SIBO Part B: What the Experts are Saying

Sibo Monster

Sibo Monster

Warning: This blog is information intense and entertainment light.

The focus here is Small Intestine Bacterial Overgrowth (SIBO) and will discuss some highlights from two very different (yet oddly similar) conferences.  One by Naturopaths and Functional Doctors in Australia and one by Research Gastroenterologists in America.

See SIBO Part A for an overview of this four part series.

The conferences where:

First what are breath tests.


My Last SIBO Breath Test

The most common way to diagnose (and check progress on) SIBO is via breath testing.   Here is a good description and links to videos etc.

The test is done by drinking a glucose or lactulose solution then breathing into sample bags every 20 minutes over three hours.

Depending on the balance of bacteria in the small intestine, the breath test will show up either with hydrogen or methane (as different bugs produce different gases after eating your food).  Usually those people who are methane dominant have constipation.   There is also those that “flatline” showing low levels of both.  In this case Hydrogen Sulfide producing bacteria are suspected.

Shown above are my results. I am Methane dominant. I am actually IBS-M (Irritable bowel syndrome mixed type).  Which just goes to show even in medicine it’s hard to put people in boxes.

Common Themes

Here are some key learnings that were common themes across the conferences:

  1. SIBO reoccurs after treatment in around two thirds of people (welcome to my life).
  2. Diet alone is rarely enough to treat SIBO.  Other approach such as antibiotics, herbal antimicrobials or an elemental diet (fluid only) may be required.
  3. SIBOs existence and link to IBS is not contentious in the research (only in practice).
  4. You need to get at underlying causes and risk factors for those causes. Some examples of underlying causes; low stomach acid, poor gut motility, obstruction.
  5. PPIs (proton pump inhibitors) widely prescribed for reflux, gastritis, or just for fun you might think looking at the statistics, are a risk factor. It is unclear if this is because of a common third factor or if it is causal i.e. do PPIs cause SIBO? (UPDATE maybe not see here)
  6. Whether you have methane or hydrogen (or hydrogen sulfide) dominant SIBO is important to the treatment approach.
  7. Don’t snack between meals to give your migrating motor complex (MMC) time to work.  The MMC is the cleansing wave that pushes stuff through your small intestines.
  8. Prokenetics (herbs or drugs that give the MMC a helping hand) – are as important as diet in maintenance and avoiding re-occurrence of SIBO.
  9. Symptoms are unreliable – retesting (via breath tests) multiple times is important to know if you are making progress, and hence what next steps you should take. Retesting is also to see if maybe symptoms remain for other (maybe undiagnosed) reasons.

Differences within the expert schools.

The first point of contention among experts is: To feed or not to feed the bacteria while treating with antibiotics? What I mean is should you eat high carbohydrate or high fermentation foods that the bacteria feed on or avoid them completely.  The next blog covers the diets in detail.

This debate was only mentioned in passing briefly, however I found a little more about it afterwards, because it is important for so many of us.

Here is a quote from Dr Pimentel on the topic, in an interview with Chris Kresser:

“I have told my patients from day one of rifaximin or treating with antibiotics — and this goes back to the 1980s; this is an old microbiological concept — happy bacteria, happy and well-fed bacteria, are more sensitive to antibiotics and are easier to kill.  What that means is that most antibiotics work on the replicating cell wall of bacteria.  When bacteria are in hibernation, starving, distressed, they wall off, don’t replicate, and they just sit there, waiting for conditions to improve.  That’s a survival mode.  So when the bacteria are in survival mode, antibiotics won’t penetrate and won’t work as well……If you give guar gum or you augment their eating — so now you’re feeding them, they’re thrilled, they’re enjoying all that food — they’ll be more sensitive to rifaximin.  So when I treat with rifaximin, or antibiotics, in general, for these IBS patients, I don’t want them to be on a low-FODMAP diet simultaneously or any kind of carbohydrate restrictions.  I want those bacteria happy and fed because they’ll respond better, in my experience”

Dr Hawrelak would disagree that guar gum (specifically Partially Hydrolyzed Gaur Gaum – PHGG) is just feeding the bad bugs and hence making the antibiotics work better. Dr Hawrelak is a serious gut bug geek and researcher. He argues if that was the case then PHGG given without antibiotics should cause symptoms.  This is not what the research says as he and a college undertook a detailed and structured review of it (I don’t think this has been published however sorry).

The other real difference I notice was subtle and unsurprising: the GIs are more pharma based and the Naturopaths more herbs based.  However it seems to be done with respect for each other and cross over.  The Naturopaths using antibiotics and the GIs starting to get interested in more research on herbs, e.g. Allicin (garlic extract used in treatment) was specifically mentioned.

Lastly the Naturopath based diets tend to be stricter, lower carb, totally crap free etc.

