The nine variations of small intestinal bacterial overgrowth including SIBO, SIFO, LIFO and IMO. What they all mean. What causes them, how to test for them, how to treat them and how to stop it coming back.

8 Symptoms that suggest you may have SIBO

  1. Abdominal bloating after eating
  2. A feeling of fullness under the ribs after food
  3. Heartburn
  4. Belching or a high level of flatulence
  5. Abdominal discomfort
  6. Constipation OR diarrhoea or loose stools
  7. Muscle of joint pain and headaches
  8. A red butterfly rash across the cheeks and nose- rosacea
  9. Brain fog, memory issues and irritability

Small intestinal bacterial overgrowth (“SIBO”) is a bit of a catch-all phrase for overgrowth of a range of organisms in the upper bowel.

We say organisms because they could be bacteria, fungi (like candida), or archaeon – let’s refer to them collectively as bugs. Archaeons are single-celled organisms without a nucleus called prokaryotes, so are not technically bacteria.

In fact there is often a mixture of all of these components and all of these conditions often occur in a mixed pattern

Small intestinal bacterial (bug) overgrowth

When we eat food digestion starts in the mouth. Chewing not only breaks down food mechanically, but the release of amylase enzymes also starts the digestive process.

Next, the food is passed into the stomach, which stores food until it is passed into the small intestine at a controlled rate. 

Food is mixed with acid in the stomach which not only aids digestion, but also denatures a lot of the ingested organisms before food is passed into the small intestine where digestion and most of the absorption of nutrients occurs.

Our digestive system

Most of the digestion in our body occurs in the small intestine. Enzymes are released into the small intestine from the pancreas to break down macronutrients into smaller absorbable molecules. Bile acids are released to help break down fats. 

These digestive secretions are essential – it is how we break down and extract energy and nutrients from the food we have eaten.

There are, however, numerous foods like fibres that we are not able to break down. Once we have extracted what we can in the small intestine the remnants are then swept into the large intestine.

Think of the large intestine as a composter.

Here a sea of bugs are waiting to go to work on the leftovers. A mass weighing about 3 pounds thrives on our leftovers and they pull out more energy and produce a range of helpful products including short chain fatty acids and vitamins along with anti-inflammatory by-products.

The make up of this mass really depends on what is being fed to them and this anaerobic digestion is a careful balance.

As the remnants (or prebiotics as we refer to them) are broken down, by-products (referred to as postbiotics) are produced and it is these by-products that we have now become reliant on and are essential to keep us healthy.

The study of the microbiome has only been possible in recent years due to the advances in 16s genetic analysis, a test we often perform at humanpeople to assess the gut.

These bacteria are referred to as “good” when they are present in the right place in the right numbers.

It is when they turn up in the wrong place, i.e. the small intestine, or in overwhelming numbers that they cause problems and our immune system goes on alert.

This means the body enters an inflammatory state, which is sometimes helpful, but at other times can lead to further damage or even autoimmune conditions.

When our bugs are in harmony they produce food stuff for the lining of our gut like butyrate (makes up about 30% of our energy), but they also produce other by-products like lactate that stops the overgrowth of unwanted bacteria and fungi.

So for all of this to work properly there are some essential elements:

  1. Ample acid in the stomach to keep the small intestine sterile.
  2. Ample digestive secretions are produced.
  3. The powerful peristaltic contraction to sweep the food remnants and any bacteria into the large intestine is working efficiently. This contraction is part of the migrating motor complex (“MMC”) that is a key issue in SIBO. More on the MMC later.
  4. There is a valve separating the large intestine from the small intestine, the ileo-caecal valve. This needs to be working efficiently and not allowing backward flow of bacteria-rich content into the small intestine.
  5. The balance of the bacteria in the large intestine has not been altered so the “good bacteria” stop overgrowth of other types that will cause problems.
  6. There are no blockages along the path of the gut wall that slows down progress.

These six functions underlie the root causes of SIBO.

So, what goes wrong?

The MMC can be underactive due to hormonal imbalances like hypothyroidism or can be affected by an overactive sympathetic system in stress or be damaged by an (anti-vinculin) autoimmune reaction following food poisoning.

What causes it?

