Healing SIBO Naturally: 4 Steps to Total Gut Restoration!

Grace Clark-Hibbs

June 14, 2024

For many, healing SIBO naturally can feel like an impossible task. With so much conflicting and outright wrong information available on the internet, it’s no wonder you’re feeling overwhelmed and confused about where to even start.

But it doesn’t have to be that way!

This article will review what SIBO is, compare the research behind the most common treatment methods currently available, and break down the exact process I use to naturally heal SIBO is my clients.


What is SIBO?

Simply put, small intestine bacterial overgrowth, or SIBO, is an overgrowth and/or alteration of the bacteria in the small intestine. (1) Currently there are three types of SIBO – hydrogen, hydrogen-sulfide, and methanogen overgrowth.

Under normal circumstances our small intestine has a small number of bacteria living in it compared to our large intestine. While our bodies are designed to protect us from these bacterial colonies multiplying out of control, SIBO occurs when one or more of these protective mechanisms fail.

This overgrowth results in a variety of uncomfortable symptoms including gas, bloating, food sensitivities, constipation, and diarrhea. It can also result in malabsorption (i.e. the body being unable to effectively absorb nutrients from food), unintended weight loss, and nutrient deficiencies. (1, 2)

Once SIBO has been diagnosed, the only way to effectively get rid of it is to identify and address the root cause, eliminate the overgrowth and repopulate with “good” bacteria, address any nutritional deficiencies, and repair the integrity of the gut lining (i.e. “leaky gut”). (2)

Learn more about the different types of SIBO, how to differentiate and diagnose them, common risk factors, and more in our article Demystifying SIBO: An Ultimate Guide to Understanding & Conquering It.

SIBO treatment options

The most common treatment options used are antibiotics and herbal antimicrobials.

Other options that may have popped up during your search for answers include, The Elemental Diet and a variety of elimination diets, such as the Specific Carbohydrate Diet, the Bi-Phasic Diet, the Low FODMAP Diet, etc.

Let’s break down each of these.


The basic definition is that prescribed antibiotics are made in a lab, treat only bacterial infections, and usually attack only one stage of the bacteria’s life cycle. For example, they can either: (3)

  • attack the cell wall/outer coating of the bacteria
  • interfere with the reproductive process of the bacteria
  • OR block protein production

The primary antibiotic used for treating SIBO is rifaximin (brand name Xifaxan) because it has the most amount of research available to support its use. 

Practitioners like it because it’s a GI-selective antibiotic, meaning it stays in the gut and is not absorbed systemically. It also does not appear to negatively impact the “good”, or healthy bacteria, in the gut. (4

Herbal antimicrobials

In contrast, herbal antimicrobials come from whole plants, are made up of a variety of compounds and therefore have multiple uses. This means they are broad-spectrum and can have anti-bacterial, anti-fungal, and anti-viral effects, which is very helpful for clients who struggle with more than one type of overgrowth. 

There are a wide variety of herbal options for naturally treating SIBO available and the exact combination of these herbs should be customized to the specific needs of the client. 

While there isn’t as much research available investigating the effectiveness of natural SIBO treatment methods, recent research shows that healing SIBO naturally can be just as effective as rifaximin. (5)

The Elemental Diet

This is a meal-replacement diet that contains all the essential nutrients for survival broken down into their simplest forms. For example, proteins are in the form of amino acids, carbohydrates are in the form of short-chain maltodextrins, and fats are in the form of short-chain fatty acids. 

The elemental diet requires you to only consume powdered, predigested nutrients mixed with water for 2-4 weeks and nothing else. The idea is that the nutrients will be completely absorbed at the beginning of the small intestine and not be available to feed any of the bacteria downstream – essentially “starving” them out.

Some of the cons associated with this treatment method is that it is not sustainable for most clients, it’s very expensive (~$50 per day), and it has a high risk of recurrence. If even one bacteria remains in the small intestine after treatment, it will multiply as soon as regular food is eaten again. 

SIBO diets

There are a variety of SIBO diet plans that have been developed over the years. Their intent is to be used to assist an overall treatment protocol by depriving the overgrown microbes of their preferred food source. 

There is a lot of controversy within the functional nutrition world around their effectiveness and necessity. These types of diets are highly restrictive, cut out a lot of plant foods (and therefore fiber), and don’t actually address the root of the issue. 

