SIBO Testing Guide


Small Intestine Bacterial Overgrowth (SIBO) is on the increase. I have my suspicions why, which we’ll come to a bit later, but for now, let’s get started on this guide to everything you ever wanted to know about SIBO testing – and I’ve added some of my thoughts on treatment for you too as they came out whilst I was writing the testing guide! Strap yourself in..

Warning! This is a mammoth blog post so you might want to bookmark it to read again later. I also know some of you like to see stuff so I’ve also done my first ever video to take you through some of the most common SIBO test result patterns – eek, don’t judge me; I’m a newbie! Do read the whole post though as it has a lot of other stuff in it. Here’s the video if you can’t wait! 

a lab icon productsWhen you’re ready, you can order your SIBO tests here.

What is SIBO Exactly?

Simply put, it is where bacteria and microorganisms that usually live in the colon (the lower gut) somehow takes up residence and grow in your small intestine (the upper gut).  They then have a party on any fermentable food that comes along, give off gases, predominantly hydrogen (H2) and methane (CH4) and you look like you swallowed a balloon with enormous bloating.

The bacteria involved are normally gram-negative types including proteus, enterobacter or Klebsiella, to name a few.

What SIBO symptoms might I get?

Bloating is the number one clue, especially if it is pretty much there all the time and doesn’t just come on after eating – although it will worsen then quite often. The other symptoms are a bit what we describe as IBS – cramping pain, diarrhoea, constipation, heartburn and nausea.

It’s not just about the gut, though. You might also suffer food sensitivities, including histamine issues (more on why below), headaches, joint pain, respiratory disorders, skin, brain or mood issues. Rosacea is particularly thought to be SIBO-linked.

SIBO also leads to malabsorption of fats, fat soluble nutrients, B12, iron, folate and Vitamin A, so you may have symptoms related to those such as poor mood control, neurological stuff like restless legs, migraine, fatigue and poor immunity etc.

Interestingly, SIBO can blunt the villi in the small intestine. You normally associate that with coeliac disease malabsorption and is usually the reason for people’s anaemic conditions. Histamine intolerance also goes hand in hand with SIBO often because the DAO enzymes on the tips of the microvilli are damaged and you need DAO to break down histamine in the body. More SIBO = less absorption and less DAO = more histamine = more reactivity generally. Treating SIBO has been shown to improve villi absorption and lower histamine for this reason.

Who gets SIBO?

It might happen in people who’ve had an infection somewhere in the body, especially if they are immunodeficient (low IgA or T cell levels, or after chemotherapy, for example). If someone has had bowel surgery or an obstruction in the gut of some kind. Diverticula are little pockets in the digestive tract where bacteria can ‘pool’ so that would be a risk factor.

SIBO is thought to be a significant factor in the syndromes like Fibromyalgia and Chronic Fatigue Syndrome. In fact, there is some correlation between high hydrogen levels and pain in FM sufferers ie. when the hydrogen level is raised, so is the pain. So, worth checking this out.

More research is needed, but these conditions are all somewhat associated with high risk or prevalance of SIBO too: Crohn’s, coeliac disease, IBS, liver disease, restless legs syndrome, rosacea, Parkinson’s, hypothyroid, rheumatoid arthritis and interstitial cystitis.

How does the bacteria get in the small intestine, then?

How indeed? I suspect we are seeing more SIBO over recent years because more people are low in stomach acid levels and so many are taking antacid and proton pump inhibitor meds!

There should be enough stomach acid to stop any ‘baddies’ getting further down into the small intestine. Our stomach acid tends to wane as we get over about forty years old, but it can be much lower before and after then because of a lack of zinc, B vitamins or histidine amino acid. Many people with high stomach acid problems who are taking meds to lower acid production are doing precisely the opposite of what they need to be doing. I find most of them have low stomach acid, yet you get the same acidity symptoms as if it were high. Low stomach acid = lack of killing ability = more bacteria, yeasts and other organisms getting into the digestive tract. Quite simple when you think about it. You can read more about stomach acid here.

