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SIBO - How to clear small intestine/fix motility?

Background: growing up always had a bit of an off gut, loose stools, bloating etc. Also had terrible seasonal allergies and some urticarcia. Also mood issues, irritability/anxiety.

October 2016 - Took high dose probiotics (Bifido/Lacto mix) for the first time to see if it improved gut and other things. Developed severe brain fog and anhedonia. At the time did not recognise it was probiotics causing, over the next few years I did a lot of courses of probiotics, also thinking maybe it was 'die off' and I needed to 'keep pushing' - mistake.

2017, 2018 and 2019 - dealing with fatigue, severe brain fog, anhedonia, feeling spaced our/disorientated, itching, urticarcia/hives and just general malaise.

Tried a ton of different supplements too long to list here, nothing really providing any obvious benefit.

April 2019 - had a really random bout of intense urgent and watery diarrhea, which is totally out of the norm. Have had a suspectibility to looser stools, but never water. I think I triggered this by dehydrating myself, certainly didnt appear to be result of sickness ( I was on a strict keto diet and decided to cut all electrolytes, was trying anything and everything, doh. )

After the diarrhea, ALL of the symptoms cleared. I felt amazing, 10/10. Oddly, not only the best I'd felt in 3 years but the best i'd ever felt in my life. No itching, no urticarcia, no fatigue, no anxiety.

This lasted around a week feeling amazing, then another couple of weeks being good but not as good, stupidly I took even more probiotics (at this point it still hadnt clicked even though I'd suspected sibo) and declined right back.

2020: I've tried a 7 day water fast, didnt fix, oddly didnt even dissipate all symptoms, still had itching.

Tried Rifaximin, 0 effect. No benefits, no side effects.

When it clicked that it was probiotics that caused it, and also that one component appeared to be histamine intolerance (which I'm assuming is the result of sibo as it is commonly claimed), I tried high dose bifido.

I was able to take 70 billion bifido with 0 negatives, if anything it seemed to some what help but not hugely.

I tried Symbioflor (E. Coli) and had to stop after a few days, started getting severe bloating and my gut felt HORRID.

So it seems that: Lactobacillus = worsening of symptoms, E. Coli = worsening, Bifido = fine. From what I Understand, both Lacto and E.Coli can survive/build up in the small intestine and can more commonly be found in SIBO, Bifido doesn't? Which if that is true, really makes me suspect again this is all down to a build up of bacteria in the small intestine.

Had a SIBO test in 2019, flatline result.. (Which could of suggested sulfur sibo) - did seem I might have had some sulfur issues before, but don't appear to now. Since taking high dose bifido, some symptoms have improved. No longer dealing with severe fatigue, disorientation and total anhedonia. However, still dealing with itching, urticarcia/hives, anxiety, mood issues.

I can't help but feel after all of my experiementation, that this is SIBO, and that this anomalous bout of diarrhea in 2019 just cleared my small intestine, which led to all of the symptoms fading.

I Had a GI MAP done:

It shows no obvious issues, which also to me reinforces SIBO in my mind. Did have some fat in stool, which I understand is also fairly common in SIBO.

So in summary:
- Probiotics made me worse
- SIBO Test Flat Line
- GI MAP shows nothing obvious
- Can take high dose Bifido, 0 issues
- Taking Lactobacillus and/or E. Coli cause negative effects
- Bout of super urgent random diarrhea in April 2019 totally eliminated symptoms
- Appear to have histamine issues, which also dissipated with diarrhea, and is often claimed to be caused by SIBO.

I have tried inducing diarrhea, no success. I tried a few methods including salt flushing and pharmaceutical laxative (Picolax), nothing I tried gave me that same super urgent "if there is a lord above, please help me" diarrhea. I also understand that picolax induces diarrhea from the large bowel, which also explains why it didnt help.

So right now I'm at a point of understanding where I believe there must be some kind of motility issue in my small intestine. My gut ironically these days is better than it was growing up, I still get loose stools at times and mucous in stool, but overall gut function is better (it almost seems that the probiotics helped in the regard, but caused 10 bigger problems).

My stomch very rarely rumbles, which I know some people claim is the MMC kicking in. I've always felt my digestion feels a bit slow/sluggish, but I don't have any issues with constipation. That was also something I noticed in April 2019 after the diarrhea, I had normal hunger, it felt like food was moving through my quickly and nicely.

I've just started some herbal antibiotics: Goldenseal, Oregano, Neem. My concern is that it seems that actually the bacteria may just be normal commensal bacteria, not pathogenic, so I'm not sure they'll be effective? I know that rifaxmin is claimed to be eubiotic and can INCREASE lactobacillus, which might explain why it had 0 benefit for me. I think it's often assumed that bacterial issues are caused by 'bad bacteria', where as I suspect this and other cases are rather down to dislocation of normal bacteria, hence the poor response to 'good' probiotic strains .

So then I'm left looking at motility. Is it the case my small intestine just isn't clearing properly? So any probiotic I can that can build up there, does. And the diarrhea in april 2019 by pure chance resulted in my small intestine flushing, clearing the bacteria temporarily, alleviating all the symptoms.

So my question is, what suggestions would people make based on this?

Does anyone have any novel ways/ideas on how you can flush the small intestine specfically, do see if I can recreate the same effect?

Has anyone found anything that helped fix motility? I looked briefly at prokinetics, I did wonder if that's what I should be trying. Ive ordered 'Iberogast' to try which is a herbal prokinetic allegedly, although it does seem to be marketed at people with really obvious GI issues, which I don't feel I do anymore.

I've heard some SIBO doctors claim that motility in small intestine can be totally indepenant of bowel movements, as it's not actually related. I.e. people assume slow motility = constipation, fast = diarrhea, so prokinetics aren't useful for loose stools/diarrhea etc which apparently isn't true.

So how can I stimulate my MMC/small intestine? What can I try to clear my small intestine, to see if I can get relief?

Thanks for reading if you made it this far and look forward to hearing your ideas! :)
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Senior Member
United States, New Hampshire
So how can I stimulate my MMC/small intestine? What can I try to clear my small intestine, to see if I can get relief?

You might already be doing this but they say that the MMC doesn't kick in until about 3 hours after you eat. So having at least 4-5 hours between meals is recommended by DR. Mark Pimentel. This gives the MMC a better chance to help clear bacteria from your small intestine.

SIBO.com is a good source of info for clearing and preventing SIBO.
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Senior Member
I have found that arabinogactan a soluable fibre, prebiotic helps motility immensely for me.


Senior Member
Have you tried other types of probiotics such as the fungal S. Boulardii or any type of baillus probiotic?

Have you ever had a sibo test come up negative and if so how did you feel then? I know that for methane sibo xifaxan alone isn't enough according to most doctors whose works ive read, perhaps the same thing is true of hydrogen sulfide sibo? If the herbal antibiotics don't work out for you perhaps a different kind of prescription antibiotic will

You know I tried iberogast at one point, the alcohol in it made my health worse, even trace amounts of alcohol in this and other tinctures have that effect on me and I know that isn't uncommon since, from what Ive read, many people with CFS have bizarrely bad reactions to alcohol so if your health gets worse on iberogast consider that it might be that and not the prokinetic effect. I couldn't find any iberogast without alcohol when i looked around.
You might already be doing this but they say that the MMC doesn't kick in until about 3 hours after you eat. So having at least 4-5 hours between meals is recommended by DR. Mark Pimentel. This gives the MMC a better chance to help clear bacteria from your small intestine.

SIBO.com is a good source of info for clearing and preventing SIBO.

It's something I've tried in the past but not lately, I will try and incorporate it back in though, as it can only help.
I have found that arabinogactan a soluable fibre, prebiotic helps motility immensely for me.

From what i'm reading, this would be more aimed at lower colon motiltiy rather than small intestinal? I'm looking for a way to stimulate the movement/MMC in the small intestine specifically. As I don't have any issues actually going to the toilet, so I don't need the large colon to move and quicker.
Have you tried other types of probiotics such as the fungal S. Boulardii or any type of baillus probiotic?

I've tried S. Boulardii, no adverse reaction, no apparent benefit as far as I can tell. Not tried bacillus, had read some horror stories about bacillus and after my experience with others am pretty reluctant to try. At this stage i'm so confident it's a case of getting the small intestine MMC going I can't see much benefit trying any more probiotics if I'm honest.

I only ever tested for SIBO the once, which was the flat line. I've heard the same thing with methane dominant sibo, I guess my other reservation around trying other antibiotics beyond the risk of the possible damage they can cause, is that it doesn't necessarily address the underlying cause and so even if it did clear it, like 2/3rds of patients I'd probably just relapse.

The experience I had last April suggest to me that the severe spasming of the colon that occured before that diarrhea must have also induced movement in the small intestine, causing it to clear and thus the symptoms disappearing..

But what I feel I need to figure out is, how do I get my small intestine to do that otherwise? I will bare that in mind with the iberogast, thanks.


Senior Member
I recently posted the following about tests and treatments ive looked into and done in searching for the cause of fat in stool and other gi issues, since you mention fat in stools i figure it might interest you, https://forums.phoenixrising.me/threads/pale-stool-and-bile-salts.79969/#post-2274251
though you're right, chances seem good it's sibo causing the fat in stool as sibo came up quite frequently as a cause of fat in stool on the websites i looked through that listed causes of fat in stool

Have you had an xray or other investigations of the small intestine done? Maybe you have some structural issue?

Also, if i remember correctly there is a test that can be run of the MMC but it isn't done frequently, I remember Allison Seibecker mentioning it, if prokinetics work and it looks like you will need them permanently then it might be something worth looking into

Finally, I put this together to use myself for figuring out what to do about sibo. I mainly took anything i thought might be useful from webinars, conferences, books, etc. and put them in different sections so i could boil it down into the most important things to focus on though I didn't include that summary section of the document here and the info was selected for whether or not it was useful to the part of sibo I've focused on so I might well not have saved much about hydrogen sulfide since none of my sibo breath tests showed a flatline. if you open below links and run a search for hydrogen sulfide you might find useful stuff i didn't save. Anyway, it's not meant as medical advice, I didn't look heavily into the background of the doctors and read all of their articles or anything but am posting this in hopes it might provide ideas, options for tests/treatments to investigate or things to look out for that might cause issues during treatment. There is a decent bit in this on prokinetics of various kinds as well

hope it helps


From someone who had CFS and probably SIBO as he has stated: I have been able to control the proliferation of this bacteria by eliminating its food source through Elaine's diet.
Through the help of a Naturopath I have changed the intestinal environment so that it is more
acidic and not alkaline. Pathogenic bacteria do not thrive in an acidic environment. I have added lemon juice(freshly squeezed) and ginger extract along with colloidal bentonite clay, digestive
enzymes, vitamins and minerals under the guidance of Dr. Jack Larmer N.D.

{02} SCDlifestyle​

What to do if sibo test comes up methane dominant https://scdlifestyle.com/2017/05/new-solution-for-sibo/#more-13520


SIBO webinar

This one features a Dr. who specializes in SIBO

The doc says she prefers a hydrogen/methane breath test that goes on for 3 hrs as all the research studies done have been w/ 3 hr tests and there have been cases where, had she not done the 3 hr testing, she would have had a false negative.

Says she prefers, when doing a breath test, to use lactulose as opposed to glucose as lactulose will reveal SIBO in the lower small intestine where as glucose wont. She says she has found lower small intestine sibo more commonly than higher small intestine sibo. Glucose is all absorbed in the first two feet so it wont show you the lower small intestine.

