Ultimate SIBO Natural Treatment In 2023 | Symptoms, Causes & More

The Ultimate Guide To Know Everything About Natural SIBO Treatment Plan


Small intestinal bacterial overgrowth (SIBO) is a serious medical condition in which, as indicated by its name, there is an overgrowth of bacteria within the small intestine. Scientific research on SIBO has found that this condition is closely related to irritable bowel syndrome (IBS). In fact, the SIBO Theory for IBS, which states that SIBO causes IBS symptoms, supports the fact that up to 78% of IBS patients may also have SIBO 14.

Patients with SIBO often experience symptoms such as distension (bloating), flatulence (gas), abdominal pain/cramping, altered bowel habits, such as diarrhea or constipation, malabsorption of nutrients, brain fog, and much more. Many of these symptoms have been linked with increased production of hydrogen, methane, and hydrogen sulfide gases that occur as a result of increased bacterial fermentation of food within the small intestine.

If you have tested positive for SIBO, or your doctor suspects that you may have this condition, you may be wondering what type of pharmaceutical and/or natural remedies are available.

There are currently several different ways in which physicians choose to treat SIBO patients, which can include natural remedies, conventional medical treatments, or, which is most commonly used, a mixture of both.

The aim of this article is to provide you with a simple, effective, and natural SIBO treatment plan that is supported by several different published scientific studies. By the end of this article, you will have the knowledge on how to eliminate SIBO from your life without needing any pharmaceutical antibiotics, if you choose not to use them.

What Causes SIBO?

what causes sibo

Before you can tackle SIBO, it is imperative to understand some of the leading theories for why this condition occurs. By understanding these concepts, you will have a better understanding of how each natural remedy discussed here specifically targets those issues.

The two primary proposed underlying causes of SIBO include:

  1. Small intestinal dysmotility
  2. Malabsorption

There is a detailed interview with SIBO expert Dr. Weinstock and to understand the mechanisms that causes SIBO.

Any type of condition that has the potential to contribute to either of these two underlying causes can play a role in promoting the overgrowth of intestinal bacteria.

For example, structural or anatomical abnormalities of the gastrointestinal (GI) tract, such as diverticulosis or side effects of gastric bypass surgery, can contribute to slowed motility and malabsorption, thereby ultimately leading to SIBO. Other diseases that can slow motility of the small intestine and therefore also contribute to the occurrence of SIBO include Crohn’s disease, celiac disease, and small bowel adhesions, which is a term used to describe the presence of scar tissue in the small intestine 15.

Food poisoning is also an extremely important health condition that has been shown to directly cause IBS and/or SIBO. It is necessary for all to learn how to avoid food poisioning. In fact, it has been estimated that 10% of people who experience severe food poisoning will develop a type of IBS termed post-infectious IBS(PI-IBS) or SIBO.

With this in mind, there are still many other ways in which a person can develop SIBO. Regardless of the causal factor, keep in mind that SIBO will still be directly related to impaired intestinal motility, which describes the movement of the muscles of the GI tract, and some level of nutrient malabsorption.

Understanding How SIBO Treatment Works


With the general knowledge of how SIBO arises, we can now discuss some of the proven strategies that can be used to treat this potentially debilitating condition.

The main SIBO treatment methods typically fall into one of the four following categories:

  1. Diet changes
  2. Probiotics
  3. Antibiotics
  4. Prokinetics

The primary goal of each of the aforementioned treatment strategies is to reduce the overgrowth of bacteria within the gut, rebalance intestinal flora, as well as improve intestinal motility.

Although treating SIBO may appear to be a straightforward process, there are many factors that complicate the ability to fix this condition in your gut. For example, it can take a significant amount of time for some patients to rebalance a healthy intestinal flora and to achieve proper digestive motility after becoming ill.

The SIBO Natural Treatment Process

sibo treatment diagram

The rest of this article will include a 7 step natural treatment process that will help rebalance the gut. This 7 step process works in a chronological sequence that begins with important foundational steps that are just as crucial as the therapeutic strategies that will follow.

By establishing a strong foundation, SIBO patients can start to improve health from the root up and then work through each subsequent treatment strategy which will work better once the foundation is in place.

