SIBO, small intestine bacterial overgrowth, is a hot topic right now. It is thought that most suffering from IBS and possibly even fibromyalgia, actually have SIBO. The current treatment for SIBO is an antibiotic called Rifaximin. I have been to at least four conferences where this treatment has been presented and one thing that the presenter always says is, ‘this antibiotic is okay because it is not well absorbed and only affects the small intestine.’ This seems to satisfy most of the practitioner’s fears that we are prescribing yet another antibiotic and now that we know that it doesn’t affect the large intestine, it is okay… but is it?

From time to time I hear incorrect assumptions about the small intestine versus large intestine, when it comes to gut flora. If you have read any articles about the flora in your gut, it is almost always referring to the large intestine.

A quick anatomy lesson – your stomach, which is up behind your ribs, empties into the small intestine – there are three sections in the small intestine – the first section is called the duodenum, the middle small intestines is the jejunum and the third section of the small intestines is the ileum. The ileum junctures with the large intestine right by your upper right hip. The large intestine moves up your right side (ascending colon), goes straight across your body to your left side (transverse colon) and then moves down your left side into your bowels (the descending colon).

It is true that in the large intestine, at this juncture point where the small intestine meets the large intestine, that we find the largest amounts of gut flora. This is where you recycle digestive enzymes, assimilate and absorb fat soluble vitamins… you could call this the last stage of digestion. Here’s an interesting fact, your bowel movement is 50% gut flora by mass. Think about how much turnover these flora must have to keep their colony levels up.

The point here, the small intestine is definitely not sterile. Let’s talk about the small intestine for a minute – this is where the majority of the immune system operates, the mucosal lining that protects your body from the outside world is one cell layer deep, this is the site of critical nutrient digestion and absorption and this is where food sensitivities are triggered. Matter moves through this area fast, so we don’t see huge colonies of flora here like we do in the large intestine, where matter moves through much more slowly.

Remember the three sections in the small intestine? In the duodenum, there are 1,000-100,000 cfu (colony forming units) of bacteria present per gram, in the jejunum there are 100,000-10 million cfu/ g and in the ileum there are 10-100 million cfu/ g (this is per gram – this is definitely not an insignificant amount of flora). In the small intestine we see bacteria present in the millions. When we look at the large intestine we see bacteria present in the billions. So you can see why there is an emphasis on the large intestine when discussing gut flora.

In the small intestine, Lactobacilli are of the dominant flora in the duodenum and jejunum, and bifidobacteria are one of the dominant flora in the ileum.

"Reading a great post about SIBO on Clean & Lean Revolution"

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The consequences of SIBO are that gas producing organisms take up residence in the small intestine and cause inflammation, systemic immune responses, digestive unrest and simply unpleasant gut reactions pretty much every time the person eats. SIBO organics are gas producing –hydrogen gas producing, methane producing or hydrogen sulfide producing. For those with methane producing issues, this isn’t a bacteria overgrowth, in fact the organism isn’t a member of the bacteria family at all; it is another species called Archaea group called a methanogen.

SIBO treatment does not often include probiotics. The common assumption is that this is a bacteria overgrowth and that you will need to take an antibiotic to knock it out. So why would you take a probiotic and risk putting more flora in that area??

Here’s why – SIBO becomes an issue because of stress, antacid use, low stomach acids and dysbiosis (an imbalance of gut flora) in the small intestine. If there is no biofilm layer of lactobacillus in the duodenum, then the preferred pH of 6.5 – 7.5 will not be obtained. The surface will become more acidic and this will lower the body’s defenses.

Now, I do not recommend massive dose probiotics (really larger doses of probiotics do not mean that the probiotic will work better), I don’t recommend spore forming soil probiotics either, as these have the ability to turn pathogenic. Feed the gut what it prefers to have in this area to heal the area and address the inflammation that SIBO created. This will only be corrected and prevented from reoccurring when the dysbiosis is addressed. If this is not addressed and antibiotics are used without a replenishment phase, then what this will do is further damage the small intestine and it will open the door to everything that we see with chronic gut inflammation – immune dysfunction, food sensitivities, metabolic conditions and autoimmune conditions, if genetically susceptible.

SIBO is present because of dysbiosis and a dysfunctional gut lining in the small intestine. Replenishing lactobacilli and bifidobacteria has to be part of the treatment. This should be free of FOS (prebiotics) – simply lactobacilli and bifidobacteria. I prefer a powdered probiotic that I titrate up slowly. If there is a gut reaction from taking these probiotics, this is simply shedding light on the fact that there is dysbiosis present and this has to be addressed.

I have heard SIBO being referred to as a chronic condition and frankly, I am not buying it. You can treat SIBO by bringing your digestion back into balance from the top down, addressing stomach acid levels, digestive enzymes, rebalancing gut flora and of course, addressing your eating and lifestyle habits. Stress is a big contributor to SIBO and SIBO reoccurrence. By treating the whole body, SIBO can be knocked out for good.