I personally do not find them helpful and therefore do not use them in my practice. My approach is to help my clients gradually expand their diets and to ultimately incorporate as much variety (especially plant and fiber variety) as possible. 

Learn more about one of the most popular SIBO diet plans, The Bi-Phasic Diet, here.

How to choose the treatment option that’s right for you

In general, you should consider the following when deciding which treatment option is best for you:

  • Effectiveness (7)
  • Cost
  • Side effects
  • Length of time before improvement
  • Accessibility

If you’re still not sure, consult your provider or find a provider who specializes in SIBO to guide you through the decision making process.

Comparison of herbal treatment & antibiotics for SIBO

How long does it take to heal from SIBO?

The amount of time it will take to fully heal from SIBO will depend on a variety of factors. Some of these factors include:

  • The root cause/s
  • The length of time the SIBO has been present
  • Coexisting conditions
  • Compliance with the treatment plan, including diet and lifestyle recommendations

We’ll get into this in more detail in the following section, but in general the entire SIBO treatment protocol will last 12-28 weeks depending on the individual. 

This includes an initial, foundation laying phase that can last between 4-8 weeks (sometimes more). 

Followed by an active “kill” phase that will depend on whether you choose antibiotics or a natural SIBO treatment method. A round of rifaximin will usually last about 7-10 days depending on the dose. (6) While herbal antimicrobials will typically last between 4-12 weeks.

Finally, the gut repair phase typically lasts 6-8 weeks.

Now, let’s get into why you’re here.

How to heal SIBO naturally

We’re going to take a deep dive into the proven 4-step method I use with all of my SIBO clients.

Step 1: Identify & Address (the root cause)

This first phase of any plan to heal SIBO naturally should always focus on getting to the reasons why the SIBO developed in the first place, AKA the root cause. Because aren’t we all looking for a way to enjoy the foods we love without fear of how our body will react? I know I am!

The most common root causes I see in my clients include an altered migrating motor complex (i.e. dysmotility), poor digestive function (including low stomach acid), and stress (physical and emotional). And usually it’s not just one of these, but a combination. (1, 8, 9)

Let’s start with the first one.


Simply put, this is any change to the speed (increased or decreased) of the migrating motor complex (MMC).  

What is the MMC?

This is an involuntary action of your stomach and small intestine that occurs while you are fasting and stops as soon as you eat. The MMC is what moves your food through your gastrointestinal (GI) tract so that nutrients can be absorbed and waste can be removed. (10)

Slow gut motility

If this mechanism isn’t working correctly and transit time has slowed, resulting in constipation (i.e. fewer than one complete bowel movement per day) it can lead to bacterial overgrowth. (11, 12)

One way to address this is by taking prokinetics. Prokinetic agents are a group of drugs/supplements that cause the nerves along your GI tract to contract. This effectively increases the gut’s transit time and therefore increases the frequency of bowel movements. (13

These can either be prescribed or not, so work with your healthcare provider to determine which option is best for you. Examples of commonly used prokinetics for SIBO include:

Prescription Prokinetics:

  • Low Dose Naltrexone
  • Low-dose Erythromycin 
  • Low-dose Prucalopride

Non-prescription motility agents: (14, 15, 16, 17, 18)

  • MotilPro
  • Triphala
  • Iberogast
  • Ginger
  • Artichoke extract

I have used Naltrexone, MotilPro ginger, and artichoke extract to assist with my own dysmotility, as well as with my clients, and have seen great results over time. 

Poor Digestion

Our digestion is complicated and requires many processes to function smoothly and completely in order for the body to properly digest and absorb nutrients. These processes also act in a “domino-like” fashion. Meaning, the completion of each step triggers the next step.

A good example of this is the effect low stomach acid has on the release of pancreatic enzymes. The release of pancreatic enzymes can’t occur unless there is enough stomach acid present. The HCL, or hydrochloric acid, in stomach acid will trigger the release of pancreatic enzymes that will continue the digestive process. (19)

I always say that if something isn’t working well in the early stages of digestion (i.e. low stomach acid, poor pancreatic enzyme output, poor bile flow, etc.), digestive issues are going to snowball out of control as food moves into the small and large intestines. Creating an environment that is ripe for SIBO development. 