7 Steps to a Healthy Gut:

  1. Diet and Lifestyle
  2. Supplemental Support and Probiotics
  3. Antimicrobial treatments
  4. Prevention and Motility Support
  5. Food reintroduction and fiber
  6. Elimination testing
  7. Underlying cause investigation

It is important to note that people who are experiencing less severe symptoms will probably only need to complete steps 1 and/or 2 before they will be ready to reintroduce a wider variety of foods and begin to eliminate any supplements. At the same time, individuals who are experiencing more severe symptoms will probably need to complete each of the first 4 steps prior to incorporating any food(s) or fiber into their diet. This process for people experiencing severe symptoms will typically proceed at a slower rate as compared to those with less severe symptoms.

If none of the first 4 strategies prove to alleviate your symptoms, it may be an indication that a more thorough investigation into the causes of your illness may be required. To this end, it is advisable for you to consult with a medical expert who is experienced in treating patients with SIBO and IBS.

7 Step SIBO Treatment Process Instructions:

  • To begin, follow the foundational step of “Diet and Lifestyle.” Once you go through this initial stage, carefully work through each step until you are executing it effectively. Remember, regaining your health will require time and commitment!
  • Continue to steps 1-4, in chronological order. Be sure to provide yourself with enough time to evaluate your symptom improvement after completing each step.
  • In order to evaluate how well a treatment step is working, it is recommended to follow the guidelines of a step for at least 1-2 months. Since symptomatic relief will vary between individuals, some may notice symptom improvement quicker than others. Regardless, continue with each step for the recommended time frame; however, if you find that the step is not improving your symptoms at all, proceed to the next step.
  • Once you feel that your symptoms have been significantly reduced with a given treatment plan, continue with this step for at least 3 months. At this point, you can proceed to step 5 and begin reintroducing a wider variety of foods and fiber into your diet. Once you begin this recovery process, it is also recommended that you begin to come off some of your support.
  • If diet, lifestyle, probiotics and other supplements do not appear to improve your symptoms and you instead require antibiotic treatment, it is not as important to restrict your diet. In fact, it may prove beneficial to broaden the diet while on antimicrobial treatment.


SIBO Treatment Step 1: Diet and Lifestyle


As mentioned previously, the foundational steps of modifying your diet and lifestyle play a tremendous role in the initial process of healing the gut. In fact, many patients with moderate SIBO symptoms will find that making these changes will alleviate their symptoms altogether.

However, regardless of the severity of your symptoms, making changes in your diet and lifestyle are important before proceeding with the following steps of this treatment plan.


How can a diet be used to treat SIBO?

Making changes in your diet will require a significant amount of time and discipline to accomplish. Many doctors will recommend that patients complete at least 1 month on a healthy SIBO-friendly diet to evaluate its effects on improving symptoms. If healthy diet modification improves at least 30% to 50% of SIBO symptoms, it is recommended that individuals continue with this diet to determine whether it further improves symptoms.

The following diets are commonly recommended for people with SIBO and IBS:

  1. Low FODMAP diet
  2. Simple low fermentation diet
  3. SCD diet

Of these, the most widely studied and recommended diet for the treatment of SIBO and IBS is the Low FODMAP diet.

In recent years, data from several randomized controlled, case-controlled, and observational studies have found that the Low FODMAP Diet provides a significant amount of relief in the management of SIBO and/or IBS symptoms.

In fact, each of these scientific studies has provided consistent results on how this treatment option allowed IBS patients to experience a wide range of symptomatic benefits.1

Click Here to See the ultimate SIBO Cookbook

The term FODMAP is an acronym that stands for:

Fermentable, Oligosaccharides, Disaccharides, Monosaccharides, and Polyols

Each of these macromolecules is a poorly absorbed carbohydrate that can be found in various foods. For example, food products containing garlic, dairy with lactose, onions, apples, and beans are often high in FODMAPs.

See more detailed information on SIBO Diets here.


chakra yoga posture

The lifestyle modification aspect of this step involves stress management, exercise, and healthy social activity.

