SIBO Guide (to help you eliminate IBS)


Irritable bowel syndrome is commonly known as IBS and it is estimated that this affects around 11% of the population - SIBO is the main cause of IBS and as many as 60-80% of people with IBS have SIBO.

Have you been told you have IBS, and you will just have to put up with it? In this SIBO guide, we are going to break down the step-by-step process to see if you have SIBO and what are the best treatment options for SIBO.

Have you tried increasing fiber or adding probiotics only to find that your IBS symptoms are worse?

If this sounds like you then you may have SIBO.

First, let’s look at what SIBO is, what causes it and how to identify if you have SIBO or if your gut issues are caused by something else.

What is SIBO (and what’s the connection to IBS)

SIBO stands for Small Intestinal Bacterial Overgrowth and while it is coming to the attention of more and more doctors, for many doctors it is not on their radar as they were not taught about SIBO in medical school.

Much of the research into SIBO has taken place in the last ten years, so unless your doctor is keeping up with the latest research they are probably not testing you for SIBO, and if you have digestive symptoms you are probably given the label of IBS.

You should have lots of bacteria in your large intestine but very little in your small intestine, so if you get an overgrowth of bacteria in the small intestine this is known as SIBO.

The bacteria in the small intestine can ferment fiber and starches from the carbohydrates you are eating, this produces gases that damage the small intestine, and cause symptoms such as bloating, pain, diarrhea, constipation, and reflux.

Do these symptoms sound familiar? They are all of the symptoms of IBS, so if your doctor does not test you for SIBO and can find nothing else wrong then you are labeled as having IBS - rather than given a step by step treatment plan.

This can be frustrating, especially if you have had a colonoscopy, gastroscopy or an ultrasound and they can’t find anything wrong - that is because these tests can only identify structural or physical issues like gastritis, polyps or cancer

While it is great to rule out serious pathologies these types of tests don’t identify SIBO.


Symptoms of SIBO

You don’t need to have all of these symptoms if you have SIBO, sometimes people can just have 1 or 2 while in severe cases you may have all of these symptoms.

  • Bloating and gas 
  • Constipation/diarrhea 
  • Abdominal pain
  • Leaky gut symptoms: rashes, food allergies 
  •  Belching, flatulence
  • Reflux
  • Nausea 
  • Steatorrhea (fat in your stool)

As well as the digestion symptoms listed, SIBO can also cause a number of other digestion problems.

  • Microvilli damage - this can lead to leaky gut, food intolerances, histamine intolerance and damage to the brush border enzymes that can affect the absorption of nutrients.
  • Bile acid deconjugation - leading to fat malabsorption which can lead to deficiencies in your fat-soluble vitamins A, D, E and K
  • Impaired motility - this makes the problem of SIBO worse as it is harder to clear the bacteria and causes constipation
  • Nutrient deficiencies - especially vitamin B12, magnesium, zinc, and iron (but be careful with iron supplements as this can make SIBO worse)

SIBO and Associated Symptoms

Besides the specific digestive symptoms that SIBO can cause it is also associated with a wide range of other health conditions.

  • IBD
  • Fibromyalgia
  • Interstitial cystitis
  • Restless leg syndrome
  • Acne Rosacea
  • Atherosclerosis
  • Diabetes
  • Hypothyroidism
  • Scleroderma
  • Fatty liver
  • Chronic prostatitis
  • Diverticulitis
  • Gallstones

If you are suffering from IBS or some other digestive or hormonal issue and can't figure out the right course of action, then just click the button below and schedule a consultation with me and I can help you resolve your digestive or hormonal issues.

Rather than a one off SIBO test to diagnose SIBO I recommend a device called Food Marble as it costs about the same as a SIBO test but you can use it to test for SIBO many times, as well as your reactions to specific foods.

To do SIBO testing with Food Marble you need to be connected to a practitioner, my clients get a 15% discount on the Food Marble Aire 2 device and you can schedule an appointment below.

Different Types of SIBO

Types of SIBO

There are two main types of SIBO.

