Demystifying SIBO: An Ultimate Guide to Understanding & Conquering It

SIBO has become a hot topic on the internet over the past 10 years, which usually means there’s a lot of misinformation out there. 

This article is designed to provide a comprehensive, research-based overview of what it is, what the risk factors are for developing it, how to test for it, and possible treatment options. 

Lots to cover, so let’s get started!

What is SIBO?

SIBO, or small intestine bacterial overgrowth, is when too much bacteria is present in the small intestine. This is an issue because your small intestine is where the majority of your digestion and absorption happens and should be almost completely sterile. (1)

When bacteria and other microbes find their way into your small intestine they are met with an unlimited food source and they start to grow out of control. Think of it like weeds in a garden – if given the opportunity, these microbes will happily take over the “empty field” of your small intestine and crowd out everything else. 

This overgrowth leads to the unabsorbed carbohydrates in your gut to ferment, which leads to gasses being produced as byproducts. These gasses include hydrogen, methane, and hydrogen sulfide. The type of gas that’s produced is determined by the type of bacteria that are present and the amount of time they’ve been growing. 

The longer the microbes are present, the more fermentation that occurs, and the more fermentation that occurs the more gasses that are produced. This leads to more uncomfortable symptoms, like bloat, changes in bowel habits, food sensitivities, fatigue, and nutrient deficiencies. And before you know it, you find yourself in a very vicious cycle.


In a 2023 research article, SIBO was detected in almost 34% of patients struggling with gastrointestinal (GI) issues that were instructed to take a breath diagnostic test. (2) Another study found that 31% of people who have been diagnosed with irritable bowel syndrome (IBS) also had SIBO. (1) Despite this prevalence, many conventional practitioners are unfamiliar with how to effectively address SIBO with their patients.

Risk Factors 

There are a wide variety of conditions and circumstances that put you at higher risk for developing SIBO. Some of these include: (2)

  • Diabetes
  • Heartburn/GERD medications (i.e. Proton Pump Inhibitors or antacids)
  • Gallbladder removal
  • Diet low in fiber and protein
  • Chronic alcohol use
  • Abdominal trauma or surgery
  • Celiac disease
  • Inflammatory Bowel Disease
  • Liver disease
  • Hypothyroidism

Hydrogen vs. Hydrogen Sulfide vs. Methane SIBO

Let’s dive into the three known types of SIBO – hydrogen, hydrogen sulfide, and methane – what they are, how they’re different, and an overview of the signs and symptoms of each.

Hydrogen SIBO

This is often considered the first step of developing SIBO. It is associated with loose stools or diarrhea accompanied by rotten egg smelling gas, but not always. Other possible symptoms include:

  • Bloating
  • Undigested food in the stool
  • Abdominal pain
  • Nutrient deficiencies
  • Headaches
  • Food sensitivities
  • Skin rashes

In general, the steps of hydrogen SIBO development are:

  1. Opportunistic bacteria find their way into the small intestine.
  2. Bacteria causes unabsorbed carbohydrates to ferment. 
  3. Bacteria feed on fermented carbs and multiply, leading to the bacteria growing out of control.
  4. Overgrown bacteria produce hydrogen gas as a byproduct of consuming fermenting carbohydrates.
  5. Excess hydrogen gas leads to uncomfortable gut symptoms.
Infographic explaining the cycle of how hydrogen SIBO develops and multiplies.

Hydrogen-Sulfide SIBO

The bacteria present in this situation are called sulfate-reducers and will feed on the hydrogen that is produced by other bacteria. The sulfate-reducers then produce hydrogen sulfide gas as an additional byproduct. 

Hydrogen-sulfide SIBO is often considered the most uncomfortable form of SIBO. Some of the additional symptoms experienced by people with hydrogen sulfide SIBO include:

  • Bladder irritation/interstitial cystitis
  • Intolerance to noise
  • Body pain
  • Extremely tingly
  • Histamine intolerance
  • Sulfur smelling gas
  • Nervous system strain (i.e. anxiety, hypervigilance)
  • Alcohol sensitivity (hives, severe headaches)

Please note, this is the newest form of SIBO to be identified and studied, therefore published research on this condition is limited.

