SIBO – A Basic Guide



For the last month or so I have been reading and looking into something called Small Intestine Bacterial Overgrowth or SIBO for short. You see back in 2014 I was (privately) diagnosed with it and I have been taking antibiotics combined with two ways of eating (paleo and ketogenic) to help manage/ combat the symptoms. Unfortunately it hasn’t been enough to clear up the overgrowth and as a result I have been suffering. I have been back and forth to my GP who have told me that it’s IBS and there is nothing I can do about it! After trying to manage the symptoms by myself, I returned to my GP who referred me and I underwent a procedure known as a flexible Sigmoidoscopy; due to intolerance’s to the ingredients in the prep sachet’s, I was unable to have a full colonoscopy which was what I had originally been referred for!.

From my research and experience it seems that the NHS don’t really do much for the treatment of IBS symptoms and their SIBO treatment is limited. Other than prescribing antibiotics (for SIBO) which can often aggravate it, or giving relaxant medication to help with the pain/ inflammation (for IBS) they don’t actually TREAT the underlying problem! As my SIBO was discovered through private testing, the NHS won’t accept the diagnosis. As a result I decided it was time to up the tempo and aim to target the SIBO all guns blazing (so to speak!).

What is SIBO
The small intestine is part of the digestive system, connecting to the stomach and large bowel. Its main function is to digest and absorb food into the body. Food empties from the stomach into the first part of the small intestine known as the duodenum; the food makes its way through the jejunum (the second part of the small intestine) and into the third and final part known as the ileum, which then empties undigested food into the large intestine (also known as the colon).
The gastrointestinal tract is the whole system in your body that works together to digest food and it (normally) contains bacteria; the number of bacteria is at its highest in the colon and at the least in the small intestine, the types of bacteria also differ from one organ to the next.

SIBO is when there are abnormally large numbers of bacteria in the small intestine and the types of bacteria are more like the ones found in the colon. Usually the gastrointestinal tract (a muscular tube), moves food through the small intestine and into the colon; However its thought that if this system is interrupted/ slowed and the gastrointestinal tract isn’t as active as it should be, it can allow bacteria to stay longer in the small intestine and multiply. It’s also thought that the lack of activity can allow bacteria to spread backwards from the colon and into the small intestine.

What causes it?

There are a whole range of reasons for the normal activity of the gastrointestinal tract to slow down and they are:-

•Recent antibiotic use – antibiotics can interfere with the levels of bacteria, leaving the gut susceptible to colonisation by pathogenic bacteria
•Proton pump inhibitors PPIs can reduce stomach acid and impact on the bacterial growth in the stomach
•Neurological and muscular diseases can alter the normal activity, for example Diabetes mellitus damages the nerves that control the intestinal muscles and Scleroderma which damages the intestinal muscles directly.
•Partial or intermittent obstruction in the SI, obstructions include things such as adhesion’s or scarring from past surgery (e.g. Crohn’s disease)
•Diverticuli – small pouches in the small intestine can allow bacteria to multiply
•Alcohol consumption
•NSAIDS such as ibuprofen can damage the intestinal wall
•Chronic pancreatitis
•Poor diet – bacteria love carbohydrates and sugar
•Lactose intolerance
•Malabsorption disorders such as fructose or glucose malabsorption
•Coeliac disease
•Food poisoning

What are the symptoms?
The symptoms of SIBO are often the same as that for intestinal candida infection and many other gut issues such as IBS; the most recent research even suggests that as many as 50% of those diagnosed with IBS may actually have SIBO! (Shocking huh?!)