  • SIBO-C which is predominantly constipation and this affects about 35% of people with SIBO
  • SIBO-D which is predominantly diarrhea or loose stools and affects about 40% of people with SIBO
  • There is also a third type called SIBO-M where you can alternate between constipation and diarrhea and this affects about 25% of people with SIBO

The gases that are predominant in SIBO:

  • Methane Gas - main symptoms are constipation, nausea, and belching
  • Hydrogen Gas - main symptoms are diarrhea or alternating diarrhea/ constipation, abdominal cramping and fibromyalgia-like symptoms
  • Hydrogen Sulfide Gas - main symptoms are diarrhea, foul gas, bladder pain, and joint pain

What Causes SIBO

There are several causes of SIBO from food poisoning to physical adhesions and identifying the underlying cause is important for long term treatment success.

Here are the 4 key areas that can lead to SIBO

  • Damage to the migrating motor complex (MMC) and Enteric Nervous System
  • Bacteria not cleared out of the small intestine leading to overgrowth
  • Can be caused by Traumatic Brain Injury (TBI) which affect the vagus nerve and the messages to the gut
  • Low thyroid function leads to slower motility and constipation
  •  Chronic infections from the large intestine, important to assess large intestine with a stool test like the GI-MAP test
  • Mold toxicity can be a cause and a contributing factor to why SIBO treatments are not successful
  • Diabetes leads to slower motility and gastric emptying
  • Scleroderma due to a weakening of the gut muscles
  • POTS or Mast Cell activation syndrome can also affect motility leading to SIBO
  • Altered Anatomy/Structure
  • Bacterial clearance blocked by abdominal adhesions from surgeries
  • Ileocecal valve dysfunction 
  • Endometriosis is the most common cause of non-surgical adhesions
  • Altered Physiology/Function
  • Bacteria not killed in the stomach because of low stomach acid - test for H.pylori
  • Chronic stress, in constant “flight or fight” - assess adrenal function
  • Secretory IgA deficiency which can lead to dysbiosis
  • Poor bile flow
  • Dysbiosis and overgrowth of opportunistic bacteria
  •  Medications
  • Opiates and antispasmodics which slow motility
  • Proton pump inhibitors which lower stomach acid
  • Tricyclic antidepressants can also slow motility

Diagnosis of SIBO and IBS

The best way to diagnose SIBO is with the Food Marble breath test, as you can use this to do multiple different tests with glucose, lactulose, and fructose.

The reason it is better to test with multiple different challenge agents is that you may not show a positive result for glucose but can a positive result for fructose, this is because different bacteria will react differently to fructose, glucose and lactulose.

So if you have done a SIBO test which came up negative but you have the classic signs then you may have had a positive results using a different challenge agent.

There are also other signs and symptoms that can be present to help you identify if SIBO is the cause of your IBS symptoms

  • Your symptoms get worse with prebiotics or probiotics! Both prebiotics and probiotics can be fantastic to improve gut health but prebiotics in particular and some probiotic supplements can make SIBO worse
  • Symptoms start after a case of gastroenteritis! Food poisoning can cause severe digestion symptoms but after a few days you should be getting back on track, but if your symptoms continue the food poisoning may have lead to SIBO
  • Your symptoms improve while you are taking antibiotics but return again after a week or two. Antibiotics can often suppress the SIBO bacteria without fully eliminating it so while you are taking the antibiotics you feel better (this does not happen to everyone with SIBO and some people feel worse)
  • Taking fiber supplements leads to your constipation getting worse. Fiber is great for gut health but if you have SIBO it can “feed” the bacteria in the small intestine and affect motility leading to a flare-up of your symptoms
  • Symptoms worsen with xylitol and other sugar alcohols as they are high FODMAP foods that can also “feed” the bacteria in the small intestine
  • Celiac patients who continue to have symptoms whilst on GF diet

While these signs and symptoms can give clues to whether you have SIBO the best way to diagnose is with the breath test.

Glucose is used to assess SIBO but this is absorbed in the upper part of the small intestine so it may lead to more false negative results.

Lactulose is the more common agent used but this has the potential to have false positives.

Fructose is rarely used but this is another way of assessing SIBO and it would be very expensive doing 3 different commercial SIBO tests so this is why I recommend the Food Marble device - and there is no cost to retest.

SIBO Preparation Guidelines- what to avoid

1 month prior to testing:

  • No Colonoscopy
  • No antibiotics

1 week prior to testing:

  •  No probiotics including fermented foods
  • No herbal antimicrobials (unless re-testing)

1 day prior:

  • No laxatives
  • No digestive aids like Betaine HCL and digestive enzymes

NOTE: proton pump inhibitors are no longer to be discontinued but you can stop one day before testing.