The lactulose will feed the small intestinal bacteria if they are there, that is how the gas is produced by feeding those bacteria but be aware you may feel temporarily worse

She strongly rec a followup breath test to make sure it is gone. If you are using a quick killing method like antibiotics, herbal antibiotics, or elemental diet you should do your followup breath test within two weeks after the last day of the quick killing method you used, preferably within 5 days, this quick followup is because the bacteria can recolonize the gut in around two weeks after your quick killing method if it is going to recolonize so you want to get the breath test done quickly to know how much of an impact your intervention had on the microbes

Mentions that elemental diets may not work if you have SIBO all the way up to your stomach as at that point the microbes might be absorbing the nutrients, elemental diets work best on lower small intestinal sibo as the nutrients in the elemental diet are predigested and will be absorbed very early on in the digestive tract, maybe even before the small intestine altogether, don’t know, she didn’t specify that clearly

Says that she often sees cases where diet isn’t enough to fix SIBO and where antibiotics are needed, these cases are often the ones who have constipation and are methane predominant, says methane predominant ones are in general much harder to treat and she will often need to use all three methods(antibiotics, herbal antibiotics, and elemental diet) in succession to treat them

She says that nuts, beans, lots of carbohydrates(from fruits), and yogurt seem to cause a lot of problems for scd people

Says that SIBO can cause fructose malabsorption which will leave fructose available for the bacteria to feed on which is why some scd people can have issues w/ honey

Says that Dr. Haas, the inventor of the diet, went very slow with veggies and fruits when introducing them.

Says that the soonest any of the cases of Dr Haas got over their symptoms on the diet was 3 months, it takes a long time, some people feel really well early on but they will take months to several years to become symptom free

Mentions prokinetics: erythromycyin and acitromycin or something, says that they are antibiotics but are used at levels where they wont function as antibiotics, you have to go to a compounding pharmacy to get them at these low doses. These prokinetics may be needed to fix your sibo or it may be that hydrochloric acid is needed or bitters or ACV and water to increase the HCL or that enzymes are needed. Alternative to prokinetics you could go to an acupuncturist and have them treat you for gastroparesis, which is also known as stomach paralysis, and there are some good studies showing that acupuncture can work for that.

Try and take 3-5 hrs between meals in the day to increase MMC, take things to increase MMC right before bed as the MMC is most active during sleep

{03} BTVC book​

quite early in SIBO the normal absorption of vitamin B12 is disturbed. There is considerable evidence that B12 is poorly absorbed in microbes multiplying within the small intestine prevent uptake by the ileum. P 13

problems resulting from bacterial fermentation are: (one) production of excess amounts of short-chain volatile fatty acids (organic acids); (two) lowering of the pH of the blood as these acids are absorbed; (three) overgrowth of bacteria as the undigested carbohydrates provide food for bacterial proliferation; (four) mutation of some bacteria such as E. coli because of the change in pH in their colonic environment; and (five) excess toxin production caused by the overgrowth of some pathological bacteria P 55




Gastric achlorhydria
Due to long term use of a proton pump inhibitor [Lombardo et al. 2010; Compare et al. 2011; Hamvas, 2012] or autoimmune etiology (chronic atrophic gastritis)
Anatomic abnormality of the small intestine with stagnation
Afferent limb of Billroth II gastrojejunostomy, small intestine diverticula [Krishnamurthy et al. 1983], obstruction, surgical blind loop, radiation enteritis
Small intestine motility disorder
Diabetic autonomic neuropathy, scleroderma, chronic intestinal pseudo-obstruction, small bowel diverticulosis, irritable bowel syndrome (IBS) [Pimentel et al. 2000]
Gastrocolic or coloenteric fistula
Crohn’s disease [Funayama et al. 1999], malignancy, surgical resection
AIDS, chronic pancreatitis (in 30–40% of cases [Trespi and Ferrieri, 1999]), liver cirrhosis (in up to 60% of patients), IgA deficiency, combined variable immunodeficiency, nonalchoholic steatohepatitis [Compare et al. 2012; Machado and Cortez-Pinto, 2012], fibromyalgia, celiac disease [Ghoshal et al. 2004; Krauss and Schuppan, 2006]


In many patients, it is necessary to exclude lactose from the diet, to reduce other simple sugars, to increase coverage of energy needs by fat and to administer medium-chain triacylglycerol (MCT) oils [Bures et al. 2010]. In cases where there is decreased motility, such as chronic pseudo-obstruction, methods to enhance motility can be attempted. Prokinetic agents that are commonly used and are available in the US include metoclopramide and erythromycin.


There is no common agreement concerning the choice, dosing and duration of antibiotic therapy. Broad spectrum antibiotics which affect enteric aerobes and anaerobes and numerous choices are available (Box 3). These include ciprofloxacin, norfloxacin, amoxicillin/clavulanate, metronidazole, cephalexin and more recently rifaximin. Rifaximin has gained popularity since it is nonabsorbed, has few side effects and little evidence for resistance [Frissora and Cash, 2007; Koo and Dupont, 2010]. Rifaximin may therefore be the antibiotic of choice as clinical resistance is seen far less frequent than with other antibiotics


Bacteria in SIBO might significantly interfere with enzymatic, absorptive and metabolic actions of a human. Due to injury of the brush-border of enterocytes, the activity of disaccharideses may be decreased. If bacteria simultaneously metabolise fructose, lactose and sorbitol, malabsorption of saccharides may occur. Injured small intestinal mucosa can have undesirable consequences in increased intestinal permeability and/or protein-losing enteropathy. Deficiency of vitamin B12 results from the consumption of this vitamin by anaerobic micro-organisms. Bacteria may also utilise intraluminal protein in the small bowel, this may lead to protein deficiency for the macro-organism and excessive production of ammonia by bacteria. Deconjugation of bile acids by bacteria results in malabsorption of fat and liposoluble vitamins. Extensively formed lithocholic acid is poorly absorbable and acts enterotoxically

Bacteria produce various toxic agents that may have surprising systemic effects. These agents are ammonia, D-lactate, endogenous bacterial peptidoglycans and others. SIBO is regularly associated with increased serum endotoxin and bacterial compounds stimulating production of (pro)inflammatory cytokines[7,96]. SIBO might be associated with endogenous production of ethanol (probably synthesised by Candida albicans and Saccharomyces cerevisiae). Serum ethanol disappears after successful treatment of SIBO

SIBO may be clinically asymptomatic or can resemble irritable bowel syndrome with non-specific symptoms (bloating, flatulence, abdominal discomfort, diarrhoea, abdominal pain). In more severe cases, there are signs of malabsorption (weight loss, steatorrhoea, malnutrition), liver lesion, skin manifestation (rosacea), arthralgias and deficiency syndromes (anaemia, tetany in hypocalcaemia induced by vitamin D deficiency, metabolic bone disease, polyneuropathy due to vitamin B12 deficiency, impaired barrier function of the gut, etc.). Anaemia is usually macrocytic (megaloblastic) due to vitamin B12 deficiency. It could also be microcytic iron deficiency (due to occult gastrointestinal blood loss)[could this be the cause of my occult blood] or normocytic (as anaemia of chronic disease)

The most important thing is always treatment of the basic underlying disease if possible. Nutritional support is mandatory in SIBO associated with malnutrition, weight loss and nutrient deficiency. We usually use individualised diet, enteral nutrition by fine-bore naso-jejunal tube or nutritional support by sipping of polymeric formulas. In several patients, it is necessary to exclude lactose from the diet, to reduce other simple sugars, to increase coverage of energy needs by fat and to administer MCT oils (medium-chain triacylglyceroles).

Prokinetics seem to be a logical therapeutic step in SIBO due to motility disorders. Several studies tried metoclopramide, cisapride (which was later withdrawn from the market), domperidone, erythromycin, itopride, tegaserod and octreotide. However, there are only limited data suggesting that this treatment would be effective over the long term[7,71]. Cyclic lavages of the small bowel (e.g. by polyethylene glycol) can be considered as supportive therapy in cases of relapsing SIBO[7].

Surgical treatment must always be considered where possible to correct gastrointestinal pathology (entero-colic fistulae, blind loops, bowel obstruction, multiple small intestinal diverticula, etc.). Specialised non-transplant surgery can provide interventions in short bowel syndrome improving intestinal motility (STEP - serial transverse enteroplasty), slowing intestinal transit (valves, reversed segments, colon interposition) or increasing mucosal surface area of the gut (creation of “neo-mucosa”, sequential intestinal lengthening)


dr siebecker rec the elemental diet formula Vivonex Plus which dr Pimentel uses in his research and has found to have a high success rate for eradicating SIBO, about the same 80-90 percent success rate that pharmaceutical antibiotics(rifaxamin) have, she also says that herbal antibiotics have a similar success rate in her practice but that there aren’t studies around to say that they are as good.

Says when she is using the elemental diet she has the patient do it for 2 weeks and does an in house sibo breath test on the 14th day and if it’s still positive then she has them continue for another week. Says it is difficult to do elemental diet, some people feel hungry the whole time and the powder tastes bad

She likes to test the patient in 5-14 days after the treatment of antibiotics has concluded as it takes around 14 days for the gut bacteria to regrow and if you test before it regrows you can tell if your treatment is making a difference or if it is failing, for instance, if your treatment brings your gut’s hydrogen gas down by 40 points it is doing something and you should continue using that same treatment, you just didn’t use it long enough in other words(or maybe you did if bringing it down by 40 points brings it down all the way but if it brings it down only part way and the test is still positive for sibo you need more of your treatment), but if the gas didn’t even budge you’ll have to try something else

Says a lot of patients come to her from other doctors who have been treated with xifaxan and felt immensely well for several weeks or months only to relapse and she will ask if they used a prokinetic and typically their lack of prokinetic use turns out to be the issue

Rec clover honey, says a number of honeys aren’t tolerated by people who malabsorb fructose but that clover honey is just fine for fructose malabsorbers as are any other honeys which are 50% glucose/50% fructose.

Says she sees patients who have been on SCD or GAPS for years and years and who still have SIBO despite, so, diet alone is seldom enough to eradicate SIBO

The guy above who interviewed dr siebecker also has a full package of similar digestion experts he interviewed available for $100


$400 for full access to large amounts of SIBO info, should be last resort

If it turns out http://www.townsendletter.com/index.htm was right about needing either an antibiotic or a year and a half on scd to eliminate sibo consider subscribing to them


Stuff caused by sibo:

Malnutrition may result in weight loss, and progress to excessive muscle wasting (cachexia). Inability to absorb fats in the diet may lead to steatorrhea (excess fat in the feces) that results in foul smelling oily stool, and may cause some anal leakage or fecal incontinence.


A group of 104 patients who tested positive for newly diagnosed SIBO took either a standard, high dose of rifaximin (1200 mg daily) or two capsules twice daily of each of the two supplements in one of the two following herbal protocols:

The products were specifically chosen because they contained antimicrobial herbs, such as oil of oregano, thyme, berberine extracts, and wormwood, shown to provide broad-spectrum coverage against the types of bacteria most commonly involved in SIBO.

Of the patients who received herbal therapy, 46 percent showed no evidence of SIBO on follow up testing compared to 34 percent of rifaximin users. Those using a natural SIBO treatment were significantly more likely to test negative for SIBO at follow up than those taking rifaximin.

The participants who did not improve on the rifaximin were then prescribed either one of the herbal protocols or triple antibiotics (clindamycin, metronidazole, neomycin) for four additional weeks. Of the 31.8 percent of rifaximin non-responders that then took the herbal therapy, 57.1 percent tested negative for SIBO compared to 60% of those taking the triple antibiotic therapy.

Adverse effects reported among those taking rifaximin included anaphylaxis, hives, diarrhea, and Clostridium difficile, while only one case of diarrhea and no other side effects were reported in the herbal therapy group.

“Herbal therapies are at least as effective as rifaximin for resolution of SIBO …” concluded the study authors.

(lane’s note: study is below with relevan data posted


One hundred and four patients who tested positive for newly diagnosed SIBO by lactulose breath testing (LBT) were offered either rifaximin 1200 mg daily vs herbal therapy for 4 weeks with repeat LBT post-treatment.

SIBO is widely prevalent in a tertiary referral gastroenterology practice. Herbal therapies are at least as effective as rifaximin for resolution of SIBO by LBT. Herbals also appear to be as effective as triple antibiotic therapy for SIBO rescue therapy for rifaximin non-responders. Further, prospective studies are needed to validate these findings and explore additional alternative therapies in patients with refractory SIBO.