Infographic explaining the cycle of how hydrogen-sulfide SIBO develops and multiplies.

Methane SIBO

Similar to hydrogen-sulfide, methane SIBO develops as a second stage to hydrogen SIBO. In this case, microorganisms called archea consume the hydrogen gas produced by the hydrogen producing bacteria. Then the archea produce methane gas as a byproduct of this process. Methane gas slows everything down in the digestive process, often leading to constipation and bloating. It has also been associated with a strong, “barnyard-like” body odor.  

This becomes a vicious cycle and it can be difficult to identify which came first, the slow motility or the bacterial overgrowth. Getting rid of methane SIBO is more challenging than hydrogen SIBO and usually takes more time. 

Infographic explaining the cycle of how methanogen overgrowth (methane SIBO) develops and multiplies.

While it can feel daunting to address methane SIBO it’s important to find a practitioner who is well versed in treating SIBO because there are long-term negative effects of not addressing it. Some of these consequences include:

  • Malnutrition
  • Nutrient deficiencies
  • Decreased quality of life
  • Social isolation

Overlap with Other Digestive Issues

A question that comes up a lot is how to identify whether you have irritable bowel syndrome (IBS), SIBO, or both because there are a lot of overlapping symptoms. In fact, a recent research review showed that 31% of study participants with diagnosed IBS also had some form of SIBO. (3)

IBS is considered a functional gastrointestinal (GI) disorder that is characterized by abdominal pain, bloating, and altered bowel habits. (4) As you can see, this definition is very broad and often becomes the “catch-all” diagnosis for all gut issues that can’t be confirmed with a conventional test or procedure, such as a celiac blood test, colonoscopy, endoscopy, etc. 

If you are experiencing chronic constipation and/or loose stools, foul smelling and trapped gas, bloating no matter what you eat or drink, and probiotics often make you feel worse, I recommend working with a practitioner to test for SIBO. 


There are two direct ways of identifying SIBO – an intestinal culture and a breath test – and one indirect way – a stool test. We will break down all three in this article. 

Small Intestine Aspirate Cultural

This procedure involves an upper endoscopy in which ~3 mL of fluid is collected from the duodenum (this is the first section of the small intestine and is connected to the bottom of the stomach). This fluid is then sent to the lab to be tested for the presence of bacteria. (5)

Widely considered the gold standard of SIBO testing, however it is not done very often. This is because it’s incredibly invasive to complete, is time consuming, and is very expensive. It’s also not widely known or performed in conventional GI doctor’s offices. 

Breath Testing

There are two breath tests that are most commonly used to diagnose SIBO. One is a glucose breath test and one is a lactulose breath test. 

Both require the person to drink a special liquid (either glucose-based or lactulose-based) and then measure the levels of hydrogen gas produced through the breath at set intervals after ingestion. (6) These tests are not as accurate as the small intestine aspirate culture, but they are much more accessible and far less invasive. 

However, they do require strict pre-test preparation. This preparation includes following a special limited diet the day before and day-of testing, stopping the use of laxatives, stool softeners, stool bulking agents, and antacids one week before the test, and waiting at least two weeks after taking antibiotics or antifungals. Not following these preparation guidelines may result in an inaccurate result. (7)


The GI MAP is a stool test that must be ordered by a practitioner and is completed in the comfort of your own home. After collecting your sample, you will send it back to the processing lab and the results will be sent to the practitioner who ordered the test. All instructions, collection materials and shipping supplies are included with the test. (8)

While the GI MAP can’t officially diagnose SIBO, it can provide valuable insight into what may have caused the SIBO in the first place, aka the root cause. It does this by providing detailed information about what’s going on throughout the digestive system, including:

  • Is dysbiosis (imbalances of “good” and “bad” gut bugs in the large intestine) present?
  • Is fat digestion effective?
  • Are enough pancreatic enzymes present?
  • Are the liver/gallbladder functioning optimally?
  • Is the gut immune system suppressed or overactive?
  • Is inflammation present in the gut?
  • Are there any active gut infections?
  • Are there any parasites/worms present?
  • Is the gut lining healthy or are there signs of gut permeability (aka “leaky gut”)?