Symptoms include
Excessive fullness after a meal
Gas/ bloating
Abdominal pain
Cramping after meals
Abdominal fullness

Research also suggests that those with SIBO tend to have secondary conditions such as:-
Rheumatoid arthritis
Magnesium deficiency
Folate/ iron/ B12/ fat soluble deficiencies
Carbohydrate and protein mal-absorption
Weight loss

When an overgrowth is prolonged and severe, the bacteria can interfere with digestion and absorption of food leading to deficiencies of vitamins and minerals. It can cause patients to lose weight, suffer with pain and fatigue – symptoms not directly thought of as gastrointestinal. When bacteria digest food in the intestine they produce gas which can cause bloating and distension which can cause abdominal pain; increased gas causes flatulence. The bacteria convert food into substances that are toxic to the inner lining of the SI and colon, causing diarrhoea.

Methane or hydrogen?
As if it’s not complicated enough, research indicates that depending on the type of organisms that dominates your overgrowth, depends on what type of SIBO you suffer!! SIBO can be methane producing or hydrogen producing. If you suffer diarrhoea it’s likely you have methane producing bacteria, this is referred to as SIBO-D, the D is for diarrhoea; if you suffer from constipation it’s likely to be archaea (which will be explained below) as they feed off hydrogen. This is called SIBO-C, the C is for constipation.

Archaea were once thought to be a type of bacteria but they are actually a single cell organism which lacks a nucleus, has no membrane bound organelles and are what’s known as a prokaryotes.

In a healthy gut, food is broken down and absorbed into the blood through the small intestine wall; however if you have a bacterial overgrowth, high levels of bacteria cause unabsorbed carbohydrates in foods to ferment before they can be broken down. This fermentation causes a by-product called hydrogen gas. The bacterial overgrowth also produces toxins that irritate the gut lining which is what causes diarrhoea.

However, if you have archaea in your gut it’s a different story! You see when you eat fibre, the bacteria in your gut starts to ferment it. The process of fermentation produces hydrogen and archaea feed of the hydrogen, then produce methane as a by-product. The methane has a number of negative effects on the body, constipation being the one, which is why archaea SIBO is known as SIBO-C.

It’s pretty complicated because bacterial overgrowth = Hydrogen = archaea = methane gas. So it’s a little bit like the chicken and the egg – it’s hard to know which one came first.

It can help to know which type of SIBO you are suffering from because treatment can differ between the two types; however in a recent post by Dr Chris Kresser, he suggests the best treatment is to aim to remove both archaea and the bacteria from the SI to gain the best results.


Lactulose Breath Test
This type of testing for SIBO requires a simple and non-invasive breath test that measures hydrogen (H) and methane (M) gas that is produced by the bacteria in the small intestine (humans don’t produce M or H). Patients will usually follow a 1-2 day preparatory diet that aims to remove as much of the food that would feed the bacteria. On the day they will have a baseline breath test, then given a sugar solution drink of glucose (or lactulose). Humans can’t digest or absorb lactulose, only bacteria have the right enzymes to do this. Their breath is then measured to see if they react to the sugary drink. If there is an overgrowth the breath test will show hydrogen and/or methane. The way it works is that gas is diffused into the blood then the lungs where it is expelled in the breath. This type of test is useful as it can diagnose an overgrowth in the distal end of the small intestines however the disadvantage is that it is not as accurate as a glucose breath test.

Glucose breath test
This test is more accurate and successful in diagnosing proximal overgrowth. The disadvantage is that it can’t diagnose distal overgrowth occurring in the latter 17 feet of the small intestine which is thought to be more common.
Both humans and bacteria absorb glucose and in humans it is usually absorbed within the first three feet of the small intestine. If hydrogen and/ or methane gases show during this breath test it’s a reflection of an overgrowth in the proximal / upper end of the small intestines (within the first 2 feet). This test can be carried out at home or in a clinic and is usually performed after a 1 day special diet and a 12 hour fast.

Digestive Stool Analysis Testing
I personally had a comprehensive digestive stool analysis taken which picked up my small intestine bacterial overgrowth. It was done through my private specialist doctor who also interpreted the results for me. The lab that was used was Genova Diagnostics Europe. They also test for parasites too. I know that they send out test kits (you will have to contact them directly for prices), but if you decide to take this option, you will need to find a doctor who will interpret the results for you – unfortunately the NHS won’t do this for private test results!