Angela Pifer is a Functional Medicine practitioner and licensed Certified Nutritionist. Seattle’s go to nutritionist, Angela, has been in private practice for a decade. Work one on one with Angela through her private practice of

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from 7 people


I have been fighting with SIBO/or-candida, inerldibcy excessive gas and burping the last 6 weeks. Combined with leaky gut (worse form of IBS), it's really painful. No egg smell. I've done 2 rounds of Flagyl from the GI who hasn't been terribly helpful. I'm not sure it did anything. I lost 30 pounds in a month or two from cutting out carbohydrates. Now I'm to the point where I have to eat some since starvation is worse.What has really helped is reducing worry and strengthening my intestines.Magnesium/Zinc helped tremendously on the pain and mood, and strengthening the intestines. Anxiety apparently burns Mg stores.I was doing glutamine/N-Acetyl Glutamine, but cabbage is better. Eating a good chunk of cabbage a day and chewing it well really helps the IBS/leaky gut repair, which has helped my immune system as well. If your gut is permeable, and bacteria and strange foods keep getting in, it takes a a ton of energy to deal with that. Also, I could feel the toxins from whatever's living in there.Mastic gum is very helpful if you have ulcery or heartburn symptoms and it feels like acid is going straight into you. I would get this in the morning a lot or late at night. The mastic cuts it fast.Omega-3 s also help tremendously on acid or inflammation, they coat the system and reduce inflammation.Probiotics seem to help. Apparently I haven't been taking enough, thanks for the advice here of 2/per meal!Digestive enzymes definitely help. They weren't cheap, but having amylase, pancrealipase, ox bile, papain, HCl etc, work on the food does two things.1) improving digestion means you get more of your food, they get less.2) those protein-cutting enzymes attack the beasties, too.These were hard to take when my intestines were fragile and permeable, but now that the cabbage and Mg/Zn have helped, I'm taking more and feeling better.Eating more fibre to help strengthen intestines and shunt food through faster has helped. It makes some gas, yes, but that's reduced due to enzymes, and getting the food through fast and cleaning out bacteria entrenched in the mucous helps a lot. I have psylium husks, but I prefer oats.5HTP/Valerian really helped me sleep some nights from worrying. Not eating 3+ hours before bed is important so gas doesn't build up. I have had health issues the last six months, this was caused from recovering from liver issues, being ill and feeling pain inside gets old as a prison. Just being able to rest and forget is priceless. After awhile the anxiety, and the energy depletion and immune system flare-ups it causes are worse than the bacteria. You can stress yourself to the point where your body just attacks itself.Count victories. They may be small, but count them instead of worrying. How is today better than 5 days ago? There still may be pain, but is there less of it, is it shorter, is it more manageable?It's not gone, but I'm finally improving.



Hi Michael,

I would also have your COMT genes tested. If you have snips here, then high dose methylated supplements may not be the best for you long term.

It is possible to have inconsistent symptoms with SIBO - yet I don't usually see this ebb and flow over weeks. It ebbs and flows over days and across the day.

Lactobacillus is a species, as is bifido. So, you are looking for strains of these. I have all the probiotics that I work with listed here on my shop (you can reference these and discuss them with your doctor)





We are not sure if I have SIBO or not. I have not been tested. Trigger foods usually do not bother me, maybe some times. Hard to tell. I have been tested low in stomach acid, and taking Betaine HCL seems to help to resolve some discomfort. But....I still have this mild maliase/nausea like feeling in my gut, some bloating, etc... Hard to say if it's SIBO or not.

I also tested positive for MTRR ++, and am now on high doses of Methyl-B12.

In some ways, one some days I feel I can eat anything and I feel fine, then other times, I feel like crud.

Does SIBO go into hibernation at times, and other times they wreak havoc?

Also, you mentioned taking lactobacilli and bifidobacteria. Are there any good products with just those two that you recommend?

Thank you!

Michael (NW)


Hi Tamara, I am not a fan of these probiotics. I recommend strains that have been tested, no prebiotics and these are definitely too high of dose to treat SIBO. The goal is targeted strains, low dose and build your levels over time. I recommend trying probiotics prior to trying Xifaxan - if Xifaxan has already been used, then probiotics are a must on the other side. I sometimes use these during antibiotic treatment (patients come to me for adjunct support while using antibiotics as well) and sometimes I don't - it really depends on the person.




Hi Angela,
What do you think of the Garden of Life RAW Women probiotic? Also, do you recommend taking probiotics throughout the course of Xifaxan or as soon as one finishes the course?




Hi Peggy - thanks for your comment! You definitely will need to take a probiotic, ongoing. The goal is to find a probiotic that doesn't have inulin, or strains that are more likely to form D-lactate versus L-lactate. All lactobacillus species produce lactic acid, it is the form that we are interested in. In an imbalanced gut (which is present because you have SIBO) you don't have the healthy flora available to balance out these acid forms and this an lead to a more acidic environment in the small intestine. I don't recommend L. acidophilus. There are few different forms of Floranex out there - many have sugar alcohols added to them (the chewable form). I would look for a good S. boulardii probiotic to start and then find a blend of L. casei and L. bulgaricus (both form L-lactate).

There is a lot more to addressing constipation when taking xifaxan. If methane positive, if you choose to go with antibiotics, you should be taking the duel antibiotic treatment and not just xifaxan. If you have shifted to a higher protein/ fat eating plan (on any of the specialized diets to address SIBO) then the increase in protein will increase constipation. When SIBO is present, it eats your digestive enzymes, degrades the brush border (lining of the GI tract where we digest food) and uncouples bile (you'll have a hard time emulsifying and digesting fats). You may want to explore betaine HCL and a good digestive enzyme with your doctor. HCL has to be taken with the digestive enzyme, otherwise it will not be 'active' at the right pH.

Best of luck to you!!



I love this!! The only thing I don't understand .. Do we take probionic lactobacilli with it . I take floranex . So I am on Xifaxian now am confused . Read you should take it , then should not take it. I find myself full of gas that is not passable. My started with chronic acid that they could not get in control. Yes stress is a big factor. Any help would be great. I am on my 3rd day and i feel constipated as well as having small BM. Thanks


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