This may be a controversial take, but in my professional opinion it’s not as important to know the amount of overgrowth that is present as it is to know what caused the SIBO in the first place. SIBO is essentially a side effect of something else and until the root cause is addressed, a relapse is inevitable.

Now, let’s look at possible root causes of SIBO.

Possible Root Causes

What is a root cause? A functional nutrition approach differs from a conventional approach by looking for and addressing the underlying cause/s of the symptoms you’re experiencing. This is usually referred to as the root cause. 

As mentioned earlier, SIBO is often mistaken as the root cause of symptoms but it’s actually more of a symptom. The only way to get rid of SIBO and prevent it from returning is by identifying what led to the development of the overgrowth in the first place. 

Three of the most common root causes of SIBO are described below.

Poor Meal Hygiene

Meal hygiene refers to how someone eats. In other words, the circumstances that are present internally and externally while someone is eating. Examples of poor meal hygiene include eating while distracted and/or stressed, eating too fast, not chewing enough, waiting too long to eat, and drinking a lot of fluids while eating.

Digestion works from the top down and actually starts before food ever enters the mouth. This is referred to as the cephalic phase of digestion and is an automatic reflex in response to the thought, sight, and smell of food. (9

This reflex triggers important digestive secretions such as saliva, stomach acid, enzymes, etc. Skipping or rushing through this phase of digestion is going to make digestion more difficult and contribute to an environment that is susceptible to SIBO. 

Poor Digestion

Our digestion is complicated and requires many processes to function smoothly and synergistically in order to properly digest and absorb nutrients. In addition, these processes are triggered sequentially. Meaning, the next process or reaction can’t happen, or happen effectively, until the one before it has been completed. 

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 breaking down the proteins, carbohydrates, and fats present in the food you just ate. (10)

For more information on low stomach acid and how to increase it naturally, see my article, 10 Ways for Naturally Increasing Stomach Acid

Poor bile flow from the gallbladder and liver is another situation that can occur. Bile is a fluid produced by the liver and stored in the gallbladder and is released in response to consuming fat. (11) Sometimes the pathway between the gallbladder and the digestive tract can get clogged or slowed down. This can lead to slow digestion and contribute to an environment that is ripe for the development of SIBO. 

Chronic Stress

This is probably one of the most significant underlying causes of SIBO because of the impact stress has on the entire digestive process. It’s important to remember that for our purposes, stress can be good or bad. 

In fact, stress is considered any internal or external circumstance that causes a biological response. (12) 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: (12, 13)

  • 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 

There is even research to show that stressors experienced in childhood can contribute to gut inflammatory diseases (like Crohn’s disease) in adulthood. (14)

Other common stressors on the body include:

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

Other Possible Root Causes

  • Slow gut motility (how quickly food moves through the digestive system)
  • Dysbiosis (an imbalance of “good” and “bad” gut bugs) in the large intestine
  • Hormone imbalances
  • Poor thyroid function
  • High inflammation
  • Drug side effects
  • Chronic excessive alcohol intake

SIBO Treatment Options

Currently there are two primary treatment options for SIBO – prescription antibiotics and herbal antimicrobials – and one that is not very common for a variety of reasons that we’ll go into – the Elemental Diet. 

It’s VERY important to receive a personalized treatment plan that is based on your symptoms and medical history and takes into account what you have tried in the past. This is for a couple of reasons. One, because your root cause is going to be different from someone else’s. And two, your body and GI system may be more sensitive and require a gentler approach. 

It’s also VERY important to work with a healthcare provider that is well-versed and familiar with SIBO. Having someone who has a clear roadmap of where to start, who can support you throughout the treatment process, and who can help troubleshoot situations and symptoms along the way is invaluable. 

SIBO treatment is not a linear journey, there will inevitably be ups and downs along the way, so find someone who you trust will be in your corner every step of the way. 

OK, let’s dive in.


Rifaximin is the primary pharmaceutical used to treat SIBO today because it has the most research to support its effectiveness. 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. (15) A round of rifaximin treatment usually lasts about 7-10 days depending on the dose. (16

So, how effective is rifaximin?