1. Antibiotics (2 weeks)

There are several pharmaceutical antibiotics which are commonly prescribed for SIBO: Neomycin (better for Methane dominant), Metronidazole, and Rifaximin. The benefits of antibiotics top out after 3 weeks, so a 2 week course is the sweet spot.

Rifaximin (generic: Xifaxan) has the best reputation of the group, even among naturopaths, as it’s an antibiotic with “eubiotic effects.” It specifically targets the area we need to eradicate—only killing bacteria in small intestine. According to studies, the side effects are mild and the die-off of beneficial species of bacteria in the colon is minimal. For those who are wary of antibiotics, this isn’t a bad one.

However, the main problem with Rifaximin (and all other pharma options in this category) is that with repeat use, you increase the likelihood of becoming resistant. Meaning, it might be worth one try, but you don’t want to get into a cycle of use, especially when there are other natural options that have been proven equally effective with fewer long-term risks.

2. Herbal Antibiotics (4 – 6 weeks)

People don’t necessarily gravitate towards herbal options just because they’re more “natural.” Rather, certain combinations of herbal antibiotics have been proven in studies to be just as effective, if not more effective than their pharma counterparts.

The downside: more pills, for longer, with the possibility of GI side effects. Just because herbs are natural doesn’t mean they’ll be tolerated by everyone. I certainly experienced discomfort and an increase in my constipation symptoms while on the Biotics formula.

The upside? You can purchase these herbs without a prescription and experiment on your own. Which, considering you can now take a SIBO test at home, is an affordable option for those who aren’t able to invest in the helping hand of an integrative doctor.

So what are the best protocols for herbal antibiotics? The two most commonly used herbal blends in Dr. Alison Siebecker’s practice, who is commonly thought of as the pioneer of SIBO, are:

Metagenics Candibactin-AR + Candibactin-BR (this is the most studied option)

Biotics FC Cidal + Dysbiocide (the one I used!)

Typical dosing is: 2 caps, twice a day, for 4 weeks. For what it’s worth, I did the Biotics system for 6 weeks.

The two protocols above combine several individual herbs that are thought to be helpful, including berberine herbs, ginger and oregano. There’s definitely a big pro to having a formula already sussed out for you. But another route is to design your own treatment using a combination of the below herbs. Dr. Allison Siebecker recommends 1-3 in combination, for 4 weeks, at highest dose suggested on product labels.

Allicin: Though it’s derived from garlic, this strong antimicrobial doesn’t contain the FODMAP’s found in other parts of the clove. The highest potency formula is Allimed. This is the only single use herb that’s been studied with SIBO, and was found to be effective for methane-dominant SIBO. It can be added to one of the above protocols, or used in conjunction with Berberine and Neem.

Berberine Complex: these herbs are also found in the Metagenics formula. It’s derived from Goldenseal, Oregon Grape, Barberry, and other herbs. Many use this in conjunction with oil of oregano and neem for hydrogen-dominant SIBO.

Neem Plus: Neem is a tropical evergreen tree and is said to enhance the positive effects of the two herbs above.

Oil of Oregano: This herb has been known as a longtime antifungal, antimicrobial, antiviral powerhouse. During my Biotics protocol, I habitually added two drops to my water or took a veggie capsule of it with my other pills.

3. The Elemental Diet (2 weeks)

If all else fails, there’s always the elemental diet. It is thought of as a last resort because of the extreme unfun-ness of the protocol, which involves drinking a medical solution for all meals for a 14 day period. I can’t imagine ever doing this, but it’s a relatively quick strategy that’s proven 85 percent effective at starving out the bacteria, while, on a purely elemental level, feeding the person.

The mixture includes liquid nutrients in an easily assimilated form that is used in hospitals on GI patients whose system needs to heal. The nutrients get absorbed quickly and easily in the first leg of the digestive labyrinth, meaning they never make it to the area of the small intestines where unwanted bacteria congregates in SIBO patients.

The protocol is suggested for 14 days, with a retest taking place on the 15th day. Overnight results should be requested so that you can immediately start the diet for an additional week if there’s still a positive.

Again, this is if all other protocols fail. It’s not recommended to take antibiotics or herbs during the elemental diet because the bacteria, without food sources, will essentially be hibernating or die off on their own, as intended by the diet



Iberogast oral drops 100ml Iberogast oral drops is a herbal medicine formulated to treat digestive disorders, gastritis, stomach pain, abdominal bloating, flatulence, gastrointestinal colic, nausea and also heartburn. In the composition of Iberogast oral drops a variety of medicinal plants that their joint action allows to effectively combat the symptoms mentioned above. These plants are as follows: Angelica archangelica L. (angelica) Melissa officinalis L. (melissa) Carum carvi L. (caraway) Chelidonium majus L. (celidonia) Chelidonium majus L. (licorice) Matricaria recutita L. (chamomile) Silybum marianum L. Gaertner (Marian thistle) Mentha piperita L. (peppermint) The dosage, dosage and method of use of Iberogast oral drops are detailed below: in adults, adolescents and children over 12 years must take 20 drops of Iberogast, 3 times daily before or after meals, mixing the drops with a little liquid. If after 2 weeks of treatment the symptoms do not get better or worse you should consult your doctor. The most common side effects of Iberogast oral drops are very few and very unusual: have reported hypersensitivity skin reactions such as rashes, itching or respiratory discomfort.

100 servings per bottle


I have taken FC-Cidal and Disbiocide by Biotics Research. The two work well to cure SIBO. However you need to take this between meals and not with food. I've tried it both ways and found it didn't work when I took it with meals. You also need to lower your carbohydrate intake. This last round I discovered that sugar and fruit do not aggravate SIBO but bread products certainly do. I suspect simple sugars and fruit are absorbed before they reach the site of infection (distal small intestine) where bread products are still present and feed the bacteria. That would also explain my observation that if I eat a lot of non-fruit carbohydrates I develop SIBO again a lot sooner than if I just stick to fruit.

The beneficial effects of these bacteria are eradicated when large numbers of foreign bacteria – chiefly those which are found in the large intestine – begin to grow in the small intestine. Once the small intestine is colonized by these strains, there is a multitude of consequences. The orderly process of digestion is now undermined by bacteria that deconjugate bile before it can be used, leading to an inability to digest fats and producing nausea and cholecystitis-like symptoms. Carbohydrates, which are normally broken down in the large intestine, are now fermented in the jejunum, leading to bloating, distension and gas. Moreover, the action of these bacteria on proteins leads to excess ammonia production, which, in essence, acts like a poison if not adequately cleared from the system. Once digestion is impaired (dysbiosis), deficiencies of fat soluble vitamins (A, D, E), as well as deficiencies of B12, thiamine (B1), and nicotinamide (an amine of B3 involved in cognitive function) will result. Most deleterious of all is the resultant inflammation of the lining of the intestine, which leads to malabsorption, leaky gut, immune system upregulation and numerous food allergies and sensitivities. Because SIBO affects every aspect of small intestine digestive function, it produces a wide range of GI symptoms: diarrhea, weight loss, GI pain, anemia. SIBO has also been linked to the inflammatory skin condition, rosacea. Several studies have shown that once SIBO is treated, rosacea disappears.

Joint pain related to inflammation also improves dramatically when SIBO is treated. Interestingly, treatment of SIBO improves cognitive symptoms in CFS/ ME patients, providing further evidence of the link between the gut and the brain. The most common cause of SIBO is antibiotic treatment. Slow motility can also lead to SIBO as can hypochlorhydria. Diagnosis of SIBO is made through breath testing. Because Xifaxan is a non-systemic antibiotic, it is currently the drug of choice for treating SIBO. Generally, antibiotic treatments are given for one week once a month until the infection has cleared. The second line of treatment, often given simultaneously and/ or immediately after treatment with antibiotics, is probiotics. In milder cases of SIBO, antibiotics may be skipped altogether in favor of a probiotic course of treatment. Probiotics of varying strains have been used for treating SIBO, but the more successful varieties have been Acidophilus GG (marketed as Culturelle), and Bifidobacterium infantis (marketed as Align).

Follow a low-carbohydrate diet. Enteric-coated peppermint oil has been shown to be lethal to bacteria. In one case study, only ten days of treatment with enteric-coated peppermint oil resulted in not only a significant reduction in hydrogen production in the hydrogen breath test, but a reduction in bloating, pain, and belching. It is important to note that the peppermint oil must be enteric coated in order to avoid heartburn. Increase stomach acid. Hypochloridia is so common in CFS/ ME patients that low stomach acid is among the most likely culprits of SIBO. Fortunately, increasing stomach acid is fairly easy. Supplementation with Betaine Hydrochloride (HCl ) will increase stomach acid and aid the production on pancreatic enzymes. Start with one tablet with a meal. If you get heartburn, stop and try again in a week or so. (Don't take the supplement before or after the meal, but during.) Stomach acid can also be aided by taking vitamin C with a meal, or by sipping a dilution of apple cider vinegar (1-2 TBS to 4 oz water.) Pancreatic enzymes are important adjuncts in SIBO treatments. Enzymes are frequently under-utilized in people with SIBO, due to hypochloridia and bacterial deconjugation of bile. Supplementation with Ultrazyme or another broad spectrum enzyme will aid the process of digestion

Alpha Ketoglutarate rec for aid in krebs cycle(ATP production), for fighting SIBO, strengthening intestinal mucosa, and producing several nonessential amino acids(lots more info on AKG in section)

finally a weak ileocecal valve (the valve that separates the bacteria rich: contents from the ileum, the final segment of the small intestine) can lead to overpopulation ans small intestinal bacteria. A weak ileocecal valve is most often the consequence of long-term constipation or straining excessively at defecation; in both these cases a low fiber diet is most often responsible.

From Valerie balandra: mentions biocidin as an antimicrobial for sibo, she also rec rifaxamin for it

Dr mark Pimentel on chris kresser


any methane rise over 3ppm in breath test is 90% of the time a positive test

2/3rds of SIBO patients relapse after rifaximin(and I think for that matter any antimicrobial for sibo), those that relapse within a week or two often have issues going beyond a weak migrating motor complex, something like damage to the gut systems that would need to be investigated

Says rifaximin doesn’t affect the microbes in the colon for some unknown reason, it works fine in the small intestine but is rendered ineffective once it enters the colon. Rifaximin isn’t causing increase in yeast or any sort of change whatsoever in the microbiome of the colon

Bacteria are much more vulnerable when they are able to eat, when they aren’t able to eat they go into dormant mode and wall themselves off making it hard for the antibiotics to harm them. When you give guar gum or other prebiotics they start eating and their defenses go down. Patients shouldn’t be eating low fodmap or low carb diets while on rifaximin or other antibiotics that are designed to treat sibo.

As for prokinetics he doesn’t like to use don peridon(might have misspelled) b/c of heart related side effects. The two he uses is very low dose erythromycin, at that dose it is prokinetic without any antibiotic effects(erythromycin is usu a antibiotic), resalor(maybe misspelled) is the other prokinetic he uses.

Rifaximin can be used over and over again, it causes very little resistance and when resistance does come about it disappears within a week.

{08} misc from curezone(med list overall doc)​


I will share with you what I believe are the most important things that have and are helping me. #1- diet- 95% starch free. #2- Rifaximin- I took a 10 day course and a 15 day course at 1,200mg a day.

That brought down the bacterial overgrowth and allowed me to tolerate a high enough dose of antimicrobial herbs like oil of oregano, berberine, cinnamon, thyme, amla and grape seed extract. If you can't get Rifaximin, high doses of herbs have been shown to work just as well.

#3- I take a high dose probiotic (60 billion cfu). That is basically my protocol. I have learned through trail and error, that a very low starch diet and fairly high doses of STRONG antimicrobial herbs, long term, are absolutely necessary to get rid of sibo.

By long term, I mean at least 6 months or even longer. I'm 4 months in and just really noticing some big improvements. I have been very strict with both diet and anti-microbials but I also got a big jump start with the Rifaximin.