It’s important to correct these issues first, otherwise there is a high risk of SIBO recurrence, whether you use antibiotics or a more antimicrobials. Let’s look at what natural healing options are available for some of these. 

Low Stomach Acid

Long-term use of drugs meant to treat heartburn and stomach ulcers often leads to changes in the make up your gut, AKA your gut microbiome. (20) These drugs are called proton pump inhibitors, or PPIs, and one study claims they alter your gut’s microbiome even more than antibiotics. (21)

This change to your microbiome can leave you more susceptible to gut infections and bacterial overgrowth. (1, 21, 22) Gastric bypass surgery can also have a similar impact on stomach acid and the microbiome. (23)

Knowing this, what are your next steps?

PPIs should be used in moderation, with the input of your healthcare provider, and only as a last resort. There are lifestyle changes that can help alleviate symptoms of heartburn, including:

  1. Avoid trigger foods
    1. This is different for everyone, but common ones include high-acidic foods (like tomatoes and citrus), high-fat (including fried) foods, caffeine, alcohol, and soda.
  2. Eat smaller portions
  3. Wait before lying down after a meal
  4. Eat enough fiber (i.e. whole grains, fruits and vegetables)
  5. Quit smoking

Is chronic PPI use not your issue? Check out my article on how to naturally increase your stomach acid levels. 


Stress is considered any internal or external circumstance that causes a biological response. (24

Basically, the high-achieving, busy lifestyles that are commonplace in the Western world changes many of the body’s physiological systems. These systems include memory/cognition, the immune system, the cardiovascular system, and of course, the digestive system. 

If we look deeper into the effect stress has on our GI system, studies have shown that it: (24, 25)

  • Decreases nutrient absorption
  • Increases intestinal permeability or “leaky gut”
  • Decreases mucus/stomach acid/enzyme secretion
  • Increases inflammation
  • Alters gut motility
  • Negatively impacts the gut microbiota 

The most common stressors I see with my clients include:

  • Skipping meals
  • Undereating/overexercising
  • Never-ending to-do lists
  • Inadequate sleep
  • Mold exposure

It can take a while for my clients to fully accept the role their stress is playing on their symptoms. For many of them, it’s much easier to take the supplements than it is to make impactful changes to their lifestyle.

But I can speak from personal and professional experience, if your nervous system is constantly in “fight or flight”, your blood sugars are not being balanced, and you’re not getting adequate rest, no amount of supplements will be able to heal your SIBO.

Here are some of my favorite resources to help with stress management and nervous system regulation:

If you’re struggling with chronic bloat and would like help figuring out your root cause, check out our “Why Am I STILL Bloated???” quiz. In just 10 questions, you’ll get answers to what’s causing your bloat, plus actionable tips you can take today to start finding relief. 

Step 2: Eliminate & Replenish

It’s important to remember that healing SIBO naturally requires a series of layers – each new layer building on the one that came before it. As mentioned before, jumping straight to this step will only lead to modest improvements and significantly increases the likelihood of recurrence.

Therefore, an effective Eliminate & Replenish phase involves building on the foundations that were laid in the previous step. It will incorporate a combination of herbal supplements that rebalance the good and bad gut bugs, start fixing any gut permeability (AKA “leaky gut”), and reverse any nutrient deficiencies and/or inflammation. 

Common herbal supplements for naturally healing SIBO

An effective elimination phase will include a combination of the following:

  • Antimicrobial herbs (to kill off the overgrown bacteria)
  • A binder (to attach to the bacterial byproducts and pull them out via detox pathways)
  • A biofilm disruptor (in some cases you will need extra support to break through the outer protective layer of the bacteria)
  • Immune support (improves food sensitivities and helps eliminate harmful substances)
  • Digestive support supplements (i.e. stomach acid support, pancreatic enzymes, bile flow support, etc.)
  • Prebiotic fiber (important food source for the good bacteria and important especially when the diet is lacking in it)

The most common antimicrobials used in our practice include:

  • Biocidin – This is a blend of herbs including bilberry fruit extract (26), oregano oil (27), garlic bulb (28), and grape seed extract (29) that helps get rid of the bad bacteria and reduces bloating and gas.
  • Candibactin AR + BR – The active ingredients in this combo of supplements include berberine (30) and oregano oil to help rebalance the gut microbiota. Candibactin BR also contains ginger, licorice, and skullcap to support healthy liver and gallbladder detoxification.
  • Atrantil – This is a polyphenol-based supplement that addresses bloating and constipation, which are most common in methanogen overgrowth. The active ingredients here are quebracho heartwood extract (31), horse chesnut extract, and peppermint leaf.