  • In the 24 hours before the test you need to follow a special low fermentable carbohydrate diet

Rather than a one off SIBO test to diagnose SIBO I recommend a device called Food Marble as it costs about the same as a SIBO test but you can use it to test for SIBO many times, as well as your reactions to specific foods.

To do SIBO testing with Food Marble you need to be connected to a practitioner, my clients get a 15% discount on the Food Marble Aire 2 device and you can schedule an appointment below.

Interpreting SIBO Results

This is where it pays to work with an experienced practitioner as SIBO test results are not always “black and white” and can be open to interpretation.

Also, different labs will have different reference ranges and it is important to take into account your signs and symptoms, the level of bacteria rise and when that bacteria rises during the testing period.

The key things to focus on with SIBO results:

  • We are focusing on the first 90-100minutes from baseline as past 120 minutes a rise in gases could be caused by fermentation in the large intestine
  • Hydrogen (H2) – rise of 20ppm
  • Methane (CH4) – rise of 12ppm
  • Combined H2, CH4 – rise of 15ppm
  • We cannot directly test for hydrogen sulfide YET but if a client has the signs and symptoms of hydrogen sulfide and gets a flatlined close to zero result on the SIBO test that could indicate an overgrowth in hydrogen sulfide. 

Other Tests to Consider (NOT Diagnostic for SIBO)

Organic Acids Test

Organic Acids Test as this is one of the best ways to assess candida and it can also show other markers indicative of SIBO. This is also a good test to assess for reasons behind fatigue and mood problems.

Blood Tests

Blood tests - low chloride could indicate hypochlorhydria (low stomach acid), high folate is possible because of increased bacterial production and low B12 due to poor absorption.

Vibrant Wellness Gut Zoomer Stool Test

The Gut Zoomer stool test can also be helpful in assessing the health of the large intestine, plus other intestinal health markers like digestive enzymes, SIgA, fecal fat and Zonulin which can be impacted by SIBO.

The Gut Zoomer also has a section on the bacteria levels of common bacteria associated with SIBO. If you have gut issues and you are wondering if you should do a SIBO test OR a stool test I would always recommend the Gut Zoomer test first as it gives us so much more information.



SIBO Treatment


SIBO Bi-Phasic Diet

The regular SIBO bi-phasic diet has been around for a few years and now there is also a vegetarian version of the SIBO bi-phasic diet.

Other SIBO diet options that I use with clients are the low histamine and low sulfur versions of the SIBO diet. 

The vegetarian version of the SIBO diet is great as I find that a lot of vegetarians can have SIBO due to the high fiber that comes with a vegetarian diet.

Aim of the SIBO Bi-Phasic Diet

  • Reduce fermentable carbohydrates
  • Reduce symptoms to provide relief while implementing a treatment plan
  • The first phase is stricter and we often implement this phase while we are waiting for the SIBO results to return
  • The second phase increases some of the carbohydrate foods which can be effective when using antimicrobial treatment during the “killing” phase of the bacteria overgrowth.

The SIBO Bi-Phasic diet is not a long term diet and ideally, this will be a 10-12 week plan with more and more foods being able to be added in as the treatment plan progresses.

For some people, as they reintroduce foods into the diet they may notice that certain foods can trigger symptoms, if this is the case these foods need to be eliminated and we can try adding them again later.

Phase 1 of the SIBO diet is the most restrictive.

No grains, dairy, honey, legumes, fruit. Basically protein and vegetables. 


The aim of phase one is rapid symptom relief, once symptoms improve by 50-60% we can then start to reduce foods from phase 2.

If someone is already very underweight I might only do phase 1 of the diet for a few days and then introduce more carbohydrates in the form of plain white rice.

NOTE: It is important to be cautious of someone has a history of eating disorders if they are planning to do the SIBO diet, they may be advised to do a modified version of phase 2 so that it is not so restrictive.

Phase 2 of the diet is less strict.