Other reasons include low pancreatic enzymes, low bile production or a reflux problem with the ileocaecal valve which should normally stop any bacteria going backwards back up the tract.

The really major cause, though, is simply a lack of movement in the gut for some reason so stuff is just sitting around and not being processed through properly. That might be because someone has had surgery and the scars (adhesions) have caused the tract to ‘kink’ up like a garden hose. (Look into visceral manipulation to break those adhesions down if this is you.) Or, they might be taking meds or supplements that slow things down like opioid painkillers (can you swap to a different type, take a lower dose with your docs’ help?). It could be that the whole body system is slowed down by an underactive thyroid (take the free basal temperature test here and read the Thyroid Factsheet here if it’s positive).

If none of those are applicable to you, then you can assume there is probably something going on with your MMC.

Beg pardon?

MMC stands for the Migrating Motor Complex and it’s what keeps the gut moving via electromechanical peristaltic waves, which should sweep through the gut regularly between meals and during the night to keep everything moving forward. This is termed the gut motility. It is responsible for moving the bacteria from the small intestine to the colon and should inhibit the migration of the bacteria backwards.

Only it doesn’t sometimes.

Why is that? Well, my theory is that the MMC works best in a fasting state and if yours is sluggish or not functioning all that well and you eat regularly through the day, snacks every few hours etc, then maybe it is not getting enough space and time to do its stuff, if you see what I mean? One well-known way to get the MMC moving is to space meals out every 4-5 hours, maybe with coffee or water in between and give it a regular 12 hour overnight fast so it can relearn how to work and have the space to do so. You can use what are called ‘prokinetics’ to help too. These are meds like low dose erythromycin, low dose naltroxone (LDN) or natural ones like a combination of ginger and 5HTP, digestive bitters (also talked about in the Stomach Acid & Enzymes Factsheet) and a herbal mix called Iberogast, all of which help stimulate the MMC directly.

So, you can see that most people’s attempts at killing off the bacteria will only work up to a point. You need to address the causes too if relapse is to be avoided.

OK, how do I test if my problem is SIBO?

The established medical gold standard way to diagnose SIBO is to have an endoscopy – where the camera is inserted into the throat. This is not exactly pleasant, but actually it has some serious failings too. The main issue is that the tube can only reach as far as the top third of the small intestine, so you’re not going to get samples from the middle or lower small intestine. You can go upwards to get to the bottom third of it if you have a colonoscopy, but that still leaves the middle small intestine section unreachable, so any results are going to have to bear that in mind.

That’s why the breath test is now being used much more, certainly in functional medicine clinics anyway. The breath test kits used to be really unreliable, but labs have done an awful lot of work on them and I’d say they are now more reliable than the supposed gold standard.

What is a SIBO breath test, how does it work?

Simply put, you follow a preparation period to ensure you are able to measure the true level of bacteria in your gut and not what you are fermenting from your last meal or what your last lot of antibiotics, probiotics or even exercise did to your gut. Then, you drink a sample of either a lactulose or glucose solution and breathe into a collection bag in a specified way so we know we are collecting lung air and not the air in your room.

These air samples are taken at specific times, usually every 20 minutes, throughout a three hour period on your testing day and each time you deposit the air into a labelled, timed sample vial until you have completed all the vials. Then, you send the vials to the (UK) lab to be analysed.

There is a really good video here showing how to do it – it’s quite simple. The most important thing to remember is that your results will only ever be as good as your samples so it is important to get the preparation and breath samples done right. I’ve never had anyone have issues but just saying so you know.

What’s the difference between lactulose and glucose tests?

There’s a lot of confusion about this. Essentially either will give you a good test if you have an average small intestinal transit time, which is around about 90 minutes. In one review of studies which analysed 315 adult cases, the transit time ranged from 15 minutes to 5 hours (!), but 83% of people had a transit time of less than 2 hours, and the mean transit time was 84 minutes.