Studies have shown mixed results in its effectiveness at eradicating SIBO, with a range of 49% to 64% of participants having a normal breath test immediately after treatment depending on the study. (17, 18) Another study found that 47% of participants (35 out of 80) had a recurrence of their SIBO nine months after a week-long treatment of rifaximin. (19

Administering multiple rounds of antibiotics runs the risk of causing antibiotic resistant bacterial strains to develop, making this treatment method less and less effective. This highlights how important it is to address the root cause in order to prevent a relapse and to promote long term relief – simply killing off the bacteria is not enough. 

Herbal Antimicrobials

There are a wide variety of herbal options available and the combination of these herbs should be customized to the specific needs of each client. They are also more broad-spectrum than antibiotics. Meaning they can get rid of bacteria, viruses, fungi, and parasites, which is helpful for clients who struggle with more than one type of overgrowth. Treatment length will vary depending on the types of herbs being used, but will typically last between 4-12 weeks. 

So, how effective are herbal antimicrobials?

One study found that a 4 week round of herbal therapy was slightly more effective at eliminating SIBO than a round of rifaximin (46% compared to 34% respectively). (18) Another study found it to be as effective as rifaximin and just as safe. (20

While there is no risk of developing antibiotic resistance with herbal treatments, we are still learning about effective dosages because there aren’t as many published studies on this treatment method. This makes it extra important to vet the practitioner supporting you through this process. 

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.

So, how effective is the elemental diet?

A 14-day trial of this treatment method resulted in 80% of the study participants having a normal breath test at the end. (21) While this sounds like the most effective option, this study did not follow-up with these participants after they resumed eating their normal diets. 

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. 

Other Supplements

Other types of supplements can be helpful tools for addressing the root cause of the SIBO, supporting a healthy gut long-term, and preventing a relapse, but they are not an effective treatments on their own. Let’s look at a few that get asked about a lot.


Pre- and probiotics are essential components of a well-rounded SIBO treatment plan. Probiotics help replenish the “good” bacteria that are necessary for establishing a healthy gut microbiota, thus preventing a relapse. And prebiotics act as an important food source for those beneficial bacteria, helping them to reproduce and “crowd-out” the overgrowth long-term.

There is limited research on the use of probiotics as a SIBO treatment on their own and the studies that do exist have shown mixed results. (22) However, one study determined that administering probiotics alongside antibiotics as a maintenance regimen provided better protection from a SIBO recurrence than antibiotics did on their own. (23

Digestive Enzymes

Insufficient digestive enzyme secretion from the pancreas and/or small intestine can contribute to the development of SIBO. Therefore, in some cases it is necessary to supplement with digestive enzymes before, during, and possibly after treatment to help facilitate proper digestion. 

This is part of addressing the root cause, supporting the body’s natural processes, and preventing the overgrowth from returning.

Stomach Acid Support

Stomach acid, which consists primarily of hydrochloric acid (HCL), is an essential component of healthy digestion, especially protein digestion. A condition called hypochlorhydria, or not having enough stomach acid, is widely considered a risk factor for developing SIBO. (6, 7, 18, 22)

Digestion starts at the top and if anything is not working well early in the process –  not chewing enough, low stomach acid, insufficient pancreatic enzymes, etc. – the problems are only going to get worse down the line. 

Not having enough stomach acid slows down digestion by causing the food to take longer to break down enough to be able to move on to the next stage. HCL is also an important trigger for the release of pancreatic enzymes. Meaning, inadequate HCL will lead to inadequate pancreatic enzymes, which will lead to food sitting in the small intestine and fermenting. As we learned earlier in this article, this is what will eventually lead to bacterial overgrowth.

All in all, SIBO treatment is highly individualized and requires looking at the entire digestive process to be effective. 

Final Thoughts

Small intestine bacterial overgrowth, or SIBO, occurs when opportunistic bacteria are able to grow out of control in the small intestine. This leads to fermentation and gas production, which often leads to changes to bowel movements, uncomfortable bloating, food intolerances, and nutrient deficiencies. 

For many, being diagnosed with SIBO brings a sigh of relief because they finally have a reason for their discomfort. However, this is only one piece of the puzzle. Figuring out what factors led to the development of the overgrowth in the first place (i.e. the root causes) is the key to finding long-term, sustained relief.

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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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