Treatment Flow for Addressing SIBO

  • Consultation and organize tests
  • Once testing is finished start the phase 1 restricted diet until we wait for the results
  • Consultation to go over results and assess changes from phase 1 diet
  • Implement a treatment plan based on the results*treatment is typically 8-12 weeks depending on the results
  • Schedule follow up appointment and assess treatment plan and whether to retest - if results are clear focus on gut healing and motility.

SIBO Antimicrobial Treatment Plan

We have 3 main choices when it comes to the treatment of SIBO

  • Herbal Antimicrobials and nutritional treatments which is usually my first choice
  • Antibiotics like Rifaxamin which can be expensive and difficult to get, plus they are not more effective than herbal antimicrobials
  • Elemental diet for 2-3 weeks which is probably the most effective treatment but being a liquid only diet is difficult for most people to do. It is possible to do a partial Elemental diet and have this for one meal of the day.

Herbal and Nutritional Medicines to Treat SIBO

  • Herbs often have multiple effects and can treat both the large and small intestine, they can treat bacteria, parasites and fungal infections
  • Herbal medicines can also help to treat motility issues
  • There are great natural biofilm treatments
  • Don’t damage the beneficial bacteria in the same way antibiotics can
  • You can use specific probiotic strains to complement the treatment plan
  • The treatment plan is normally 8-12 weeks which is longer than antibiotics which are 2-4 weeks and the Elemental diet which is 2-3 weeks
  • Quality herbal products can be expensive (though still often cheaper than Rifaxamin)
  • Some people can react to herbal treatments, especially if there is an underlying mold toxicity

Herbal and Nutritional Medicines and SIBO - things to consider

  • It is important to use practitioner quality products and make sure that you are taking the correct dose, as low dose supplements will be ineffective.
  • Address low levels of stomach acid and pancreatic enzymes if necessary
  • Biofilms are likely with long term bacteria and fungal infections, it is usually best to treat biofilms with a quality biofilm product like Interfase plus or Biofilm defense. Biofilms are like a protective mucous shield that surrounds the bacteria and make it difficult for herbal antimicrobials and antibiotics to kill the bacteria.
  • If constipation is an issue then you also need to treat motility with magnesium based products or herbal motility products like Iberogast. Specific strains of bacteria can also help with constipation like Lactobacillus reuterii DSM17938 and Bifidobacteria lactis HN019.

Antibiotic Treatments for SIBO - Rifaximin (Xifaxan)


Rifaxamin is one of the better antibiotics available as it mainly works in the small intestine and does not have the negative effects of other antibiotics on your “good” bacteria in the large intestine. Rifaxamin is not a "magic" solution for SIBO and many people take this and do not get results.

However, to make Rifaxamin more effective it is often combined with another antibiotic like Neomycin or Metronidazole, and these antibiotics can affect the beneficial bacteria in the large intestine.

Rifaxamin is more effective for hydrogen dominant SIBO, and its benefits have shown to be enhanced when using Partially Hydrolyzed Guar Gum (PHGG)

A typical Rifaxamin treatment is for 2 weeks which is probably why it does not have a high success rate as often a 4-week treatment is needed.

One of the negatives of Rifaxamin is that it does not address fungal infections which are also present, so you may want to consider adding in an anti-fungal treatment at the same time.

Elemental Diet and SIBO


The Elemental Diet is one of the most effective treatments for SIBO, but it is not always my first choice of treatment as for many people it is difficult to follow.

The Elemental Diet is a complete liquid meal replacement using a specially formulated combination of free form amino acids, rapidly absorbed glucose and MCT or another type of quality fat.

This formula is rapidly absorbed in the upper part of the small intestine so essentially it starves the bacteria of any food but still provides enough calories and nutrients for the patient.

It is not a low-calorie diet but because you are consuming the same liquid formula for two weeks people often struggle to have enough calories in a day so it can lead to weight loss and is mentally challenging to do. So the Elemental diet is not ideal if you are already underweight.

The Elemental diet is done instead of herbal antimicrobials or antibiotics, but sometimes in difficult cases, I have done herbs either before or after the Elemental diet.

There are several commercially available formulas and with my clients I recommend the Moss Nutrition brand, this requires a consultation and a practitioner code to be able to order this brand.

SIBO and Bacteria “Die-Off”


Die-off, also known as a Hercksheimer reaction is a massive increase in lipopolysaccharides (LPS) and other bacterial and fungal toxins as these organisms die and this can lead to fatigue, headaches, diarrhea in the first few days of treatment.