Like I said though, if you can tolerate fairly high doses of antimicrobial herbs, they are just as effective, but take longer to work. I think you will need very strong antimicrobials like oil of oregano, neem, thyme, cinnamon extract, at fairly high doses to get sibo/dysbiosis under control, based on my experience, but it IS do-able!

{09} Genova​

SIBO clinical considerations gdx https://www.gdx.net/clinicians/medi...ebinars/small-intestinal-bacterial-overgrowth

Lactulose is a synthetic sugar that wont pass through the gut wall and so will only be digested by gut bacteria, when the breath test results come back and the levels rise slowly to a single peak at or near the end that is likely not SIBO but when it rises to a peak near the beginning, goes down, and rises again to a peak that represents SIBO as the small bowel produced the first peak which then receded as the lactulose passed through an uncolonized part of the small bowel before reaching the colon which is supposed to be colonized.

The small intestine aspirate and fluid culture, something done by the mayo clinic, involves passing a tube through the upper gut into the small intestines to take a culture from there to be grown out, this test unfortunately has many false negatives.

Breath tests should look for more than hydrogen alone since in many people hydrogen gets converted into methane. So by getting a test that includes both hydrogen and methane you avoid false negatives.

Sibo therapeutic interventions

  • Rifaximin
  • Rifaximin in combination with other antibiotics (neomycin)
  • For methane predominant SIBO
  • Herbal antibiotics
  • Dietary interventions
  • Low FODMAPs
  • Low Carbohydrate diet
  • Elemental diets
Another option is to treat the underlying cause such as maldigestion(hypochlorhydria/pancreatic insufficiency), motility issues, poor diet (high starch/refined carbs)

“while there has only been one published report of herbal antibiotics in the treatment of SIBO, our experience is that they have similar effectiveness to antibiotics. We have used the following botanicals: Allium sativum, Hydrastis Canadensis, and other berberine containing herbs, Origanum vulgare, cinnamon, and azadirachta indica. We have used these as both single angents and in various combinations at dosages that are at the upper end of lael suggestions x 30 days. Specific single dosages we have used include allicin extract of garlic: 450 mg b.i.d.-t.i.d., goldenseal/berberine: 5g q.d. in split dosage, emulsified oregano: 100mg b.i.d., and neem: 300mg t.i.d. our breath testing has validate the need for the longer treatment period of 30 days for herbal antibiotics compared with 14 days for antibiotics. We have also observed with this method prolonged dio-off reactions, which can last for the duration of treatment course. Studies on herbal antibiotics for SIBO are needed, particularly to identify botanicals effective in reducing methane.

from http://www.townsendletter.com/FebMarch2013/ibs0213.html

Other tests that may be helpful in the case of SIBO:

  • GI effects can identify:
Pancreatic insufficiency



Yeast overgrowth

Parasitic infection

  • Food antibody panel
  • Celiac and gluten sensitivity panel


GI effects profile can not identify SIBO

There are markers on this profile that can be suggestive of SIBO in the right patient population:

  • Elevations in products of protein breakdown
  • Elevations in fecal fats (due to interrupted enterohepatic recirculation
  • Unexpected or extreme elevations in beneficial SCFAs and n-butyrate
If any of these is elevated and the patient is symptomatic you may consider doing a SIBO breath test to be definitive

Nutritional testing (nutreval/ION) if you suspect SIBO is causing deficiencies on the level of B vitamin status, fatty acid profile, fat soluble vitamin status.

Additionally, if you suspect leaky gut has arisen from prolonged SIBO leading to gut damage(leaky gut) you may run an Intestinal permeability panel and a Food antibody panel

When working to eliminate SIBO probiotics are a good thing to take but make sure there are no prebiotics taken as part of that same capsule or separately, prebiotics are meant to feed bacteria in general and wont distinguish between helping probiotics and pathogenic bacteria. Prebiotics are things like FOS, inulin, arabinogalactan, and GOS (galactoligosaccharide).. Though if the patient gets worse on probiotics then it might be a good idea to back off on them

From http://www.townsendletter.com/FebMarch2013/ibs0213.html

(If it turns out http://www.townsendletter.com/index.htm was right about needing either an antibiotic or a year and a half on scd to eliminate sibo consider subscribing to them)

The following may indicate SIBO:

• when a patient develops IBS following a bout of acute gastroenteritis.
• when a patient reports dramatic transient improvement in IBS symptoms after antibiotic treatment
• when a patient reports worsening of IBS symptoms from ingesting probiotic supplements which also contain prebiotics
• when a patient reports that eating more fiber increases constipation and other IBS symptoms
• when a celiac patient reports insufficient improvement in digestive symptoms even when following a gluten-free diet
• when a patient develops constipation type IBS (IBS-C) after taking opiates
• when a patient has chronic low ferritin levels with no other apparent cause

An important protective mechanism against SIBO is proper small intestine motility via the migrating motor complex because stasis promotes bacterial growth.18 Also key in prevention is gastric, pancreatic, and gall bladder secretion, since hydrochloric acid, enzymes, and bile are bactericidal/static.19 The use of proton pump inhibitors encourages overgrowth, especially of the hydrogen producing type.20,21 We also suspect an important role for proper ileocecal valve function in preventing reflux of colonic bacteria into the small intestine.22

Methane has been shown to slow gastrointestinal motility by 59% in animal studies, and the volume of methane overproduction correlates with the severity of constipation

Therefore when both hydrogen and methane are present, diarrhea, constipation, or a mixture of both can be present based on the relative amounts of gases.29 The bacterial consumption and uptake of host nutrients, such as B12 and iron, can lead to macrocytic and/or microcytic anemia or chronic low ferritin, in addition to general malabsorption and malnutrition in more severe cases.8,33 Finally, continuous fermentation of host nutrition by repeated exposure to daily meals, perpetuates bacterial overgrowth and its symptoms, creating a vicious cycle

Preparation for the (hydrogen/methane breath) test varies from lab to lab, but a typical prep diet is limited to white rice, fish/poultry/meat, eggs, clear beef or chicken broth (not bone broth or bouillon), oil, salt, and pepper. The purpose of the prep diet is to get a clear reaction to the test solution by reducing fermentable foods the day before. In some cases, two days of prep diet may be needed to reduce baseline gases to negative. Antibiotics should not be used for at least 2 weeks prior to an initial test; some sources recommend 4 weeks.39

We have found that an absolute level of gases at or above the positive ppm levels provided by Quin Tron, without a rise over baseline, correlates well with clinical SIBO. This is especially true for methane gas, which can have a pattern of elevated baseline (over 12 ppm) which remains elevated for the duration of the test. In cases such as these, methane may only rise 5 ppm over baseline, but the ppm level is consistently above positive. Interpretation of elevated hydrogen or methane on the baseline specimen (pre-lactulose ingestion) is controversial, but we prefer to consider a high baseline to be a positive test.31,40

The classic positive for SIBO has been considered to be a double peak, with the first peak representing the SIBO and the second peak representing the normal large intestine bacteria. This is an infrequent presentation in our experience. More frequently we see one peak that rises highest in the third hour, representing distal SIBO and then the normal LI bacteria.

If the measured gases do not rise until after 120 minutes, it is possible that this is due to a prolonged transit time, which we have seen in patients with severe constipation. In such a patient with the expected symptom picture for constipation type SIBO, a significant rise at 140 minutes may be interpreted as a positive test.

SCD(specific carbohydrate diet) or (GAPS) Gut and psychology syndrome diet are rec for sibo patients

We have found that using the SCD or Gut and Psychology Syndrome Diet (GAPS) as the core diet (Table 1), with the incorporation of the fruit and vegetable recommendations from the Low FODMAP Diet (Table 2), is an effective approach. The Low FODMAP Diet is an IBS treatment diet that has investigated the fermentable levels of carbohydrate foods (fruits, vegetables, and grains) and has a success rate of 76%.47 The FODMAP Diet is not specifically designed for SIBO and therefore does not eliminate polysaccharide and disaccharide sources such as grains, starch, starchy vegetables, and sucrose. Eliminating these poly- and disaccharides is essential in SIBO because SIBO creates a situation in which these normally well-absorbed carbohydrates, foods that usually go to feed the host, can now feed bacteria inappropriately located in the small intestine, creating symptoms and worsening the problem

Low-carbohydrate diets are weight-loss diets. Particular attention must be paid to those who are low weight or underweight. If a low-carb SIBO diet is causing too much weight loss, this dietary strategy will need to be altered to allow for more carbohydrates. In these circumstances, one or more of the other three treatment options should be considered along with white rice, glucose, and other carbohydrate sources.

Diet is also essential for prevention, post SIBO treatment.

Elemental Diet
An elemental diet can be used in place of antibiotics or herbal antibiotics to rapidly decrease bacteria. Elemental diets are powdered predigested nutrients that are mixed with water and used in hospitals for various gastrointestinal disorders to give digestion a rest. The concept behind this treatment for SIBO is that the nutrients will be absorbed before having a chance to feed the bacteria, thus feeding the person but starving the bacteria. It is used in place of all meals, for 2 to 3 weeks, and has a success rate of 80% to 85%.48 Elemental diets are not protein powders or cleansing/detox formulas. They are available over the counter and are not covered by insurance, which can make this treatment course costly.

SCD resources: breaking the vicious cycle by Elaine gottschall. www.breaking the visciouscycle.info www.scdlifestyle.com

GAPS resources: Gut and psychology syndrome by dr. Natasha Campbell-mcbride. Gaps guide by baden lashkov. Gutandpsychologysyndrome.com

See: sibo fruit and veggie guide which is an image saved in documents giving info on fermentability

Rifaximin is local and does not act as a systemic antibiotic. rifaximin has several unique benefits: it does not cause yeast overgrowth, it decreases antibiotic resistance in bacteria by reducing plasmids, antibiotic resistance does not develop to it, making it effective for retreatments, and it is anti-inflammatory, decreasing intestinal inflammatory cytokines and inhibiting NF-kb via the PXR gene.52–54 Rifaximin is best used for SIBO when hydrogen is present, but when methane gas is present, double therapy of rifaximin plus neomycin (500 mg b.i.d. × 14 days) is more effective.55 Many gastroenterologists use metronidazole (250 mg t.i.d. × 14 days) as an alternative to neomycin (unpublished). Since different antibiotic regimens are recommended based on the gas type, breath testing is necessitated when considering this treatment.

SIBO is a disease that relapses because eradication itself does not always correct the underlying cause.57,58 Pimentel's 2006 treatment algorithm includes 2 essential preventions: diet and a prokinetic (motility agent). Our approach offers 3 optional additions: hydrochloric acid, probiotics, and brush border healing supplements

A key underlying cause of SIBO is thought to be deficiency of the migrating motor complex (MMC), which moves bacteria down into the large intestine during fasting at night and between meals.59 Prokinetics stimulate the MMC, symptomatically correcting this underlying cause. Prokinetics studied for SIBO include low-dose naltrexone 2.5 mg q.d., h.s., or b.i.d., low-dose erythromycin 50 mg h.s., and tegaserod 2–6 mg h.s.59,60 Tegaserod has a higher success rate for SIBO prevention versus erythromycin, but has been withdrawn from the US for safety reasons.59 Prucalopride 1–4 mg h.s. is not yet available in the US but is a safer alternative to tegaserod.61 A trial removal of the prokinetic at ≥ 3 months is suggested but continued long-term use may be needed.

To our knowledge, only one study has examined the rate of healing post SIBO, which found that intestinal permeability normalized four weeks after successful SIBO eradication in 75% of patients.37 While this report is very encouraging, it may or may not reflect the other repair needed post SIBO. Therefore we currently suggest continuing a SIBO diet for three months post successful eradication. At this point, the Cedars-Sinai Diet, FODMAP Diet, or a similar lower-carb diet may be adopted long term, as the patient tolerates. Spacing meals 4 to 5 hours apart, with nothing ingested but water, allows migrating motor complex (MMC) to occur.28 We have found this to be very helpful clinically. If a low-carb SIBO diet does not correct hypoglycemia, this strategy will need to be altered to allow for more frequent meals.