The thing to know is that lactulose doesn’t get absorbed at all anywhere in the small or large intestine whereas glucose is absorbed in the small intestine. So, if someone was a bit slow in transit time, they would be better to use a lactulose test because it will find a distal overgrowth ie. at the furthest end of the small intestine. Conversely, if someone has a fast transit time, the result might reflect a colon infection rather than SIBO. This is why it is all in the interpretation and dependent on your particular body and symptoms.

Most SIBO issues will show within the first 90 minutes (and by then the glucose is more or less absorbed), but if someone was slow, it might not show until 110 or even 120 minutes so you wouldn’t find it as easily if you had used glucose. Some experts are now saying that the glucose being absorbed doesn’t seem to make any difference, but I still err on the side of caution if a person tends to be on the constipated side.

What are we looking for in results exactly?

The two gases being measured are hydrogen (H2) and methane (CH4) as well as a score of the two combined. Most people are predominantly hydrogen-producers, but 30% of the average population are methane-predominant, hence the need to look for both. Methane is often seen in people who have constipation. I assume this might depend on the type of diet people have and how they ferment food individually. Many labs, certainly in mainstream medicine and, I’m told, some pretty well-known highly-regarded ones, still use hydrogen-only machines, which would mean they could miss a load of SIBO sufferers!

We’re essentially looking to see if the hydrogen, methane or a combined score is too high at specific times that relate to the small intestine. Labs do sometimes score these differently, just to make it nice and easy for us!

I have decided to follow the guidelines given by a consensus group of SIBO experts in 2017 put together to try and devise standardisation of SIBO testing and interpretation. Plus, I am using Aero Diagnostics as the SIBO lab because that’s what they specialise in.

You can get the AeroDx breath test here.

So, this is what I see as positive:

Using lactulose

SIBO report

For hydrogen, a positive result for SIBO is usually >20 over baseline figure within the first 90 minutes.

For methane, a positive result for SIBO is usually >10 over the baseline figure at any time. However, the experts believe that anything over 3 if the symptoms fit could be seen as positive.

For combined scores, a positive result for SIBO is >15.

Using glucose

For hydrogen, a positive result for SIBO is usually >12 over baseline at any time.

For methane, a positive result for SIBO, for me using the same reasons as above, is usually >10 over the baseline figure, but remember over 3 can be significant.

For combination scores, a positive result is usually >12.

Flatliners – a special case

There is one big exception to this to watch out for: the so-called flatline type of result. This is where you see both hydrogen and methane pretty flat right through the test – a seemingly negative result. But is it? You might have all the symptoms of SIBO but then get this result. The first thing to do is check if the samples were viable, which you can check easily on the report. If they are, you ask yourself if your poop smells really strong, somewhat like rotting food or egg? Nice. If so, you are likely to be positive and you are producing hydrogen sulphide instead which uses up all the hydrogen and methane molecules, leaving nothing left to test! Still positive for SIBO, just a different gas. You can actually test for hydrogen sulphide levels if necessary to confirm it.

If no rotten egg smell, the other reason for this could be that it was too soon after antibiotics or treatment to test viably and you would re-test according to the patient preparation advice given.

Don’t forget, I’ve done a video for you where I run through the results reports. You can get that below.


If your SIBO test result is negative, what else could it be?

Well, first check the person analysing your results knows what they are talking about!  Have they read the results correctly; does your graph reflect a fast or slow transit time or some other anomaly? Next, think about what else might be causing your symptoms. Might it be a problem somewhere else in the gut – low stomach acid or enzymes (or often both!), a parasitic, yeast or bacterial infection in the lower gut? Review the Gut Tests here.

Could it be a food sensitivity or a gluten related disorder? Quite possibly. Check here for that. I often see this. Bear in mind, it is often a combination of factors.

Can other tests give you any clues whether you have SIBO?