Not everyone experiences die-off and many people think that it is a reaction to the supplements.

The best option is to reduce the supplements and then very slowly increase the dose to the therapeutic dose, this helps to minimize symptoms.

Other options to improve the bodies detoxification pathways and minimize the negative effects of die-off include:

  • Sauna
  • Exercise
  • Ensure that you drink optimal levels of fluids
  • Activated Charcoal, or Bentonite Clay or Zeolite

What if SIBO Symptoms are Not Improving?

Many people get significant improvement in the first month or two of treatment, especially with bloating and stool quality, but what if you not seeing improvement, what can be done?

The first thing I check is to make sure that the supplement dosage is correct and that a biofilm agent is being used as this is a common reason for people not getting results with their treatment.

If you have not already done a stool test like the Gut Zoomer / or the GI Map test/ Organic acids test then this is a good idea to assess for other possible infections like candida or mold.

Other infections like Helicobacter pylori, mold or Lyme disease can also affect treatment outcomes so assessing if these could be contributing factors is a good idea.

If constipation is the main symptom making sure that you address motility is important - hormone issues like low thyroid function can affect motility and should be ruled out if you have chronic constipation.

You may need digestive enzymes, betaine HCL or bile support. 

Sometimes we just need to switch around the treatment plan, for some people different herbal formulas will be more effective - this is why I don’t recommend one particular brand of supplements as there are many different options that can work.

Finally, stress can be a big factor in not progressing with treatment and there is a big connection between gut health and the brain. There are a number of different things that you can do to help address this like meditation, breathing exercises and a great program is the Gupta Program which helps to retrain the brain.

Stress affects the Vagus nerve and the Gupta program focuses on improving the gut/ brain connection.

SIBO and Healing the Gut


If you have had SIBO then there is a good chance that you have intestinal permeability, also known as “leaky gut” as SIBO can be a major contributing factor to intestinal permeability.

The small intestine has a single layer of epithelial cells covered by mucosa, this can regenerate every 5 days and help to protect us from microbial invasion.

The gut lining can be affected by:

  • Medications like antibiotics and NSAIDs
  • Food allergens like gluten and casein
  • Toxins
  • Alcohol
  • Diet
  • Chronic stress
  • Pathogens and lipopolysaccharides (LPS)

It is these last two, that we are concerned about with SIBO because of the overgrowth of bacteria and LPS that can damage the small intestinal mucosa.

Leaky gut is one of the reasons why gut infections can cause a wide range of symptoms not relating to your gut health.

Symptoms of Intestinal Permeability

  • Rashes
  • Joint Pain
  • Food Reactions (allergies, sensitivities)
  • Abdominal discomfort
  • Headaches
  • Brain fog
  • Anxiety/depression
  • Overweight/obese
  • Autoimmunity

Fixing a Leaky Gut

The first step is to remove the underlying cause, whether that is SIBO, medications or a food intolerance as it will be harder to fix if the underlying trigger is still there.

Lifestyle tips include:

  • Breathing exercises
  • Meditation
  • The Gupta Program
  • Time in nature
  • Hot and cold showers to improve circulation

Probiotics in Leaky Gut Treatment

  • S.boulardii – increases sIgA and anti-inflammatory
  • Nissle strain E.coli - motility, anti-inflammatory, abdominal hypersensitivity 
  • Lactobacillus rhamnosus GG - motility, abdominal hypersensitivity, anti-inflammatory
  • Soil-based probiotics  – decreased LPS absorption

Nutrients for a Leaky Gut

  • Glutamine which is essential for the gut epithelium - the dose is important and you need 20 grams a day however most supplements only have 1 to 2 grams
  • Other amino acids include glycine, proline, serine and threonine and these can be found in bone broth or collagen powder
  • Zinc carnosine
  • DGL licorice
  • Aloe Vera juice
  • Slippery Elm powder
  • Quercetin
  • Bovine IgG or colostrum powder

Learn how to treat Leaky Gut here: Healing a Leaky Gut

SIBO Cookbooks

SIBO Family Favourites


SIBO-Friendly Recipes

  • Gluten-free
  • Dairy-free
  • Refined sugar-free
  • Soy-free
  • Almost grain-free
  • Low FODMAP options
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