Probiotics are a controversial intervention in SIBO because lactobacilli have been cultured in SIBO and there is concern about adding to the bacterial overload, particularly in this situation of dysfunctional MMC.25 Despite this, the few studies that have focused directly on SIBO have shown good results, with a SIBO eradication rate of 47% from Bacillus clausii as the only treatment, and a clinical improvement rate of 82% from Lactobacillus casei and plantarum, Streptococcus faecalis, and Bifidobacter brevis (Bioflora) as the only treatment.63,64 Probiotic yogurt containing Lactobacillus johnsonii normalized cytokine responses – reducing the low-grade chronic inflammation found in SIBO, after 4 weeks.65 We have used various multistrain and single probiotics as well as yogurt and cultured vegetables in our SIBO patients, with good results.

Brush border healing supplements may be given to assist the repair of small intestine tissue. While mucilaginous herbs are traditionally employed for this purpose (licorice, slippery elm, aloe vera, marshmallow), their use is controversial post SIBO, due to their high level of mucopolysaccharides, which could encourage bacterial regrowth. Specific nutrients that we have used include colostrum: 2–6 g q.d., L-glutamine: 375 mg–1500 mg q.d., zinc carnosine: 75–150 mg q.d., vitamins A and D, often given as cod liver oil: 1 Tbs q.d., curcumin: 400 mg–3 g q.d., resveratrol: 250 mg–2 g q.d., glutathione (oral liposomal): 50–425 mg q.d. or glutathione precursor N-acetylcysteine 200–600 mg q.d. Supplements are given for one to three months, though may be continued long term for general benefit. Higher dosages of curcumin and resveratrol are given for two weeks for the purpose of downregulating NF-kb, a mediator of increased intestinal permeability, and then reduced to maintenance levels

In our practices we have found that the following circumstances increase the chances for an unsatisfactory patient outcome:

Failure to continue treatment courses until SIBO is eradicated (negative breath test or patient ≥90% better).
Failure to use double antibiotic therapy for methane producers. Methanogenic bacteria need different antibiotic treatment than hydrogen-producing bacteria.
Failure to utilize breath testing to identify if the patient has SIBO, the type of gas he/she produces, and the overall level of gas. This information is necessary for diagnosis, treatment choice, duration, and prognosis.
Failure to use a prokinetic immediately following treatment. Prokinetics along with diet are needed to prevent relapse of this commonly recurring condition.
Failure to use a low-carb preventative diet following treatment. Diet along with prokinetics are needed to prevent relapse of this commonly recurring condition.
Failure to tailor diet to individual tolerances with personal experimentation. No fixed diet can predict an individual's complex bacterial, digestive, absorptive, immunological, and genetic circumstances; therefore customizing is necessary.
• Failure to identify underlying causative conditions. A recent report found the following conditions led to a poor response to antibiotics: anatomical abnormalities, chronic narcotic use, Addison's disease, scleroderma, colonic inertia, inflammatory bowel disease, and NSAID-induced intestinal ulceration.

Human Gut Microbiome

Just having positive H Pylori doesn’t mean anything, if a person is asymptomatic it doesn’t need to be treated

It isn’t that h pylori causes ulcers but rather perpetuates it. If the person is symptomatic he uses triple antibiotic therapy but makes sure to use lots of probiotics after to prevent dysbiosis.

Says he doesn’t like treating sibo w/ pharmaceutical antibiotics even if it is xifaxan. He uses betaine hcl, enzymes, herbal antimicrobials instead as the herbal antimicrobials are gentler. He prefers combination products, says they are more powerful than any one alone.

{10}Allison Siebecker


IBS/SIBO Differential Diagnosis Sx: bloating, pain, constipation, diarrhea(in other words, things that can cause sibo type symptoms):

• Yeast Overgrowth • Parasitic Infection • LI Bacterial overgrowth/ infxn • H pylori infection • Celiac Disease/NC Glut Intol • IBD: Crohn’s/ Ulcerative Colitis • Carbohydrate Malabsorption – Lactose, Fructose, Polyol… • Food Reaction: protein, histamine, salicylates… • Hypochlorhydria • Pancreatic Enzyme Insufficiency • Hypo/Hyper Thyroid • Bile Acid Malabsorption • VIPoma • Zollinger Ellison Syndrome • Abdomino-phrenic dyssynergia • Chronic Abdominal Wall Pain • Endometriosis • Cancer- Panc/St/SI/LI, Ovarian… • SI Obstruction • Immune Deficiency (CVID) • Stress • Insufficient Chewing

IBS/SIBO DDX Lab Testing:

• Carb Malabsorption: Breath- Lactose, Fructose, Mannitol/Sorbitol, Sucrose • Yeast: Blood- Candida Ab/Ag Complex. Stool Urine OG Acid • Parasite, LIBO, LI Infection: Stool • H pylori: Breath- Urea. EndoscopyCulture, Rapid Urease. Blood- Ab • Celiac: Endoscopy- biopsy. Blood- IgA: tTG, EMA, DGP, IgG: DGP. Saliva/Cheek, Stool- Gene • N-C Gluten Intol: Diet- Elim/Chall, StoolGene • IBD: Colonoscopy, Stool- Calprotectin, Lactoferrin • Immune Deficiency: Blood- Ab Total/Vaccine, T cell, WBC • Dyssynergia: Manometry • Endometriosis: Imaging, Surgery • Food Reaction: Diet- Elimination/ Challenge, Blood- Food Ig, DAO • VIPoma: Blood- VIP • Zollinger-ellison Syn: Blood- Gastrin. Imaging. Endoscopy • Cancer/Obstruction: Imaging • Hypochlorhydria: Heidelberg. 24 hr pH Metry. String? • Pancreatic Insufficiency: Stool- Fat, Elastase, Chymotrysin © Dr. Siebecker 2012 • Stress: Saliva- Cortisol/DHEA

Diagnostics Tests

1. Endoscopy: Culture • 38% reproducibility (Quigley 2006, PMID: 16473077)

2. Breath Hydrogen & Methane: Lactulose or Glucose • 92% reproducibility (Quigley 2006, PMID: 16473077)

3. Blood: Cdt B & Vinculin Antibodies (IBSChek) • Dx PI-IBS (SIBO from food poisoning); diarrhea/mixed type • 91% specificity, 95% dx accuracy (Pimentel 2015, PMID: 25970536)

Not Diagnostic

• Stool - dx LIBO not SIBO (LI different organ) • Urine OG Acid - can’t distinguish btw SI & LI • Types of Breath Tests – not all are for SIBO • Urea: H pylori • Carbohydrate Malabsorption: Lactose, Fructose, Sorbitol…

When breath testing for sibo

3 hour version of test needed for hydrogen sulfide (HS) & helps methane dx, HS causes a distinct pattern on HMBT= “flat line”/zeros entire test

Meant to lower the baseline & allow a clear reaction to the substrate. • Ideal= Meat and Fat, No Carbs • No Fruit, Veg, Juice, Nuts, Beans, Grains, Bone Broth, Milk, Alcohol… • White Rice/Wheat allowed - only if it’s known not to aggravate sx

Retesting on Prokinetics • Ok in my opinion • Not advised by Breath Testing Consensus. Concern: False (+) if substrate moves faster into LI, showing LI bact gas in SI time.

LBT Positive Test Criteria: Numbers My Opinion • Hydrogen: ≥ 20 ppm w/in 120 min, after baseline w/in 140 min with constipation • Methane: ≥ 12 ppm w/in 180 min, including baseline 3-11 ppm w/in 180 min with constipation • Combined H & M: ≥ 15 ppm after baseline • H at any time-point + M at any time-point • Hydrogen Sulfide: all zeros or close (0-6ppm H, 0-3ppm M w/in 180 min)

LBT Positive Test Criteria: Severity My Opinion Mild= up to 45ppm Moderate= 45-70ppm High= 70-100ppm Severe= 100+ppm Note: sx severity may not correlate with gas severityv

Breath testing patterns:

  • Improper Prep = High baseline that plummets over 120 min
  • highest # within 120 min is baseline, may rise in 3rd hr due to LI bact
  • Methane = starts high, stays high (no real rise) • Hydrogen Sulfide = no rise H or M in the 3rd hour: “flat line”
  • Proximal SIBO clearing On Retest= lower #’s earlier (a good sign)
  • • Hydrogen Rises when Methane decreases On Retest
  • Common; 4 H’s make 1 M
  • Double Peak- 1 st indicates SIBO, 2nd normal LI bacteria

Hydrogen Sulfide Testing

• LBT: “flat line” on 3 hr LBT (not 2 hr or GBT) • Or: 0-6ppm Hydrogen, 0-3ppm Methane the whole test • B/c 3rd hr should show LI bact gas; if it doesn’t it’s been converted to untested gas • Urine: Immune balance (Th1/TH2) urine test • Unvalidated- “research purposes only” • At home test. No Dr’s order needed (pt can order) • Urine turns dark purple quickly if (+) • Follow up testing after successful tx= paler color or turns dark slowly

Migrating Motor Complex Testing

- Antroduodenal Manometry:

• Direct test for MMC

• Endoscopy (invasive, expensive, only a few places perform it)

• Interpretation: reported by performing Dr.

-Cdt B & Vinculin Antibodies (IBSchek):

• Indirect test for MMC via ICC damage

• Blood

• Interpretation: Positive=if either Ab is (+)

• Negative= ”inconclusive” b/c can have IBS from another cause

Altered Anatomy/structure testing

Barium SI Series:

• Direct test for flow/passage through SI

• Indirect test for extra intestinal adhesions

• X-ray Imaging

• Interpretation: reported by performing radiologist

(+) narrowing with dilation above it

(+) 90 angles indicate adhesions (SI should have rounded/curved features)

The following instructions are needed on Order Form to get a sufficient test: “Rule out adhesions with multiple spot films and positional changes to visualize each segment of bowel”

1st line treatment for sibo: treat anemia/lowferritin/adrenals/thyroid/other hormones/other present conditions

2nd line treatment: probiotics:

Some docs= no Pbx in SIBO. Some= Pbx for all SIBO. – I go case by case (ask each pt how Pbx have effected them in the past, factoring in Prebx)

• Note: avoid Prebiotics as main ingredient (w/mg listing) – Inulin/FOS/GOS/MOS/Arabinogalactan. Often Ok as a base ingredient.

• Not included in Algorithm. – Good idea to use probiotics w/Neomycin, Metronidazole & Berberine. Not needed w/Rifaximin.

Patients typically relapse between 2-3 months after treatment, most patients do relapse

100% symptom resolution is not expected – 80-90% is standard. 100% can happen but it’s not standard • Underlying cause generates sx & has not been treated in most cases – I try for 90% & often get it- if 80% better = I do another round • 10-20% left – 1 st & 2nd line Therapies

Standard Tx course for the majority: – Takes months of multiple rounds to get an initial test negative – Work this through with rapid follow ups/next Tx courses, till achieved • 1-2 week break btw Tx courses, otherwise they may relapse & progress just made may be lost. Ok to go right into next Tx w/o break. Retest every 2nd round- recommended.