  1. Absent or impaired migratory motor complex i.e. a floppy small intestine that does not move food along like it should do.
  2. Previous abdominal surgery
  3. Colectomy
  4. Stomach stapling leads to a blind end
  5. Adhesions from previous surgery
  6. Food poisoning (see below)
  7. Stomach antacids reduce the acid entering the small bowel from the stomach
  8. Motility problems
  9. Connective tissue problems like Ehlers Danlos syndrome
  10. Abdominal obstruction i.e. endometriosis
  11. Altered digestive secretions allow bacteria to grow
  12. Inflammatory bowel disease
  13. Coeliac disease

Other associated medical issues

  1. Thyroid issues can both cause and be caused by SIBO. Hypothyroidism messes with the normal function of the MMC and the peristaltic wave in the gut.
  2. Diabetes affects all nerves including those in the gut. There is a gut-brain connection that controls these contractions.
  3. Head injury. We postulate that the change in gut absorption associated with head injury is strongly associated with the MMC.
  4. Chronic stress. The fight or flight (sympathetic system) stage of chronic stress sidelines processes ruled by the rest and digest (parasympathetic system).

Food poisoning. What’s the link with SIBO?

1 in 5 cases of food poisoning may cause an autoimmune reaction whereby the immune system produces antibodies against an essential protein in the gut wall called vinculin.

Vinculin is an essential part of the pacemaker wave in the gut that causes strong contractions 90 minutes after eating, removing food remnants and bugs from the gut.

This means that the small intestine is not contracting properly and SIBO can become chronic. A new commercial test is now available to look at anti-vinculin antibodies. This will confirm MMC-derived SIBO.

Food poisoning may be the most common cause of SIBO *ref

How do we test for SIBO?

The gold standard test for SIBO is to look directly at the small intestine. It is possible to see a small way into the small intestine with endoscopy, take an aspirate of the fluid and then analyse what is going on.

A less invasive way is to do a breath test.

  1. This involves avoiding all food for at least 12 hours so any food remnants should have passed from the small intestine.
  2. You then drink a lactulose (sugary) solution.
  3. Breath samples are taken in 20 minute intervals. This is then fed into a gas analyser to check for hydrogen and methane gas.

When the body is functioning properly, when lactulose is drunk it should pass into the small intestine, be broken down by our normal enzymes and absorbed. This is a non-fermentation process. Any remnants may pass through into the large intestine and then be fermented.

In the case of SIBO, the lactulose hits the bacteria in the small intestine and fermentation occurs. Due to the high absorption in the small intestine this gas is absorbed into the bloodstream and the body excretes it in the breath. It is this gas that is picked up by the analyser, leading to the detection of gut bacteria.

Numerous studies have shown the process to be reliable, certainly in the presence of normal bowel movements.

Occasionally if there is a fast transit time into the gut the lactulose is moved quickly and the fermentation occurs in the large intestine.

SIBO – hydrogen, often associated with diarrhoea and weight loss

SIBO in its simplest form is the overgrowth of bacteria, often “good bacteria” that are normally present in the large intestine, in the small intestine.

When our bacteria get to work on remnants it is usually devoid of a lot of the simple sugars and carbohydrates that are highly active and full of more inert fibres.

Therefore when unprocessed foods mix with this bacteria there is a strong fermentation with a lot of hydrogen by-product gas produced. 

This gas leaves us feeling bloating, uncomfortable and causes abdominal pain. When hydrogen is produced the body tries to flush the contents out and large amounts of water flush into the small intestine leading to diarrhoea.

The gas causes inflammation and irritation. 

The fast passage of the food means that nutrients are not absorbed and weight loss can occur.

If SIFO small intestinal fungal overgrowth is present it is common to get a lot of flatulence when sugary foods or beverages are consumed as fungi like candida break them down very quickly.

The production of hydrogen from these bacteria is key in diagnosing the presence of bacteria in the small intestine.

The gold standard is an endoscopy with aspiration of the small intestine and analysis however this is invasive.

Intestinal methanogen overgrowth (“IMO”) formerly SIBO-C or SIBO methane – often associated with constipation and weight gain

Some of us have methane producing bugs in our gut that can also overgrow in the gut. 

As previously mentioned these are not technically bacteria but prokaryotes, archaeon, single celled organisms that produce methane.

The most common of these is methanobacter brevi smithii is responsible for 95% of the methane produced, however there are some other small groups.

These organisms do not ferment food but instead absorb the hydrogen gas produced and turn it into the highly irritable methane.

This in turn causes lots of inflammation in the small gut and elicits a strong immune response.

It is thought that this also affects the integrity of the gut wall allowing leakage of some of the contents of the gut into the body.

One of these contents is LPS lipopolysaccharide that is part of the cell wall of gram negative bacteria that has been isolated in the blood of SIBO patients.

This LPS provokes a very strong immune response and may be responsible for the brain fog and inflammation that is associated with SIBO and clears up when it’s treated.