Various clinical and experimental studies have shown that psychological stresses can have a significant impact on intestinal sensitivity, motility, secretion, and permeability. Furthermore, stress has also been shown to act as an underlying mechanism of mucosal immune activation, alterations in the central nervous system, peripheral neurons, and gastrointestinal microbiota.2  

In conclusion, psychological stress can have detrimental impacts on gut motility, inflammation, intestinal microbiota, and overall gut health, each of which can already be altered if you have SIBO and/or IBS.

Some effective ways you can cope with stress include:

  • Walks in nature
  • 8 hours of quality sleep
  • Hypnotherapy
  • Sunlight exposure
  • Teas
  • Deep breathing, meditation, or prayer
  • Yoga class
  • Consistent light exercise
  • Epsom salt baths
  • Digital detoxification

SIBO Diet and Lifestyle Action Plan:

  1. Implement the Low FODMAP diet for 1-2 months
  2. Implement 2-3 of the stress-reducing and health-promoting activities every week


SIBO Treatment Step 2: Probiotics and Supplements

If you are still experiencing your symptoms after completely following the diet and lifestyle modification for a period of at least 1-2 months, the next step is to introduce a well researched and strain-specific probiotic into your daily routine, along with other supplements.

Throughout this second step, it is extremely important to maintain the diet and lifestyle changes you made during foundational step 1.

Probiotics for SIBO


While there is some controversy as to whether probiotics can be helpful in the treatment of SIBO patients, an overwhelmingly large amount of positive scientific evidence has shown that probiotics are important supplements for IBS and SIBO patients.

For example, in this meta-analysis, the researchers found that daily probiotic use successfully reduced the pain and overall symptom severity scores of patients as compared to those taking the placebo 3.

Prior to beginning your probiotic treatment plan, it is crucial to choose a strain-specific supplement that has which has been clinically studied in IBS or SIBO patients experiencing similar symptoms.

Probiotics are like different breeds of dogs. Like dogs, each breed, or strain, in the case of probiotics, will exhibit different personalities, or properties, and therefore provide different therapeutic actions when taken each day.

Here are some examples of specific probiotic strains and their actions:

  1. Saccharomyces Cerevisiae Boulardii- studied in SIBO and SBS
  2. Bifidobacterium lactis HN019- studied to help slow transit time
  3. Lactobacillus reuteri (DSM 17938)- studied to help methane and constipation
  4. Probiotic mix VSL #3- studied to help IBS
  5. Lactobacillus plantarum 299v- studied to help IBS

Digestive Enzymes


Although there has not been as much experimental support for the use of digestive enzymes for the treatment of IBS and SIBO, many patients have found that these enzymes can help breakdown foods and reduce fermentation.

Here is one study that showed some positive ways in which the use of digestive enzymes improved the symptoms of IBS patients. While this study did not compare their results to a placebo control group, it did indicate that the digestive enzyme treatment group experienced a reduction in abdominal pain, flatulence, and bloating.

Digestive enzymes are typically taken with meals throughout the day to help breakdown foods.

Here are a few digestive enzyme supplements that may help IBS and SIBO patients:

  1. Klaire Labs SIBB Zymes
  2. Rainbow light enzymes

Adrenal Support


It is not uncommon for patients with SIBO and IBS to experience fatigue, stress, depression, and/or lower strength. To alleviate these symptoms, treatment with remedies that specifically target your adrenal glands, which are the glands that are present directly on top of your kidneys, can play an important role in revitalizing your health and digestion.

Although the number of studies on adaptogenic herbs and adrenal supporting supplements is not as extensive as compared to some of the other treatment options mentioned here, there is still a considerable amount of evidence connecting these natural remedies with improved stress and energy levels in IBS and SIBO patients.

This systematic review showed positive signs for the use of Rhodiola Rosea for the treatment of physical and mental fatigue. In addition, this study found that a high-concentration full-spectrum Ashwagandha root extract safely and effectively improves an individual’s resistance towards stress, subsequently improving their self-assessed quality of life 9.

Adrenal support supplements will typically contain a combination of adaptogenic herbs, as well as other important vitamins and minerals to support the adrenal glands and optimally combat fatigue and stress in the process.