• Then Relapses begin & that can take months to get well controlled into longer remissions (however it’s usu shorter to get to neg test again)

Anti-biofilm agents offer no clinical improvements, aren’t worth using

Standard- wait at least 2 wks – For Re-Test results – To Asses Sx – For a Abx/HAbx holiday • can refresh effect of a tx that’s stopped working

Important to be on Prokinetic between Tx’s- to hold gains made

• Back to back Tx– If gas is high

• GI Docs often wait 1 month to re-test or re-treat – But 2 weeks is such a common relapse time I don’t advise waiting that long

Average Gas Reduction of Treatments Abx and HABx reduce gas by 30ppm on average, Elemental Diet = 70-100+ ppm, Diet = unknown – Fodmaps= on day 2: hydrogen ↓180ppm for IBS pt but that’s without prep diet & while eating (incomparable) –

SIBO diet could cause a lowered test score

Tx Concerns

• SIBO Diets (restricted diets) – Malnutrition - Weight loss - Hypothyroid – Microbiome alteration - Eating disorder

• Abx/HAbx – C diff infection - Side Effects, allergy – Microbiome alteration - Abx/HAbx resistance

• Elemental Diet - Side Effects -Weight Loss

• Prokinetics - Side Effects, allergy

Successive Treatment Rounds are often needed to treat sibo (Abx/HAbx) – 1 tx course lowers gas 25-35 ppm avg (Abx=2wk, HAbx=4wk)

Different Tx needed for Methane &/or constipation – Add Neomycin or Metronidazole, or Allicin

Vary Tx method PRN between Abx, HAbx & ED – Often only 1 method of 3 is effective. I use all 3 interchangeably.


siebecker talking to sean crockston(might have misspelt his last name)

2 studies showed that those w/ sibo have a 50/50 chance of having leaky gut, healthy controls only have a 4% chance of having leaky gut

In one study, 100% of leaky gut was healed once the SIBO was eradicated. In the other study, 75% of the people had their leaky gut healed upon eradication of SIBO. The only thing these patients did to heal their leaky gut was eradicate the SIBO. In the studies, this was done using pharmaceutical antibiotics. No supplements or diet intervention was given. This proves that when you remove the cause, the body will heal on it’s own.

Siebecker’s experience, roughly ¼ of her patients with SIBO also have Candida. Therefore, SIBO and Candida don’t go together. Candida can also cause leaky gut, just like other infections.

Herbal antibiotics are also antifungals, so they can treat SIBO, candida, and parasites.

When choosing a probiotic, look for one that makes you feel better and stick with it. The three most beneficial strains for SIBO have shown to be bifidus infantis, bifidus lactis, and lactobacillus plantarum.

Biofilm disruptors do nothing to treat SIBO but are important in treating candida

Herbal antibiotics can disrupt gut microbiota. One herbal antibiotic that has shown not to kill probiotics, specifically lactic acid bacteria is allicin from garlic.

Some peoples iliocecal valves are open too much and allow bacteria from the colon to invade the SI, there are different massages the patient can do to correct this or they can go to a chiropractor to have it fixed

Q: How long does it take to heal from SIBO and Leaky Gut?

A: Everyone is different, so there’s no solid answer. Studies on patients with alcohol-induced leaky gut showed 2 weeks to heal the gut. Patients with Celiac seem to take longer; between 6 months to 1 year. For patients with SIBO and leaky gut. Leaky gut generally heals less than a month after SIBO is eradicated.

The time is takes to get rid of SIBO can take 2 weeks to 1 year depending on the method used. It usually takes about 2 months. In many cases of SIBO, there is damage to the ICC cells which are responsible for the migrating motor complex. It can take 1 month to 6 years to heal these damaged cells.

Q: How do you prevent a relapse of SIBO?

A: Prevention requires some type of low carb diet with a prokinetic. There are both pharmaceutical and natural options for a prokinetic. According to Dr. Siebecker, the pharmaceutical options are the best. These include Erythromycin, Resalor, and LDN (Low Dose Naltrexone). While many people love LDN because it has a number of other benefits, it isn’t strong enough for everyone. For approximately ¼ of people, LDN doesn’t work well enough. In that case you can switch to a stronger prokinetic or add a natural prokinetic with the LDN. Resalor is the strongest and Erythromycin is in the middle.

If you prefer to avoid prescriptions and go the natural route, your options include Iberogast, MotilPro, and ginger. Ginger seems to work well, but many people become tolerant to it, so it stops working after a few months. Additionally, ginger can cause acid reflux and what’s known as “ginger burn”. MotilPro is a combination of ginger and 5-HTP. Many people also have problems with it because of the “ginger burn”. In terms of natural prokinetics, Dr. Siebecker recommends Iberogast. It’s been around for many years, and it’s been well studied. In fact, studies have been done comparing Iberogast to 2 pharmaceutical prokinetics (not the ones mentioned above), and Iberogast was shown to work better.

Below is Dr. Siebecker’s recommended dosing for all of the prokinetics mentioned.

**All prokinetics should be taken at night before bed.**

Erythromycin – 50 mg

Resalor – ½ mg

LDN – 2.5 mg for those who tend toward diarrhea, 4.5 or 5mg for those who tend toward constipation

Iberogast – 20 drops

MotilPro – 2-3 capsules

Ginger – 1000mg


bone broth often bothers people with SIBO cause the mucopolysaccharides in the joints/bones feed bacteria. Rec meat broth instead and only cook the meat broth for a shorter amount of time as opposed to the long cook times on bone broth

the writer of the GAPS diet doesn’t like the use of baking soda as it can be alkalinizing which can go against the stomach HCL so when baking don’t use baking soda

lot of people cant tolerate the squashes in the SCD diet, electrolytes can get low on the scd, and on the scd it is important to get carbs, honey and whatnot

slideshow by dr siebecker on sibo




indigestible to us cause no enzymes to break bonds

digestible to bacteria because they have enzymes

fiber exclusively feeds bacteria is therefore prebiotic

soluble fiber: inulin, psyllium, flax, chia, hemp, gums(guar, xanthan, locust bean, acacia/Arabic, mastic), beta glucan (oat bran/mushroom), alginate, glucomanan(konjac mannan), carrageenan, agar agar, arabinogalactan, pectin

0ligosaccharides:FOS, GOS, MOS

Sibo pathophysiology:

Sibo causes increased inflammatory cytokines, deconjugates bile, and destroys the brush border which can lead to steatorrhea and fat soluble vitamin deficiency

The damage to the brush border leads to decreased disaccharidases, reduced carb transporters, blunted villi, elongated crypt depth and intestinal permeability. Can’t tell for sure but it looks like she’s written that everything here but the intestinal permeability causes GI sympotoms and that the intestinal permeability causes systemic symptoms(more likely) or maybe that all of these issues cause both gi sx and systemic sx(less likely)

Indications of sibo

Chronic low ferritin with no other cause

Pancreas obscured by gas bubble on CT scan


Take for 3mo after tx, take at bedtime:

prucalopride 1-4mg hs

Erythromycin 50mg hs

LDN 2.5-5mg

Key sibo treatment points for success

Multiple rounds of treatment are needed if gas is above 35-45 ppm

Avg gas decreases from abx/habx about 25-35ppm


Diets that will treat sibo over a long period of time: SCD, GAPS, Modified low fodmap diet that contains no grains, tubers, sugar, and is combined with the SCD/GAPS

Diets which are for prevention only, after sibo is gone: Low fodmap, cedar Sinai, less strict paleo/primal diets, diet may expand as tolerated by adding back in grans/tubers/sugar

and this one which is a food guide(all slides are in a file in med notes n tests) https://www.slideshare.net/maushard/sibo-food-guide-jan-13-2014

Complex clinical study review: advanced sibo and GI testing

  • https://www.gdx.net/livegdx/2019/january-complex-clinical-study-review-advanced-sibo-and-gi-testing
  • Presenter: Jill Carnahan
  • If the first reading of the sibo test comes up with high hydrogen you’re doing something wrong and the test may well be invalid, methane on the otherhand can be high to start and be high the whole way across
  • Methane over 5 is positive for sibo, used to be 3 was positive but now she says 5 is positive. 3-9 ppm methane is mild, 10 is very positive for sibo
  • Does breath testing, stool testing and organic acid testing before treating. Organic acids show markers for both bacterial overgrowth and fungal overgrowth, if they have high fungal overgrowth markers and you treat with antibiotics alone you’ll get a bad result because it’ll flare the fungus
  • Autonomic motility: diabetes, tickborne infections, and other things affect motility and can lead to sibo
  • Low IgA is a risk factor for sibo. Use S boulardii, bovine immunoglobulins, colostrum
  • Poor pancreatic function/biliary secretion is risk factor for sibo
  • Rec bitters for increasing bile acids
For hypochlorhydria she rec otc use of betaine hcl or the Heidelberg capsule to determine it. With hypochlorhydria you will often see low serum zinc, low ferratin, osteopenia, b12 deficiency; gluten sensitivity can cause hypochlorhydria. Lines and ridges on fingernails can be cause by hypochlorhydria, they are a sign of zinc malabsorption. Bloating/belching within 30min of a meal, weak peelin or cracked fingernails, acne rosacea(sibo sign too), undigested food in stool, problem with protein, chronic intestinal infections, multiple food allergies. Rec ramping the dose up till warmth/burning then lowering it. Never go beyond 3500mg per meal even if there is no warmth burning tho she has had some patients who have had autoimmune conditions that cause low stomach acid who have responded well to 16-20 caps per meal. Some people(the presenter included) don’t tolerate pepsin with the betaine HCL and so the betaine HCL has to be taken alone

3hr breath test better than 2hr

Organic acids test wont indicate sibo

Rec low fodmap diet, follow 4-6mo after treatment

She rec Allison siebeckers combination diet of FODMAP/SCD(see sibo food guide file in medical notes and test)

Elemental diet is 80-88% successful for treating sibo, very successful

Xifaxan rec, every 20-30 ppm hydrogen will be eliminated with 14 days xifaxan, so if it’s near 60ppm then 30 days straight will be needed

Neomycin or metronidazole for methane sibo, doses are 500 BID for 14 days

Prokinetics: LDN, low dose erythromycin, resolor(Canada), iberogast, ginger

Take prokinetics for 4-6mo after sibo treatment

Herbal antibiotics should be used 4-8wks, they treat not only sibo but sifo which is an advantage over Rx stuff which leaves fungus intact: berberine up to 5g’s daily(500mg-1500mg BID/TID), oregano 200mg TID x 2-6wks, garlic: allicin extract 450mg BID x 4-6wks, neem. Rec 6-8wks rather than just 14 days when using HAbx

May use biofilm disruptors if having trouble: garlic(allicin extract specifically, 450mg 2-3x/day), NAC up to 2-3g’s spread into three doses, EDTA(the product Interface Plus). Some biofilms are there with a reason so only use biofilm disruptors if needed

Use only spore probiotics during treatment, add lactobacillus/bifido after treatment but not before that

Don’t restrict diet till after treatment as you don’t want them to go dormant, guar gum is often added during treatment and makes at least rifaximin more successful. Don’t use after treatment

PAA high on organic acids(I have high PAA) can indicate pancreatic insufficiency

Rec nystatin for yeast

Methane can hide hydrogen, methane bacteria can eat the hydrogen gas so when the methane is treated sometimes you’ll find hydrogen goes up on the breath test

Xifaxan isn’t systemic, has little fx on colonic bacteria, and doesn’t cause resistance

Three hour breath test doesn’t increase data on hydrogen but does increase relevant data about methane

HAbx are good for treatment of SIBO where gas isn’t too high(like my levels feb 2019), she rec candibactin AR/BR, and that other combination from the study that compared HAbx to Abx(xifaxan) that was mentioned above in misc section

Average decrease of gas with round of antibiotics is 25-35ppm, may need successive rounds of treatment if gas is greater than 35-45ppm

Garlic extract(allicin) rec for methane sibo, sometimes biocidin and olivirex can be used as well

If failure then must use prokinetic

Diet is a must or relapse will occur

Retest 2-4wks after tx to see if issues have resolved

Don’t use low fodmap long term, fodmap diet works by starving bacteria including probiotics

Other reasons xifaxan might not work: gas levels too severe, not treating methane, bacteria don’t respond to xifaxan

Breath prep: 48 hour: no beans. 24 hour: just white rice/water then 12hr fast. Don’t do immediately on waking. Do 10 clearing breaths before(breathe in and out through the nose 10 times to make sure the airways are clear, 4 count in 4-8 counts out breath.

If Sx remain but breath and stool tests come back negative then try organic acid test which may show fungus/bacteria the other two missed. If Sx are present but dunno what is going on then use herbs, they will do less damage to probiotic populations and will also treat yeast if that is present. She has treated several patients who didn’t test positive for sibo but she treated anyway and they responded well, suspected hydrogen sulfide sibo.

