment with the goal of making bacteria easier to target. I took Interfase by Klaire Labs between meals when I remembered, though it is unclear whether it was necessary.
- Visceral Mobilization: This is a manual therapy approach that targets restrictions around the abdomen and small intestine. Some people seek out trained practitioners, while others learn gentle self-massage techniques.
There are many possible supplements for SIBO treatment, symptom relief, travel, gut healing, and relapse prevention. In SIBO Made Simple, I organize these options into an easy reference chart to make the information more practical.
For more information and links to products I keep on hand for managing symptoms, travel, leaky gut support, and treatment support, see this post on the best SIBO supplements.
DO PREBIOTICS OR PROBIOTICS WORK FOR SIBO?
Many SIBO treatment plans use a starve and kill strategy. This usually means reducing fermentable carbohydrates, such as those limited on the low FODMAP diet or Specific Carbohydrate Diet, while also using medication or herbs to reduce bacterial overgrowth. In this approach, fermented foods, probiotic foods, and prebiotic-rich ingredients are often limited because they may aggravate symptoms.
There is another perspective: using probiotics and prebiotics to help rebalance the gut ecosystem instead of focusing only on restriction.
The research on probiotics for SIBO is still limited, but some small studies suggest that probiotics do not necessarily worsen SIBO and may help depending on the strain. The effects appear to be strain-specific, which means not all probiotics should be treated the same.
As Dr. Jason Hawrelak explains in this podcast episode, probiotics may help speed transit time, stimulate the MMC, support the intestinal lining, and reduce gut hypersensitivity, which is common in SIBO.
This can feel confusing because it conflicts with the more restrictive approaches described above. The key point is that every body is different. SIBO is complex, and there is not one universally proven treatment that works for everyone.
If adding supportive organisms and fibers feels more aligned with your body than removing more foods, you can research probiotics and SIBO further or discuss prebiotics such as Allicin, Partially Hydrolyzed Guar Gum, and GOS with a practitioner.
Dr. Jason Hawrelak has argued that people with SIBO react to high FODMAP foods because something is wrong in the gut environment, not because FODMAPs are inherently harmful. From this viewpoint, using probiotics to shift the bacterial ecosystem may eventually support a healthier balance and a smaller bacterial population in the small intestine.
Here is more information on the best probiotics for SIBO treatment and healing afterward.
Low FODMAP and SCD-style diets focus on carbohydrates because bacteria ferment them. These diets can be valuable tools for reducing symptoms and giving patients a sense of control. However, the long-term goal is usually to expand the diet again, tolerate a wider range of beneficial foods, and address the underlying reasons SIBO developed in the first place.
That dietary debate, including what to eat during treatment and after treatment to help prevent relapse, is where the next part of this series continues.
OTHER SIBO RESOURCES
- The SIBO Made Simple book brings together lessons from more than 50 practitioner interviews and turns them into a practical roadmap with low FODMAP recipes.
- The SIBO Made Simple Podcast explains different parts of the SIBO puzzle in clear, accessible terms. Topics include:
- SIBO Breath Testing
- The Elemental Diet
- Methane & Hydrogen Sulfide SIBO
- Candida & Yeast Overgrowths
- SIBO & Hypothyroidism
- SIBO & Celiac Disease
- Heavy Metals, Mold & Other Toxins
- CBD Oil & SIBO
- The Low FODMAP Diet
- The Bi-Phasic Diet
- SIBO & Intermittent Fasting
- Skin Issues and SIBO
- Probiotics and Prebiotics for SIBO Treatment
- Healing Structural Issues
- Fertility & SIBO
- Histamine Intolerance & SIBO
- How SIBO Affects Depression and Anxiety
- Acupuncture for SIBO Healing
- Dr. Allison Siebecker’s site is a helpful hub of information: SIBOinfo.com
- SIBO 2.0: How to Find the SIBO Treatment That’s Right For You
- SIBO 3.0: The Best Diets and Lifestyle Changes to Treat, Heal, and Prevent SIBO From Recurring
- The Best SIBO Supplements for managing symptoms, supporting leaky gut healing, and more
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Disclaimer: This website provides health, wellness, and nutrition information for educational purposes only. The information here is not intended to replace advice from your physician or another qualified healthcare professional. Always speak with your doctor before trying any new treatment, supplement, medication, or dietary protocol.