I do like a definitive look, but there are a few other indicators to look for. For example: high faecal fats or very high short chain fatty acids and butyrate on a gut test would give a suspicion, as would any indicator of malabsorption such as low pancreatic enzyme activity or nutrient deficiencies of eg. B vitamins, folate, iron, B12, fat soluble vitamins and any sign of dysbiosis in the lower gut which could have travelled upwards.

There is also a very different type of SIBO test now from Cyrex Labs: Cyrex 22. This is very different to the breath test in that it is looking for antibodies in blood to bacterial cytotoxins released in SIBO rather than the gases we produce. It also looks for evidence to see if the cytotoxins have caused a leaky gut. You can see more info on this sheet here. It’s pretty new and not got as much of a pedigree as breath testing, but I am finding it a useful test to check for damage done by the bacteria and as a double-checker type of test for those who want one. I’ve done a few and am keeping my eye on it. You can get the Cyrex 22 here.

What do I do if my results are positive for SIBO?

The treatment is normally three-fold: diet, antibiotics (meds or herbal) with probiotics and a prokinetic. The diet is used to remove fermentable foods and those the body might have trouble digesting in a compromised gut. The antibiotics (or alternatives) do the killing stuff whilst the probiotics avoid yeast issues developing and replace the beneficial bacteria. The prokinetic keeps the gut motility action working and sweeps food and breakdown products through and out of the small intestine and prevents recurrence.

Diet is normally seen as the primary intervention, although the key experts tend to say that diet will not cure SIBO, but it will help the symptoms. People can become too focused on the diet, on what they should and shouldn’t eat and that in itself becomes counter-productive since we know stress is a big reason why people might not be able to kill the baddies off. The best advice is to follow the diet that suits you and lowers your symptoms.

Many people do well on a low FODMAP and/or SCD (Specific Carbohydrate) type of diet. For some people, they may need to go much further than that and follow a managed ketogenic or elemental diet to remove all starches temporarily. Others may find that they need to avoid too much histamine in their diet (remember the SIBO bacteria affect the DAO enzyme which breaks down histamine in the body). Be led by your practitioners, of course.

There is an argument that a low carb diet can make the bacteria you’re after go into a kind-of hibernation mode and the treatments – herbal or antibiotic – are less effective. Some doctors are now suggesting not changing the diet very much because of that. However, some of the key specialists (Siebecker and Ruscio for a start) are reporting it is not making much difference in clinical practice and people are suffering symptoms unnecessarily. As before: the best diet is the one that makes you feel better as diet is not going to kill off the SIBO; it is to help you manage symptoms mostly, so don’t stress it, end of!

The SIBO Treatment

There is quite simply no one SIBO protocol that will help everyone. Don’t shoot the messenger! Specialists often trial three main approaches and find that one of them suits a patient best. They find using antibiotics, herbal antibiotics or an elemental diet are the main ways to get rid of SIBO, but you never know really which is going to work for whom. The best advice I can give is to find a good practitioner and allow them to work through the cycles of each approach with you. Frustrating I know. Sequential treatments like this should help anyway as more and more bacteria get killed each time, one would hope. Also, don’t leave out the prokinetic; I have seen it make all the difference in protocols.

The other thing I like the sound of is a kind of staged approach where you might do the diet and prokinetics for a week to start, then continue and add in medical antibiotics for a week, followed by herbal antibiotics and probiotic therapy at the end. This has the advantage of covering most bases and herbal antibiotics will also addresses any fungal/yeast overgrowth in the small intestine – the so-called SIFO (small intestinal fungal overgrowth) which I think has been missed by many, but will become much more acknowledged before too long.

I was having a play with this and thought this is what a staged approach might look like. Note: any treatment should be carried out with your practitioner’s guidance, always. Discuss ideas with them.

This might be how I’d see it anyway. I think the protocol from the Candida Plan is a good one to use as a base, minus the diet. I have often asked people to use stage 1 from that to prepare the liver for some killing stuff to stop you getting so much die-off, which many practitioners seem to miss for some reason. Then use stage 2 for the herbal antibiotic stage. Add the prokinetic and change the probiotics as necessary. Note: I’ve suggested the TGF version of the Candida Plan here because the supplements are all grain free.