Yeast treatment with herbs: caprylic acid, grapefruit seed extract, pau da arco, ginger, oregano, unilasayic acid, turmeric.

Only use guar gum while taking rifaximin, 2g guar gum per day. Bacteria feed on guar gum and die more readily from the antibiotic

She always uses stool test, stool and organic acids first, sometimes breath test will be used right away to if ibs Sx is obvious

Sibo patients sometimes feel worse for a while during treatment

Yeast treatment is worse though and has much more in the way of die off, rec yeast treatment 2-4 months

Spore based probiotics are good for sibo patients both before and during treatment, usually she doesn’t give lactobacillus/bifido/enterococcus probiotics till after the Tx and after the 4-6months on the diet/motility agent.

Alimed/Alimex pro 450mg of Allicin extract per cap, for methane sibo 4-6 capsules per day for 4-6wks, that’s her preference.

Alinia is good for protozoa, parasites, tough sibo, methane sibo, viruses. Rec alinia 30 days for Tx. Can flare yeast. Uses it if other Tx fails

She waits 2 weeks after tx to retest, if patient is doing really well she’ll wait a bit longer, then will wait until sx return before testing again(months later usually)

She mainly mentions the fodmap diet, only one mention of the fodmap/scd diet as per siebecker so I guess fodmap diet alone is the go to diet

From another webinar in General GDX stuff:

GDX webinar: Interactions of the microbiome and the neural immune system https://www.gdx.net/clinicians/medi...-of-the-microbiome-and-the-neuroimmune-system

Says when he comes across SIBO it usually has something to do with delayed gastric emptying, decreased parastalsis, constipation, hypochlorhydria


Presenter: Allison siebecker

  • Rifaximin is not a typical antibiotic; rifampin
is not systemically absorbed (<1%)

works best in the small intestine (bile soluble)

increases Bifidobacteria and Lactobaccilli (eubiotic effects)

has anti-inflammatory activity via stimulation of human nuclear receptor pregnane-X receptor (PXR)

does not cause C. difficile or yeast overgrowth

has very low side effect profile (≤placebo)

prevents antibiotic resistance of neomycin by inhibiting plasmids

does not lead to antibiotic resistance, and continues to work after 6 rounds of treatment

  • Berberine, oregano, and neem are used in diarrhea-predominant cases; stabilized allicin is added to these herbs for constipation predominant cases
  • Overarching diet tips for active SIBO:
    • Avoid raw food, salad, and beans
    • Be careful with whole grains, nuts/seeds, winter squash
    • Choose low-FODMAP fruit and vegetables (see Monash University Low-FODMAP app)
    • Starch may be tolerated: white rice, white potato, white flour (if gluten is tolerated); often one starch is tolerated but not another
    • Lactose-free dairy, sugar, clover honey, and cocoa are often tolerated
    • Quantity matters-small amounts of individual foods may be tolerated when larger amounts aren’t
    • Experimentation and customization is necessary for best success
  • Prokinetics are used between treatment rounds and after eradication to prevent relapse by stimulating the MMC
  • Common prokinetics: low-dose erythromycin, low-dose prucalopride, low-dose naltrexone, Iberogast, MotilPro, ginger

Presenter: Nirala Jacobi, BSc, ND

  • Mucosal repair is important for both phases
  • Tight junction repair
Vitamin D helps mucosal barrier homeostasis and decreases inflammation

Vitamin A


  • Epithelial cell repair
Zinc carnosine


Increases production of human growth hormone

Major fuel source for enterocytes/epithelial cells

Supports tight junctions

Reduces interleukin (IL)-6 and IL-8, increases IL-10

comment: Jacobi stated that she sees many patients with reactions to histamine, salicylates, and oxalates.

  • Histamine can be elevated in SIBO due to 2 main causes:
Food-sourced histamine (exogenous histamine absorption)

Mast cell infiltration (endogenous histamine release)

Comment: Jacobi had 11 slides on histamine, an excellent summary of review of literature and of Charles Lewis (Enteroimmunology, Psy Press 2013). The most interesting slide was how to tame the mast cells naturally.

  • Histamine clearance
DAO supplement with food

B6, Magnesium, Copper

Pantothenic acid 1,000-2,000 mg

B12, folic acid – she stated that this needed to be started slowly

B1 100-200 mg

  • Mast cell stabilization
Vitamin C to bowel tolerance




Comment: Jacobi had 11 slides on salicylates and stated that interaction with patients who have SIBO and dysbiosis is common.

  • Salicylates
Natural plant substances, which help the plant defend itself against bacteria, fungi, and other pests. Salicylates are toxic to everyone in very high doses, but with a salicylate sensitivity the threshold is much lower before a reaction occurs.

Salicylates are chemically very similar to the manmade chemical acetylsalicylic acid, a key ingredient in aspirin and other pain medications.

Sources include:

Herbal products (most will contain salicylates)

Curcumin (especially high)

Medications: most NSAIDs

Cosmetics, fragrances, shampoo

Cleaning products

Air fresheners

Breath mints, lozenges, gum

  • Support for phase 2 clearance of toxins
Glycine conjugation: Glycine 1,000-1,500 mg daily

Glucuronidation: calcium d-glucarate 1,500 mg daily

Support for kidney clearance

Alkalizing minerals

Trace mineral

Herbal Considerations to Effectively Treat SIBO and SIFO

  • Berberine
Multiple mechanisms that overcome bacterial resistance

Inhibits biofilm formation

Reduces H2-producing bacteria

Dosage: 2-3 g/d

  • Garlic
Reduces CH4-producing bacteria

  • Syzygium aromaticum (clove)
Antibacterial, antifungal

Stimulates gastric mucous production

Cholinergic: stimulates motility in IBS-C

May increase bleeding time

  • Punica granatum (pomegranate)
Antibacterial, anticandidal, antiparasitic

Significantly enhances growth of Lactobacillus spp, Bifidobacterium breve, Bifidobacterium infantis

Inhibits growth of pathogenic Clostridia and Staphylococcus aureus

Dosage: 10 mL daily of 1:2 tincture

  • Small intestinal fungal overgrowth (SIFO)
SIFO comorbid with SIBO in 20%

SIFO found in 26% of patients with “unexplained GI symptoms”

Issues with Candida spp:

Often cause similar symptoms to SIBO

Commonly forms biofilm

Overgrowth easily evades detection

Classic antifungal herbs: Pau D’Arco, Uva Ursi, berberine-containing herbs

Essential oils of clove, oregano, and thyme


Effective against Candida spp, S. aureus, Pseudomonas a., Blastocystis hominis

Effective for SIFO and methanogens

Effective against candida biofilm

Dose: oil of oregano (50-100 mg 2x daily)

Pseudowintera colorata (horopito)

Strong antifungal activity against Escherichia coli and Salmonella, C. albicans, C. utilis, C. krusei, Cryptococcus neoformans, S. cerevisiae, T. mentagrophytes, T. ruburum and Penicillium marneffei

Moderate antibacterial activity against both gram-positive bacteria (including Bacillus subtilis and Staphylococcus aureus) and gram-negative bacteria

  • Liquid antimicrobial formulas
SIBO formula-7.5 mL 2x daily:

Oregon grape (or coptis/goldenseal)



Burr marigold

SIBO/SIFO formula-7.5 mL 2x daily:




Oregon grape (or coptis/goldenseal)

  • Herbal prokinetics
Dr. J’s Herbal Bitters formula:

Oregon grape/Gentian/Baical Skullcap/Dandelion root: 2-3 whole droppers in water 15 min before meal

"Iberogast”–Iberis amara, Angelica archangelica carumcarvi, Silybum marianum, Melissa officinalis, Chelidonium majus, Mentha piperitae, Glycerrhiza

Dose: 20 drops 3x daily before meals and before bed, or 60 drops at bed time

”Motil Pro”: Ginger, 5HTP, acetyl L carnitine, P5P

Dose: 3 caps morning and night

  • Carminatives—gas removal from GI tract
Caraway seed – very effective carminative and spasmolytic


Carminative tea (crush 1 tsp of each and steep for 20 minutes in 1 cup of water. Drink after each meal.):

Caraway seeds

Fennel seeds

Anise seeds

Comment: Parting thought: use herbs before microbiome-disrupting antibiotics

Manipulation of Gut Microbiota and GI Motility for Treatment and Prevention of SIBO

  • Dysbiosis definition=bad coexistence of host and microflora
Consequences: damage to epithelium with increased cell turnover, toxin and/or gas production, immune weakening/reaction

PPIs, H2 blockers and antisecretory drugs can profoundly influence microbiota even more than antibiotics.

  • SIBO definition: increase in number and/or change in type of bacteria (oropharyngeal or colonic)
Increased intestinal permeability occurs in SIBO with colonic type but not salivary bacterial overgrowth and is reversed when SIBO is eradicated

  • SIBO presentation
Common: gas-related symptoms (bloating, abdominal pain, flatulence, diarrhea)

Uncommon: malabsorption syndrome (B12 and iron anemia, Vitamin A/D/E deficiency, edema)

Malabsorption can occur when SIBO has been present for a long time

SIBO diagnosis is made with both presentation and breath test

Causes/risk factors

Generally: when homeostatic mechanisms that control small intestine bacteria are disrupted such as gastric acid lowering and motility abnormalities

Risk factors are endless and can include: demographics (old age), structural abnormalities (strictures, diverticula), organ system dysfunction (cirrhosis, chronic pancreatitis), and medications (PPIs, opioids)

“An absent or disordered migrating motor complex pattern is almost always invariably associated with SIBO.”

Associated conditions

SIBO and SIFO (small intestine fungal overgrowth) coexist in 34% of SIBO patients; many antibiotics (a prime treatment for SIBO) can increase fungal overgrowth.

SIBO and IBS: There is 5x more prevalence of SIBO in IBS compared to healthy controls.

SIBO is an umbrella term encompassing functional, organic, and hepatic conditions, so if you target SIBO you will be able to target many GI diseases.

  • Rifaximin
    • Rifaximin is the best antibiotic for SIBO because it is effective against gut bacteria, acts in gut only, prevents antibiotic resistance, is nontoxic, is safe in children/elderly/pregnant women, and has few side effects.
    • Rifaximin is anti-inflammatory through NF-KB and the PXR gene, a master gene critical for maintenance of intestinal integrity.
    • Rifaximin has eubiotic effects; it increases Bifidobacteria and Lactobacilli.
    • A recent meta-analysis of rifaximin for SIBO showed an average eradication rate of 70% with significant (70%) improvement of symptoms.
    • Two factors increase rifaximin eradication rate: higher dose and cotherapy with prebiotics/fiber or mesalazine (which can modify intestinal microbiota).
  • Recurrence
    • 45% recurrence by 9 months, especially if underlying cause is not corrected, which is often the case
    • Cyclic use of rifaximin (7-10 days every 4 weeks), followed by probiotics (Lactobacilli-Bifido mix)
  • Probiotics
    • 47% eradication with Bacillus clausii spores
  • Prokinetics prolong remission time
    • “Maintaining well the housekeeping activity of the intestine is a must”
    • Prucalopride is a safe option because it is very selective for the 5HT4 receptor

SIBO diagnosis and treatment 2007

The loss of activity of brush-border disaccharidases due to mucosal injury and the bacteria fermentation of sugars such as sorbitol, fructose and lactose could be responsible for carbohydrate malabsorption [4] . Enterocyte injury may alter the gut permeability, predisposing to the development of a protein-losing enteropathy. Moreover, bacteria may compete with the host for protein and lead to the production of ammonia [5] . Deconjugation of bile acids in the proximal gut induces fat and lipophilic vitamin (A, D, E) malabsorption and leads to the production of lithocholic acid, which is poorly absorbed and may be directly toxic to enterocytes [6] . Cobalamin (vitamin B 12 ) deficiency can occur in SIBO as a result of use of the vitamin by anaerobic bacteria. Levels of both folates and vitamin K, however, are usually normal or increased in SIBO as a result of bacterial production.