Note, while the current available research supporting the effectiveness of these herbs on treating SIBO is promising, it is primarily on animals. That being said, I have used all of these products with myself and my clients and have seen great success.

Another note, no one needs all of these and in no way should you start taking any of them without consulting an experienced practitioner.

What about probiotics?

The short answer is that you should wait until Step 3, the repair and seal phase.

There hasn’t been much research done to thoroughly investigate the role probiotics should have in the SIBO treatment process. But what is available supports the use of probiotics after a round of herbal antimicrobials or antibiotics. (32

Basically, now that the overgrown bacteria has been cut back, we need to fill in the gaps, so to speak, with some healthy, protective microorganisms. Based on a 2024 review, Lacticaseibacillus casei was the most effective strain for reducing symptoms related to SIBO. (32

I usually recommend rotating probiotics every 2-3 months and will use a combination of live and active cultures, as well as spore-based depending on the client.

an infographic summarizing the main points of each step in the four step SIBO healing process

Step 3: Repair & Seal

Microbial imbalances, including SIBO, inevitably cause some damage to the gut lining and contribute to the body’s inflammatory response. Therefore, the Repair & Seal phase is all about ensuring the gut lining is tight and healthy and the good bacteria are able to flourish.

As mentioned above, this phase includes a combination of:

  • targeted probiotics
  • gut lining support nutrients (like immunoglobulins or colostrum)
  • zinc carnosine for stomach and intestinal tight junction support
  • a prebiotic

It’s also important to continue addressing the root causes identified in Step 1, as these were the reasons the SIBO developed in the first place.

Step 4: Sustain

Last but not least, is the sustaining phase! How are you going to make sure you only have to go through this process once? 

Unfortunately, SIBO has a high recurrence rate in people who rely on antibiotics or supplements alone. This is why it is so important to take a holistic approach to treatment. If you fully understand your root causes and know how to troubleshoot your symptoms going forward, you have a much greater chance of kicking SIBO to the curb once and for all. 

Many providers will suggest a SIBO diet plan to follow at this point – learn about the most common ones here. The idea is that you want to deprive any remaining bacteria of their preferred food source while you finish repairing the gut. However, it’s not possible to deprive the bad bacteria of food without also depriving the good bacteria at the same time. 

Instead, I work with my clients to increase their diet variety (especially plant variety). This ensures that you get all of the nutrients required for maintaining a healthy body and the good gut bacteria get what they need to flourish.

Final Thoughts

In conclusion, healing SIBO naturally requires a 4-step, holistic process. 

Step 1 consists of identifying and starting to address your specific root causes. This is also when you should start establishing some foundational habits that will serve as the basis for your whole protocol.

Next you can move into Step 2, the active elimination phase. This is where the overgrown bacteria will actually be killed off. Followed by Step 3, which involves repairing the gut lining and repopulating the good bacteria. And finally, Step 4, the maintenance phase. 

This can be a long and challenging process, so build yourself a good support system that includes a functional provider with experience in treating SIBO. 

If you’ve been struggling with bloat, constipation or other IBS symptoms and need some insight into your root causes, check out my Why Am I STILL Bloated Quiz!

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Remember: this post is for informational purposes only and may not be the best fit for you and your personal situation. It shall not be construed as medical advice. The information and education provided here is not intended or implied to supplement or replace professional medical treatment, advice, and/or diagnosis. Always check with your own physician or medical professional before trying or implementing any information read here.

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Grace sitting

Hi, I’m Grace!

A registered dietitian & gut health expert based in Portland, OR with my husband & orange tabby, Tony.


And I’ve been in your shoes!


As someone who has struggled with my own severe, chronic, & painful bloat & constipation for over 15 years, I understand what it’s like not to get answers from conventional medical support.


This is why I’ve made it my mission to help everyone who feels held back & defeated by their gut find freedom from their embarrassing symptoms FOR GOOD!

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