Example Treatment Regimen

Specific Carbohydrate Diet (SCD)/Low FODMAP and/or low Histamine diet according to needs throughout the therapy period (3 months).

Stage 1 TGF Candida Plan to prepare the body so you get less die-off. Maybe swap the probiotic in the plan to

Ther-Biotic (25 billion multi-strain) twice a day throughout or use histamine-degrading probiotics based on infantis, plantarum and longum strains. May need to build up from low dose. After stage 1, add

Rifaximin for 7 days, taken at least 4 hours away from the probiotics. Stop, then

Stage 2 of the TGF Candida Plan using herbal antibiotics for 4 weeks. Add something like Candibactin and/or anything containing garlic, goldenseal or berberine to make it stronger. Taken well away from the probiotic again. 

Use Erythromycin low dose throughout as the prokinetic or use a natural version such as Iberogast or MotilPro in combination for 90 days, take before bed for best effect

Any other nutrients deemed necessary for eg. anaemia, magnesium, essential fatty acids etc. the TGF Candida Plan deliberately includes grain and dairy free nutrients to keep you topped up

2-3 month review. Stop the prokinetic and add foods back in gently if all OK. Retest.

6 month review

That’s a brief idea anyway in case it helps to start you off. Be led by your practitioner.

Do I need to retest?

Well, if you feel much better, that’s probably your best indicator but it might be wise. many practitioners want to see if the protocol has worked. Also, if there is some residual, it is better to get it now before it builds up again. Happily, the general consensus is that you don’t have to wait 4 weeks after the antibiotics (herbal or normal) to retest; I normally say 4-5 days is enough.

What if it comes back?

You’re allowed to have a chunter at life and kick the TV or something. Then, start again and do the next type of approach depending on what you did last time (ie. herbal if you did normal antibiotics) or try the staged approach and come at it with both bullets! Also, check your stress levels – was there a past trauma or major stress trigger right before the issues or in childhood that could be impacting on your immunity level now – don’t scoff; people miss this because they’re so focused on the bacterial stuff! You could look at your SIgA and IgA levels to see if your immunity is too low. Also, look at and correct any stomach acid and enzyme issues and consider any sugar issue like insulin resistance or diabetes which would mean more lovely carbs around for the bacteria.

Phew, that was a lot of information, wasn’t it?! I hope it helps. It’s just my thoughts on SIBO really as I went along. Finally, a couple of resources for you..

a lab icon productsYou can order a SIBO test here if you need to.

Also, I know sometimes it is easier to see what I’m talking about, so I’ve been a good girl and learnt how to show you. Here’s the video of me going through some test reports for you. I sound a bit posh-Brummy 😉

For even more info on SIBO, check my SIBO Factsheet here.

I hope that all helps. I’m off for a lie down!


7 Replies to “SIBO Testing Guide”

  1. You deserve a lie down Micki. Thank you for the excellent article which I am about to re-read! SIBO is big news at the moment and it is full of useful information.

  2. Well Micki, what a read, lots of facts, information and tips , its good to see someone explaining what the exact link is to histamine intolerance and SIBO, fat malabsorption causing deficiencies like iron, B12 , zinc etc etc, yes, the possible rise in SIBO occurrences and people taking anti acid medication makes sense too. The video explaining the breath charts was very clear I understood better the Methane significance and learnt my transit time is between 100 and 120 mins! didn’t know that before, all in all a great post , voice was fine , well spoken English accent id say 🙂 Can I Link the post to the SIBO SOS virtual summer 2017 Facebook page? its a closed group, not sure what the protocol is for sharing this sort of info. best regards Suzanne.

    1. Oh so glad you liked it, Suzanne, thanks for your feedback. A few people have emailed me to say they liked it and my first screencast video seems to have gone down well, so phew :). Yes, certainly, please share the blog post wherever you think it might help, that’s fine.

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