Rec wide spectrum antibiotics since it is hard to do testing in vitro of antibiotic vulnerabilities of bacteria

A study on patients w crohns found a good response for treating sibo using ciprofloxacin and metronidazole

Lauritano et al. [17]showed that higher doses of rifaximin (1,200 mg/day) were associated with a significantly higher therapeutic efficacy (60% of glucose breath test normalization) in terms of SIBO eradication with respect to doses of 600 mg/day (16.7% of glucose breath test normalization) and 800 mg/day (26.7% of glucose breath test normalization). Similarly, Cuoco et al. [18]assessed the efficacy of rifaximin (1,200 mg/day), followed by a 20-day course of probiotics, in the treatment of SIBO. The eradication rate of this schedule achieved 83% with a significant improvement of gastrointestinal symptoms. Neomycin, a non-absorbable aminoglycoside, was shown to be of little efficacy when used alone in SIBO. In a recent study by Pimentel et al. [19]on 111 IBS patients, treatment with neomycin achieved the normalization of lactulose breath test in 20% of patients with SIBO with respect to 2% in the placebo group. No relevant side effects were observed during the study and no dropouts occurred


Conditions That Predispose Toward the Development of Small Intestine Bacterial Overgrowth

Achlorhydria (surgical, iatrogenic, autoimmune)
Motor abnormalities
Intestinal pseudo-obstruction
Diabetic enteropathy
Abnormal communication between colon and small bowel
Fistulas between colon and small bowel
Resection of ileocecal valve
Structural abnormalities
Systemic and intestinal immune deficiency states
Surgical loops (Billroth II, entero-entero anastomosis, Rou-en-Y)
Duodenal or jejunal diverticula
Partial obstruction of small bowel (stricture, adhesions, tumors)
Large small Intestine diverticulosis
Systemic diseases (celiac disease, cirrhosis, pancreatic exocrine insufficiency, non-alcoholic fatty liver disease)

Protective Factors That Protect Against the Development of Small Intestine Bacterial Overgrowth4,8,9

• Gastric acid
• Pancreatic enzymes
• Bile acids
• Cholecystectomy
• Motility
• Migrating motor complex
• Biofilm
• Secretory immunoglobulin A

Extrinsic Factors That Alter the Gut Microbiome and May Influence the Development of Small Intestine Bacterial Overgrowth4

FODMAPsa (fructose, lactose, galactans, fructans, sugar alcohols)
Proton pump inhibitors
Anti-motility agents

Note: from personal experience It seems like FC-cidal and dysbiocide make me feel improved more if I take them an hour or more apart from one another. FC-Cidal does more for me than dysbiocide, at least, I feel better after fccidal


While some people can't tolerate probiotics during SIBO treatment, it's important to add probiotics when the time is right for you. I use spore-based probiotics and find that my patients tolerate them even during the initial phases of the herbal protocol.

Diet is part of the treatment, and carbohydrates feed bacteria, so it goes without saying that sugars from sweets, breads, pastries, soda, juices, alcohol, and others are not your best friends. Healthy carbohydrates in excess, or the wrong types of carbohydrates, can slow down your healing process as well. Some people can't tolerate simple sugars like lactose and fructose while others have a hard time with complex starches like potatoes and rice.

There's no one diet that works for everyone with SIBO, so it's important to identify which carbohydrates you can't digest and absorb because those are the ones that end up getting fermented by your small intestine bacteria. Depending on my patient's symptoms and medical history, I may use the low FODMAPs, Specific Carbohydrate Diet (SCD), SIBO-Specific (combines the low FODMAPs and SCD), or the Fast Tract Diet. Avoid fiber early in the treatment. Ultimately, your goal is to eradicate SIBO so you can reintroduce healthy foods that some of these diets restrict like garlic, onion, and apple.

What interferes with proper motility? Food poisoning and infectious gastroenteritis with certain bacteria, viruses, or parasites can damage the cells that act as the pacemaker and control the MMC.

Mentions gastroparesis as once cause of mmc not working

Unfortunately, SIBO can be stubborn to treat, and it can come back. So whether you chose antibiotics or herbals, retest within the first week of completing treatment to confirm that it's gone. If you wait too long, or never retest, and your symptoms come back a few weeks or months down the road, you're back at the starting line. When you confirm that the treatment was successful, you can confidently transition to a maintenance and prevention plan. If you test positive, your practitioner can prescribe a different medication or herbal protocol. Understand that your healing journey may include a plan B or C, or even a plan D, but without retesting, you have too many unknowns. If it turns out that your SIBO is stubborn, ask your provider about the elemental formula diet.

Make sure the root cause is treated by:

Improving gut motility

Having adequate stomach acid

Boost digestion with supplements and herbs.

Incorporate digestive enzymes, bile, and digestive bitters. The ability of your intestine cells to produce brush border enzymes on their own should start to improve as SIBO clears

SIFO can cause sibo to recur

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Psalm 46:1-3
Great Lakes
Unless I'm severely hungry, my digestive system doesn't rumble either and hasn't really for years until I followed @kurt 's advice in his recent blog posts especially this one where he speaks about using Cellulase as an antifungal: https://forums.phoenixrising.me/blo...cfs-a-complex-fungal-intolerance-part-4.2671/
After my first dose of Candex my intestines rumbled very loudly.

Also, I've always been pretty regular until I started to use thyme tea. It gives me a bit of a boost in energy so I'm reluctant to give it up since that has been the only negative.

I started on Huperzine A recently for other reasons but one of the things I found is that it seems like it assists with motility. This is only one study and on mice and it sounds like constant usage negates the benefit but I'm thinking on a rotational basis, it might be an idea. https://www.spandidos-publications.com/etm/5/3/793
I only take a 1/4 pill every other day and it has helped.

One more thing is whenever my mom and I have consistently used a product called Mycopryl, we have also been consistently regular. It is made of palm oil and in later years we developed an allergy to coconut, which is in the same family as palm. I was afraid we would develop a cross reaction to that so we have only been taking when experiencing symptoms of IBS--which it is also very helpful with.

Anyway, maybe that's all too much personal info but I wanted to offer some ideas and hope they might be helpful in some way to you.

Wow that's a lot of information, haha. I've had a quick look over and a lot of it is similar stuff I've come across in my own searches. One thing that caught my attention though was:

"Cyclic lavages of the small bowel (e.g. by polyethylene glycol) can be considered as supportive therapy in cases of relapsing SIBO"

It sounds like they're suggesting using polyethylene gylcol can flush the small intestine..? This is exactly what I'd want to try.. Do you or anyone else know anything more about this? I've not come across this is my searches.. When looking into the product it seems its sold in bulk as part of a mix for something?


Senior Member
Unfortunately I don't though you might consider getting in contact with one of the doctors who wrote the paper, I remember a few instances of people in this forum reaching out to doctors/researchers and finding that those doctors are happy to share ideas and details with the inquisitive individual

also, I just remembered the name of the test for MMC function, it's already above but I'll post it again here

Migrating Motor Complex Testing

- Antroduodenal Manometry:

• Direct test for MMC

• Endoscopy (invasive, expensive, only a few places perform it)

• Interpretation: reported by performing Dr.


Psalm 46:1-3
Great Lakes
It sounds like they're suggesting using polyethylene gylcol can flush the small intestine..? This is exactly what I'd want to try.. Do you or anyone else know anything more about this? I've not come across this is my searches.. When looking into the product it seems its sold in bulk as part of a mix for something?

It's the same ingredient in Miralax and some people use it for colonoscopy prep mixed with Gatorade. There are recipes all over the internet for that.


Senior Member
Brisbane, Australia
I have seen it suggested by a number of different sources that just doing a colonoscopy prep is enough to at least significantly reduce any bacterial overgrowth.
That would appear to be the case in this IBS study into the association of SIBO study where there was a finding of a significant reduction in positive lactulose breath tests (LBT) where a colonoscopy preceded the LBT test.

Above all, LBT after two weeks of colonoscopy may be most responsible for our paucity of abnormal LBTs. Bowel cleansing with polyethylene glycol (PEG, Colyte, 4 L) removes the bulk of bacterial flora including hydrogen producing ones26,27 and the higher rates of positive LBTs for the IBS patients correlated with a longer time limit (2 to 3 months) after colonoscopy than did our results.2,4 However, most patients with IBS continued complaining of their symptoms when they re-visited 2 weeks after colonoscopy.


Psalm 46:1-3
Great Lakes
However, most patients with IBS continued complaining of their symptoms when they re-visited 2 weeks after colonoscopy.

This was correct for me as well. Colonoscopy prep did not help with the IBS at all and indeed that is when I developed IBS-D actually.


Senior Member
Brisbane, Australia
This was correct for me as well. Colonoscopy prep did not help with the IBS at all and indeed that is when I developed IBS-D actually.
I think one inference that can be drawn from that is that SIBO is not the cause of the GI symptoms in such cases, just a reaction to an underlying condition, and I wouldn't be surprised if antibiotics had little impact on symptoms either (or just give temporary relief).


Senior Member
One thing i forgot to mention about iberogast, if you treat sibo and plan to do a retest of sibo within two weeks to check if your treatment did clear sibo, as suggested by some of the doctors in that large collection of notes i posted above, consider not taking the iberogast or whatever prokinetic until it the test has been sent out. I did a breath test 4-5 days after final dose antibiotics and had been taking iberogast since the day after that last dose of antibiotics and my breath test leaped up to the final peak at 90 min which might well mean the lactulose hitting the large intestines at 90 min which is earlier than it's supposed to be, it could be that the sibo was just that strong but usually on tests ive looked at, even with the sibo close to the end of the small intestines, the hydrogen still goes higher than that when reaching the large intestines, but at 90 min and after it stayed steadily very high up and this was on a 3 hour test.

I had 3 other sibo tests and this never happened on any of those so it is quite possible the prokinetic is responsible. In my case it doesn't matter bc I have a high methane reading on that test anyway but if i had been only hydrogen positive I wouldn't have known whether i was positive or negative. of course if you wait a week or two after the final abx to do the breath test and then start using the prokinetic you may be cutting it close since, if i remember correctly, two weeks is said to be a common amount of time that relapse occurs in those who aren't using prokinetics and/or aren't on diet to prevent sibo
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Senior Member
Disregard that last post (jun 6 2020), looked through some notes the other day and turns out i only started iberogast a few days after the sibo test

It's still possible that a prokinetic might cause such an issue but I don't know
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I had a severe SIBO infection for a year and a half. I did everything, and I mean everything. Iberogast, Berberines, Rifaximin many many times, every herb and motility supplement you can think of.

I finally ended up on the Elemental diet for 3 weeks. It was the worst, and that is when I had my first energy crash, which I thought was just related to the elemental diet.

The elemental diet took my breath test numbers waaaaaay down. I was seeing a naturapath at the time and getting the rifaximin from this total asshole doctor that didn't believe I had SIBO, but believed that rifaximin helped IBS.

I finally found a GI clinic in my hometown that did their own breath tests. Since these tests are expensive I wanted my insurance to pay for them but hadn't found a GI MD that would give me until now, and since I just finished the elemental diet I needed to do one and see where my levels were at.

So I finally got the test in an actual GI clinic, and the NP sat me down and said "well I have bad news, you have a SIBO infection and it's almost severe, as your count is 29, and 30 is a severe case".

My initial number was 146. After 6 months of herbs and rifaximin I got it down to 79. And after the elemental it was at 29! I was ecstatic. The GI clinic gave me rifaximin + metranizadole, which I highly recommend.

For motility, I highly suggest 16 oz of celery juice on an empty stomach in the morning every morning. Then nothing for 15 - 20 minutes. It took 2 months before it started working, but it works.


Senior Member
So what are your numbers now after the most recent treatment?
Has treating sibo done much for your energy or has it been more symptom treatment for gut issues?
Glad you found a treatment that's able to do something about the sibo, it's a tough condition to treat