Extras I got from the Naturopaths/Functional Doctors:









  • There is always that person that can’t tolerate anything regardless of what the research says.
  • Rifaximin doesn’t behave like most antibiotics. It is almost some sort of supper drug (not compromising your microbiome in the same way, maybe even helping it in some ways).
  • There are risks to the microbiome in low carb/high protein/high fat/Low FODMAP diets. Example one – high fat can do all sorts of freaky stuff to your microbiome e.g. decreasing bifidobacteria, and increasing endotoxin absorption. Example two – Low FODMAP can  suppress butane, increase fecal pH, reduce total bacterial abundance and more.
  • Gut parasite treatment, for those that have that too, can be very damaging in other ways.
  • Histamine intolerance can be elevated in SIBO. Symptoms include rash, bloating, headaches, cramping, allergies, insomnia, tachycardia, asthma, nasal congestion, heavy periods.  Histamine is high in foods left to age; cheese, tinned stuff, cured stuff, fermented things, alcohol.
  • Salicylate Intolerance is also common in SIBO and may be linked to extended restricted diets.
  • Visceral Manipulation might be worth considering, although the research is light, practitioners are having good results (I’ve started – will blog on it soon). Visceral manipulation is kinda like really really gentle stomach massage.
  • Pro and prebiotic fears don’t seem to have a good science backing. In fact the science points to the potential importance of pre and pro biotics in such things as improving the microbiome and encouraging the MMC.

Extras I got from the Gastroenterologists and friends.









  • Maybe fructose intolerance (as shown in FODMAP testing) is actually just SIBO and would clear if SIBO did.
  • If the breath test flat lines (with neither hydrogen or methane gas showing up much) you likely have Hydrogen Sulphide producing bacteria
  • Methane producers are not actually bacteria they are Archaea. An entire different being. Maybe this is why methane can be tricky to treat.  Also the methane producers feed off hydrogen.  Hence why you are likely to see low hydrogen with high methane.
  • Reading breath tests gets super complex as the timing includes small and large intestine where different things should happen. Plus each person has different transit speeds so when stuff moves from one to the other is a bit of guess work.
  • Latest research indicates you can retest for methane by just testing a fasting baseline. No need for the 20 minutes over 3 hours test which is the current standard.  NB: It looks from my inquiries like some labs will do this on request even if they do not advertise it.
  • There is a methane – obesity link (obviously my skinny methane dominant body didn’t get that memo).
  • Glucose tests are more likely to give false negatives. The alternative is Lactulose.  Some practitioners request both.
  • IBS isn’t a syndrome, the GIs feel it is a disease and should be rebranded, dropping the ‘irritable’ label and the associated and unfounded mental illness link. Here! Here!
  • There are likely two completely separate types of disease:
    • IBS – C (constipation dominant)
    • The others; IBS-D (diarrhea dominant) and IBS-M (mixed – you never know what you are going to get)
  • IBS-M and IBS-D are very often post infectious i.e. post food poisoning.  The extra bad news is you are even more likely to get infected a second time.  So those with this type need to travel with caution.  The good news is rifaximin can prevent food poisoning.  A lovely story was shared of a SIBO patient in recovery who went on an intrepid third world bus trip and took the antibiotic rifaximin daily and got to watch the other 18 people all get sick and she was fine.
  • Important note here: because you don’t remember having food poisoning doesn’t mean you didn’t. It could have been mild, it could have been 20 years ago. Also it you didn’t vomit it ups your chances further of getting IBS, and likely lowers your chance of remembering it.
  • The new ‘IBS Check’ blood test can be useful, however it is unlikely to show much for IBS-C.
  • There is hope in new drugs in the pipeline e.g. one to lower methane directly.
  • A great and helpful Metaphor for the human microbiome was presented. Here is my version of it – Imagine your microbiome is a city. Your ‘city’ has this basic underlying architecture. This does not change over your life (well not after 3 years when it is laid down).  However you might have say 500 rowdy lawyers visit your city for a conference, they will come, they might do some good or some bad for you but after the convention they go.  Your microbiome is like this, probiotics could be like the metaphorical lawyer convention, when you stop taking them, they leave town.   This metaphor is a bit sad for those of use with poor underlying cities, however understanding this we can carefully choose who to invite to town.

It looks like I got more from the GIs than the Naturos.  It wasn’t like that, I was impressed by all presenters from both days.  If more health professionals were like these ones we would not be in state we are in.

That is all for now as I have exceeded my word limit.

The next blog is on the diet conundrum.  The last on my personal approach from this and other information.

Until then,

Yours as Ever,

The WellbeingatWork(nearly)Dr.

Some Useful Links

UPDATE from 2018 – full list of Dr Pimentel’s publications 

Also consider Dr Pimentels Book – well worth it:








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2 Responsesso far.

  1. Heidi says:

    Really good info here! Thanks for your studies and taking the considerable time to share it.
    I have histamine intolerance ( also d frag & blasto but only some bloating and occasional diahorrea these days ) and my functional doc is testing me for SIBO.
    I’ve got a question for you … the notes with the test ask you to avoid certain fibre and carb rich foods the day prior to the self test, but my doc said to avoid all fibre whatsoever. I’m not sure I could eat much of anything if voiding all fibre and carbs.
    What do you usually do before testing ?

    • wellbeingatworkdr says:

      Thanks for your kind words Heidi. I am sorry to hear what your are going through. It is all so tough and complex and poorly understood. In terms of the testing mine is horribly strict, I live for 2 days on rice, hard cheese, chicken, egg and salt and pepper. It seems to differ by Dr/Lab etc. I can’t tell you how much I do not enjoy it, it’s no tea that does me in!!! At least I will be doing the next one with company as I am testing my 10 year old.

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