This is the tricky part because the NHS has a different approach to say private or holistic doctors. Information suggests that they usually look to find what might be causing it, e.g. is a person producing enough acid, do they have Crohn’s or have they had surgery. However NHS testing can be limited they might not be able to find out the reason. If the cause is identified and it’s possible, it will be corrected and they will use antibiotics to help reduce the numbers of bacteria. To help prevent resistance or side effects antibiotics will be rotated (also pulsing with four weeks on, four weeks off). They may refer a patient to a dietitian as they recommend a diet change such as reducing carbohydrates.

Holistic and Private Doctors may use a variety of the following:-

Diet – Most private / holistic doctors will recommend a diet change; this can be a combination of elimination diets to help identify which foods may be adding to your issue. Some foods are inflammatory and can aggravate the problem and diets such as clean eating (removing junk foods, foods which are damaging to the gut or are carby/ sugary and likely to feed the problem) or low carb/ ketogenic diets can help reduce carbohydrate foods.

Digestive supplements –If a person has low stomach acid then it would be likely that digestive enzymes, bile acids or supplements such as Betaine HCL would be recommended to help to gut to digest foods properly. Take a look at this article which explains this in more detail.

Supplements – there are many supplements about that can be taken to help SIBO, they range from those that help to fight the bad bacteria, those that help promote the good gut bacteria, those that feed the good bacteria, those to help increase gut mobility and those that help fight other issues that may be contributing such as yeast/ candida.

Below are just a few examples that I have read about:-

5-HTP is recommended for a short period to help serotonin levels in the gut, but they shouldn’t be taken if you take medications that modulate serotonin (such as those used to help mental health issues).

Triphala is an Ayurveda herb that helps increase gastric emptying, gut peristalsis, and increases gut muscle tone.

‘Kill’ supplements such as cinnamon oil, oregano oil, allicin (garlic extract) and olive leaf extract. I came across many of these when looking at natural treatments for Lyme and they tend to be used as they are a lot kinder on the stomach and aren’t as detrimental as antibiotics. They have natural antibacterial properties and some of these choices don’t kill the good bacteria – only the bad. Olive leaf extract and oregano oil do however kill some of the good bacteria so when considering them for treatment you may want to do a bit more reading.

Fermented foods – these can help establish a good environment in the good for the types of bacteria that we want also making it inhospitable to those we don’t!

Probiotic’s – they help the ‘good guys’ to flourish, it’s always worth investing in a good quality product rather than a cheap one. Also check how well the probiotic performs – research has shown that some (even big brand) probiotics don’t reach the gut alive or they are lacking in the number of bacteria they boast to have. This article from the daily mail will help you to chose which of the brands to chose from.

Soluble fibres – these are extremely important as they help to feed the bacteria that we want to keep.

The Gut Health Protocol

Just a few weeks ago I came across a book called ‘The Gut Health Protocol’ (TGHP); I had downloaded it onto my kindle and it was so good that my husband ended up buying me a hard copy. It’s full of information on gut health and the ways to treat it giving a natural approach to healing SIBO, intestinal candida, GERD, gastritis, Helicobacter Pylori (H.Pylori), leaky gut, histamine intolerance and Eczema (to name a few!).

The unusual thing is that this book is not written by a doctor but by a man who suffered for years with gut issues and ended up self-treating. Now I have to add that although it’s not written by a medical practitioner It IS jam-packed with research and it even includes all the links to the research that the book is based on. John Herron who wrote the book calls himself a ‘meta- researcher’ – he trawls through all the research studies/ journals , reading them, digesting them (‘excuse the pun!) and then explaining what they mean/ what their outcomes were.