Leaky gut

So not only does the overgrowth cause discomfort but it also causes structural damage to the gut.

This is important to remember when treating the gut, it’s not just about treating the bugs but it’s also important to support the gut when it returns to a more healthy state.


A less common type of bacterial overgrowth is one where hydrogen sulphide is produced. This is characterized by the same symptoms of SIBO but during the breath test both hydrogen and methane levels appear very low. Commercial tests for hydrogen sulphide are not yet available.


As mentioned previously it is not just bacteria and archaea that complicate overgrowth but also fungi in particular candida. These hydrogen producers are nearly always present and 23% have been shown to be the dominant problem.

When candida infections take hold they can be difficult to diagnose, an expensive urine test can look for metabolites. Signs of other fungal infections are key ie skin infections, athletes food, corners of mouth etc.

When fungal infections have “taken hold” they can be difficult to treat. The fungi will often produce a protective film around themselves that is hard for antimicrobials to penetrate. Agents that will break down the biofilm are often required alongside the antimicrobial treatment.


When fungi are dying off they release a toxin that can often cause unpleasant symptoms ranging from headaches, aches, feeling low and irritability to strong sugar cravings.

If these symptoms occur it’s important to understand what is happening but other therapeutics can be used to help. Charcoal and zeolites have been shown to “mop” up these toxins and reduce die off.


As previously mentioned one of the causes of overgrowth in the small intestine is a dysbiosis or unbalanced microbiome in the large intestine.

This can be caused by many things however the most common is the prolonged use of antibiotics or when strong antibiotics have had to be used.

The lack of presence of the house keeping bacteria like lactobacillus to produce lactic acid means that fungi can flourish and when this happens they or other bacteria can overgrow into the small intestine.

Nine types of SIBO that affect treatment protocols

So in fact all of these can exist in combination and in our practice we divide them into ten different types that will affect what treatment is used, length of treatment and recommended period of repair/ healing.

  1. SIBO-D Hydrogen dominant:
    • Breath test shows a peak of hydrogen 
    • Minimal methane gas produced
    • Usually associated with diarrhoea
  2. SIBO-C/ Methane dominant/ IMO
    • High levels of methanogens means that hydrogen is used up, however by definition this is a mixed type with high levels of methane producers.
    • Methane dominant is usually accompanied by constipation and this needs to be tackled before treatment. During treatment toxins will build up and the body needs to be able to clear them away
    • Extra microbials are needed to treat the methane producers as well as the hydrogen producers
    • Lower rate of recurrence
  3. Mixed type
    • High levels of hydrogen
    • Methane is also present but is not dominant
    • Most common type makes up about 70% of cases
  4. Hydrogen sulphide type
    • Detected by a flat gas line for both hydrogen and methane on testing
    • Characteristic foul smelling stool and “rotten egg” flatulence
    • Highly irritable to the body and strong sense of brain fog
  5. SIFO
    • Around 20% of SIBO fungal infection is also present
    • 5% is fungal only
    • Associated with certain genes like FUT2 (non-secretors of antigens into the gut mucus).
  6. SIBO + SIFO
  7. SIFO + LIFO
    • SIFO is associated with a significant large intestinal fungal overgrowth
    • Fungal infection is in the large intestine bacterial in the large intestine


Diagnosis of the overgrowth is done by collecting clinical details and performing a breath test.


  1. Stop feeding the bugs
    • Normally a high fibre diet is what we need however not in SIBO,  the bugs need to starve. We use a low FODMAP diet to reduce symptoms and to improve treatment.
  2. Kill the bugs

Clearing the bugs from the small intestine is enough in one third of cases to treat and get long term remission of SIBO.

For the other two thirds careful attention in the post “killing phase” is essential to prevent recurrence.

Understanding the initial cause will help .

The killing stage. Treatment of the bugs is done over a 2-6 week period depending on whether pharmaceutical antibiotics and antifungals are used or if herbal antimicrobials are used.

We use a proprietary blend of herbs to treat both bacterial and fungal infections together that include xxxxxxxxxxx or will use a combination of rifamaxin and metronidazole.

Before moving on to the healing phase try to ascertain the root cause to prevent recurrence

Healing phase

Depending on the cause an 8 week to 6 month healing protocol is needed.

During the first 8 weeks a prokinetic is essential.

A mixture of gut healing foods and supplements can help to support the healing of the gut.

Retest and maintain

It is important to check that the killing stage has worked and that further rounds of this stage are not needed.

Checking for vital nutrients that may not be absorbed due to gut inflammation is important.

Build these back up whilst building up the diet.