Here are a couple of quality adrenal supplements:

  1. Mega Food Adrenal Strength
  2. Gaia Herbs Adrenal Health

Probiotics and Supplements Action Plan:

  1. Try using a strain-specific probiotic for at least 1-2 weeks. If you experience a worsening in your symptoms, discontinue this specific strain and instead look to at least 1-3 other strains for potential benefit.
  2. Incorporate digestive enzymes with each of your meals as directed.
  3. Incorporate adrenal support supplements into your daily routine.
  4. If you find that the supplements in this step improve your symptoms, continue with this regimen. However, if your symptoms do not change or worsen, it may be worth speaking to a health professional to determine whether you are a candidate for antibiotic treatment. Regardless of whether you decide to move forward with antimicrobial treatment, it is recommended that you still maintain your diet and lifestyle changes, as well as continue taking any supplements that provided you with some relief.


SIBO Treatment Step 3: Antimicrobial Treatment

If the previous steps of this process did not alleviate your symptoms completely, it may be time for you to incorporate antimicrobial treatments into your daily routine. When starting antimicrobial treatment, it is important to maintain any diet and lifestyle changes, as well as the ingestion of supplements that were useful to you, throughout this process.

Although maintaining strict diet restrictions on fiber and high FODMAP intake is not as important while taking antimicrobial treatments, it is still recommended that patients continue to eat healthy whole foods.

SIBO Treatment Alternatives


Herbal antibiotics can be just as effective as conventional antibiotics for the treatment of SIBO. While this may be true, it is important to note that natural antimicrobial treatments may require more time to produce the same effect as pharmaceutical antibiotic options. In fact, the researchers of this study concluded that these therapies are at least as effective as rifaximin for resolution of SIBO by lactulose breath test10.

Doctors will typically recommend that patients undergo antimicrobial treatment for at least 1-2 months, during which some physicians may advise patients to rotate their antibiotic combination after 1 month.

The following protocols are commonly prescribed by naturopathic physicians:

Protocol 1:

It is recommended for patients to take 1 of the following combination formulas for a 1 month period:

  • Biotics Dysbiocide and FC Cidal or
  • Metagenics Candibactin AR and Candibactin BR
Protocol 2:

It is recommended for patients to take 2 of the following herbs for a 1 month period:

For more detailed information see the herbal antibiotics for SIBO page.

Elemental Diet

elemental diet

Another antimicrobial treatment strategy that has been scientifically proven to reduce SIBO symptoms is the elemental diet as a replacement for all foods for 2-3 weeks. This is an excellent option for someone who does not want to take antibiotics or who has failed to respond to other treatment modalities.

Using a half elemental diet can also provide patients with significant benefits, as this treatment option uses elemental supplements in conjunction with eating whole foods. It has been shown that a half-elemental diet can be just as beneficial as a full-elemental diet in place of all foods. This way the elemental diet acts more as a supplement for certain meals throughout the day to give the gut some rest.

In this study, the elemental diet exhibited a success of 85% in its ability to normalize lactulose breath tests after 3 weeks of this treatment method.

Some of the most commonly recommended elemental diet products include:

  1. Absorb Plus
  2. Physicians Elemental Diet

Antimicrobial Action Steps:

  1. Decide whether you want to use antimicrobials or the elemental diet.
  2. If you decide to take antimicrobials, it is recommended to continue with this course of treatment for at least 1-2 months and rotate herbs after 1 month.
  3. If using the elemental diet, it is recommended that patients order enough products that will sustain them for at least 2-3 weeks when used as a complete food placement.
  4. It is also important to note that the elemental diet can also be used as a supplement to replace 1-2 meals a day. This semi-elemental diet can be continued for a longer duration of time as needed.
  5. After completing with either treatment option, it is recommended for patients to return to the diet regimen they followed during step 1. The use of prokinetic supplements during this reintroduction phase is also crucial to maintaining digestive health after completing antimicrobial treatment.


SIBO Treatment Step 4: Prevention and Motility Support


Dysmotility has been shown to be an underlying cause of SIBO, especially in relapsing SIBO patients.3

In order to promote better gut motility (movement) and prevent SIBO relapse, it is often recommended to incorporate natural prokinetic and/or prokinetic drugs after the completion of antimicrobial treatment.