To give you an idea of how much background work has been done, the book includes over 1,200 published scientific studies! The book includes information on SIBO (types D and D), Intestinal candida, ileoccal valve, fructose malabsorption, leaky gut, GERD, acid re flux, heartburn, Helicobacter Pylori, IBS, constipation, Inflammatory bowel disease, Histamine Intolerance (HIT); It also discusses the types of diets that are useful for these conditions, the types of supplements that can be used for the various symptoms (many people with SIBO will also have other issues like intestinal candida or histamine issues). This book gives you all the information you need to treat the various issues that you have.

The protocol
TGHP is basically a three stage protocol;-

1. Kill off the bacteria/yeast that you don’t want
2. Help heal the gut
3. Maintain good gut health.

It has a basic protocol to follow which you follow and adapt to work around your issues/needs.

Firstly there is the diet – a low FODMAP and low carb diet is recommended as part of the basic protocol, but if you have other issues such as an auto immune condition like I do, you would also follow an AIP diet (auto immune protocol).

Then there are the ‘kill’ supplements; there is a list of 14 different ones to choose from. These will also be based on your needs, for example some of the supplements can cause issues with some people especially if they have histamine intolerance. By having a variety to choose from it means you can pick which of the ones suit you the most. John explains each and every supplement in the book so you know the pros/ cons of each one.

Also during the kill stage, depending on your gut issues you may need to add in further supplements to help kill other pathogens that may be at work. For example, if you also suffer from intestinal candida or parasites, then you will need to add in supplements to help kill these off too. Again, you don’t have to do any guess work; the book lists all the supplements that are recommended for each issue. All you do is pick which ones you think will suit you best.

Once you have completed the kill stage, you then move on to the heal stage where you start to take supplements to help heal the gut and to help the good bacteria to flourish. Again, it talks you through each step and explains each supplement recommended.

The final stage is what you have to do to maintain a healthy gut and prevent your gut from relapsing or regressing to its previous state which allowed the bacterial overgrowth to occur.

To help you on your journey there is a Facebook group dedicated to the book that you can join. Its run by John himself and he is on hand to answer any questions you may have. You can join the group even if you haven’t bought the book, but in order to follow the protocol you need to buy it!

Now I haven’t read the WHOLE book but I have read over half of it and as a result of reading it, I am now following the protocol suggested in the book. As I have auto immune issues I am also following an AIP diet (in addition to being ketogenic), as well as being Low-FODMAP as the book suggests. I will try to keep my blog updated on how I get on with this protocol but for the most up to date information including recipes, meal ideas and general day to day keeping’s you can follow me on Instagram, Facebook or Google Plus.

As a result of starting this protocol I will be sharing two more posts that are related, one will be about the Auto Immune Protocol diet (AIP) and another for the Low FODMAP diet.

Please Note
I have tried to be as accurate as possible with the information I have provided, but I am not a medical professional therefore I would always advise you to seek medical advice if you are suffering from any of the mentioned conditions / having other issues. I share my experiences in order to help others who may be going through similar experiences. I have listed below the websites and literature that I used to help me understand SIBO – you may find them useful too.

Information Sourced

The gut health protocol, John Herron, Second Edition – Available from Amazon (UK and Worldwide)

Chris Kresser – SIBO and Methane – whats the connection?

RHR: SIBO and Methane—What’s the Connection?

Daily Telegraph – Probiotics – how each fared and what they contain

Fix your gut – SIBO methane or hydrogen dominant, what’s the difference

SIBO: Methane or Hydrogen Dominant, What Is The Difference?

Genova Diagnostives Europe –
Genova USA –

Hollywood Homestead – treating SIBO (part 6), Hydrogen Vs Methane SIBO

Treating SIBO (Part 6): Hydrogen vs. Methane SIBO

Huntington College of Health Sciences – Digestive Enzymes

Click to access Digestive%20Enzymes.pdf

Jill Carnahan – 6 signs SIBO might be root cause of IBS

6 Signs That SIBO Might be the Root Cause of Your IBS

SIBO Testing –

The Daily Mail – Think you’re bloated, IBS

The Gut Health Protocol

Summary of “The Gut Health Protocol”

WebMD – digestive disorders, small intestine bacteria SIBO


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