Some of the most commonly used natural prokinetic agents include:

  • MotilPro
  • Iberogast
  • Ginger
  • Motility Activator

The following pharmaceutical prokinetic agents have also proven to be effective:

  • Resolor
  • Erythromycin

For more detailed information see the prokinetics page.

Prokinetic & Prevention Action Steps:

  1. After finishing antimicrobial treatment, supplement with a natural prokinetic agent for 3 months as well as the other foundational steps like the Low FODMAP diet.
  2. After 3 months you can move to step 5 if symptoms are under control
  3. This concludes the treatment steps 1-4. If the gut is healthier, move to steps 5 and 6. If you still are not getting better, move to step 7.


SIBO Treatment Step 5: Food Reintroduction and Fiber

artichoke fiber

After going through each of the previous steps that have been scientifically proven to treat SIBO, the hope is that by this stage the patient has experienced some level of symptomatic relief. By this point in the SIBO treatment regimen, patients can begin to gradually introduce a wider variety of foods and fiber into their diet.

After being on a more restricted diet for an extensive period of time, it is important to make this a slow and easy transition. To do this, it is recommended to begin with small amounts of new foods and monitor major symptom reactions you experience for re-introduced foods. If you do not experience any negative side effects with new foods, that is a step in the right direction.

However, experiencing minor symptoms is not something to overly concern yourself with either. When so many foods have been eliminated from your diet for an extensive period of time, it is natural for your body to react in some way to various different foods.

At this stage, patients can also begin to incorporate very small amounts of fiber into their diets to test its effects. The goal at this stage is to promote a healthy balance of microorganisms in your GI tract. By slowly introducing small amounts of these food products, it provides patients with the ability to accurately monitor their progress and potential dietary limitations.

The following fiber products have been widely used in IBS studies, and may be useful to try in small amounts:

  1. Partially Hydrolyzed Guar Gum
  2. Acacia fiber

In this study, partially hydrolyzed guar gum was shown to significantly improve the quality of life of IBS patients 12.

Food Re-introduction Action Steps:

  1. Gradually reintroduce some of the higher FODMAP foods into your diet and monitor any type of reaction you experience during this process. If you do not experience any negative symptoms with a food item, you can be confident that this food will not cause you problems in the future. On the other hand, if you experience any major negative side effects after ingesting certain foods, be sure to take note of your symptoms and limit this food going forward.
  2. Incorporate a very small amount of fiber in the form of PHGG or acacia into your diet. If you find that this fiber supplement improves your symptoms, continue to ingest this small amount, and gradually increase your dosage. However, if your symptoms worsen, discontinue taking this fiber supplement.


SIBO Treatment Step 6: Elimination Testing


At this stage of the SIBO treatment process, it is expected that you feel much better and are therefore ready to begin to discontinue use of some of the supplements. By eliminating certain supplements from your diet, the goal of this step is to rely on your foundational diet and lifestyle steps to maintain your long term health. While this is the goal, patients can always turn to any natural remedy they found to successfully treat their SIBO in the event their symptoms begin to flare up again.

Elimination Action Steps:

  1. Begin to eliminate one supplement at a time. Keep an accurate record of any symptoms you experience once each supplement treatment course has ceased.
  2. If your symptoms do not reappear when you have ended a supplement treatment course, it is safe to discontinue any future treatment with this supplement. However, if you feel that taking the supplement still plays a significant role in your symptom treatment, continue with what appears to work best for you.


SIBO Treatment Step 7: Underlying Cause Investigation


If you have completed each previous step of this SIBO treatment regimen and still experience significant symptoms, it may be time for you to investigate other potential treatment options. To do this, it is important to consult with a physician who has experience treating SIBO and/or IBS patients with both natural and pharmaceutical remedies.

It is not uncommon for people experiencing severe SIBO symptoms to require SIBO antibiotics or pharmaceutical prokinetics to alleviate their symptoms. Furthermore, consulting with a physician may indicate that a different type of pathological condition is contributing to your symptoms.

IBS and SIBO are both highly complex digestive disorders; therefore, treating these conditions may prove to be more difficult for some patients.

Underlying Cause Action Steps:

  1. If your condition does not improve with any of the previous steps, consult with a skilled physician who has experience treating IBS and/or SIBO in order to investigate underlying causes that may be contributing to your condition.


SIBO “Die-Off” Symptoms During SIBO Treatment

Any type of SIBO treatment strategy can cause a “die-off” reaction to occur. A “die-off” reaction will typically occur when the patient is taking potent antimicrobials, the elemental diet, or undergoing a drastic change in their diet.

A die-off reaction will typically cause patients to experience flu-like symptoms, which can include fatigue, headaches, brain fog, as well as worsened digestive symptoms, such as constipation or diarrhea, for a short period of time. The mechanism behind this reaction is believed to result from the substantial eradication of bacteria, parasites, or fungi. By killing these species so quickly, the liver and the kidneys, which are the body’s primary elimination organs, are unable to remove these species at the same rapid rate.

Although the symptoms of this reaction are not ideal, the die-off reaction actually indicates that your SIBO treatment regimen is successfully eliminating the overgrown bacteria that are causing your digestive symptoms to occur. While this may be true, if the symptoms of the die-off reaction persist after several days, it may indicate that you are instead experiencing adverse reactions to the treatment strategy you are currently following.

Check out the SIBO die off page for more information on this topic.


A Note on Methane Dominant SIBO & Constipation Treatment


The presence of methane gas in the lactulose breath test has been associated with constipation-dominant IBS (IBS-C) patients. 13  The presence of abnormally high levels of methane during this breath test indicates that any type of treatment regimen will have to specifically target the methane-producing organisms that are present within the GI tract. Although this may appear to be a straightforward process, the organisms that produce methane in the GI tract are not bacterial species, but instead, belong to the Archaea class.

One supplement that has been designed to specifically target methane overgrowth is Atrantil, which can be safely combined with many of the other treatments discussed in this article. Furthermore, Lactobacillus reuteri (DSM 17938) is a type of probiotic that has been shown to specifically target methane overgrowth as well. This strain of bacteria is manufactured in a probiotic supplement made by BioGai.

Other than requiring additional testing and certain adjustments to their treatment options, patients with methane-dominant SIBO can still continue with each of the steps of the treatment regimen discussed here. In particular, both the elemental diet and the other antimicrobial treatment options have been successful for these patients.


A Note on Hydrogen Diarrhea and SIBO Treatment

The presence of both hydrogen and hydrogen sulfide gases during the lactulose breath test is typically associated with diarrhea-dominant IBS (IBS-D).

Although the scientific research on this topic is evolving, there are various different strategies that are recommended for the overgrowth of bacteria species that cause increased amounts of hydrogen and hydrogen sulfide to be released during their fermentation.

It is generally accepted that following the steps outlined in this 7 step treatment plan can improve the symptoms of patients with a higher concentration of hydrogen sulfide-producing species in their GI tract.

Related Reading: Probiotic Tea: Types & Health Benefits Explained

Tips for Healing from SIBO

Graph up

Now that you understand the mechanisms behind the scientifically-proven steps that are incorporated into the natural treatment of SIBO, we wish you the best on your healing journey.

One thing to keep in mind during this process is that the path to better health is not straight. For many patients, this process will require continuous testing and readjustments of your diet, lifestyle and treatment methods until you can finally experience optimal health.

There is no one best treatment for SIBO. It is highly individualized.

Even after you experience a significant improvement in your symptoms, it is important to remember that it is normal to experience an occasional flare-up or relapse in your symptoms. During these difficult and frustrating times, remember to give yourself some credit for what you have accomplished so far and continue to implement health-promoting activities.

Restore Natural Gut Function Today With Our SIBO Elimination Toolkit!

Learn how to treat SIBO naturally and attain better digestive health with our SIBO Elimination Toolkit. It’s a comprehensive resource that covers everything you need to know about SIBO & IBS.


Get the Toolkit


We respect your privacy. Your information is safe and will never be shared.
Don't miss out. Subscribe today.
Share via
Copy link
Powered by Social Snap