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May 4, 2015

Is SIBO an Autoimmune Condition or Triggered by One?

Gut motility issues are center stage when addressing SIBO (small intestinal organism overgrowth). Food and digestive contents must be kept moving forward through the digestive tract, at a reasonable speed, both during meals and in between meals. This needs to happen to both prevent SIBO from occurring in the first place and to prevent SIBO from coming back after treatment. What if these waves of motion were inhibited by an autoimmune condition?

On quite a few occasions, during intake conversations with my patients, they share that their digestion simply began to stall and they don’t know why it happened. I ask them, “Did you have food poisoning three months prior to this happening?” More often than not, this is the case! So, what happened?

Beginning in the esophagus, food is moved down the tract by a process called peristalsis. These rhythmic waves of smooth muscle contractions help food continue to move forward through the digestive tract. Picture the movement of an earth worm for a moment and you will start to understand how these peristaltic waves move down the smooth muscle of your digestive tract, all the way from your esophagus, down through the small intestine.

In between meals, during a fasting state, the digestive track is swept by cleansing waves signaled by the Migrating Motor Complex.  One of its functions is to transport organisms from the small intestine to the large intestine; this includes bacteria, so you can see how important this sweeping motion is to the prevention and the treatment of SIBO. It is regulated by gut hormones and nerve signaling from the central nervous system.

When the Migrating Motor Complex kicks in, there is an increase in gastric, biliary and pancreatic secretions (stomach secretions, bile and digestive enzymes). This helps digest leftover matter in the small intestine and moves it into the large intestine.

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So, where does the autoimmune piece fit in?

Peristaltic waves are waves of contraction and release. They rely on nerve signaling of the smooth muscle that lines the digestive tract. The smooth muscle is relaxed in its normal, resting state. The nerve signals trigger the contraction of the smooth muscle and these coordinated wave like contractions move food and matter down the digestive tract. It is the ability to contract your smooth muscle that is of interest here.

If the body produces antibodies that disrupt the nerve pathways, that end innervation of nerves into the smooth muscle of the digestive tract, the peristaltic waves will be inhibited – the smooth muscle cannot contract. This is one way that gut motility is inhibited.

How does this happen?

It happens when the body is exposed to a toxin, the body then produces antibodies to the toxin and these antibodies not only attack the toxin, they also attack a protein in your gut called vinculin. This is through a process called molecular mimicry. The protein sequences in vinculin resembles the toxin closely enough that the antibodies think vinculin is a foreign invader and begin to attack it. This is an autoimmune condition, where your immune system has produced an antibody that is attacking self.

Where does this toxin come from? The short answer is a food poisoning event.

E. coli, Salmonella, Shigella or Campylobacter all produce a common toxin called Cdt-B toxin (Cytolethal Distending Toxin B). Once exposed to this toxin, some people (not all) will produce antibodies to the Cdt-B toxin. These antibodies will also attack vinculin creating an autoimmune condition.

Where does Vinculin come in?

Vinculin is a protein that connects a network of cells within the pacemaker of the gut, called the Interstitial Cells of Cajal. The pacemaker of the gut does exactly what you think it would, it is the signaling network that signals the coordinated wave like contractions of peristalsis; it sets the pace. Vinculin helps these cells connect and communicate electrical signals to contract your smooth muscle.

If vinculin is damaged or destroyed, it can’t link the cells within the pacemaker and you then can’t transmit the electrical signal to contract your smooth muscle. This stalls gastric motility during meals and in between meals.

We think that 20% of people exposed to this toxin will go onto develop SIBO, with ongoing IBS symptoms and that this takes about three months to develop. Here is what it looks like:

There is a food poisoning event and exposure to Cdt-B toxin which triggers gastritis. 20% of people will create an antibody to the toxin. They will recover from the food poisoning event – gut symptoms will return to normal. The antibodies created to address the toxin start to attack vinculin. Over time, your gut motility slows, leading to a highly fermentable environment in the small intestine and setting the stage for SIBO and IBS symptoms that appear around the three month mark.

Since the gut symptoms seem to recover after the food poisoning event and then begin to rear their head around the three month mark, many people don’t equate the gut symptoms with the food poisoning event.

Currently, a SIBO eating plan, supplemental and prescription prokinetics, stress management,  addressing meal timing and addressing SIBO with herbal therapies (so SIBO organisms do not make things worse by furthering constipating you) are the best way to treat this. The Cdt-B toxin and vinculin connection is a new discovery from Dr. Mark Pimentel’s group – that will lead to new medications that will help people treat this form of gut paresis.

Dr. Mark Pimentel and his team are currently developing a blood test that will test for the presence of this anti- antibody to vinculin. This will be the first IBS test that will allow us to quickly identify an IBS diagnosis, as it differentiates between IBS and an inflammatory bowel disease. If we can identify this toxin as a contributing factor for you acquiring SIBO, then this information will help with the formulation of both the short and long term treatment planning to address SIBO.

Gut motility will not easily be reinstated. Long term prokinetic (pro gut motility) medications and/ or supplements will need to be utilized to try to make up for this loss in gut motility. The next step is to find a medication that can target these antibodies to reduce the damage that is done to vinculin.

Angela Pifer is a Functional Medicine Nutritionist with a decade of experience, specializing in the treatment of SIBO.

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from 26 people

Hi Angela,

Really helpful post and seems to match my experience - issues a few months post food poisoning. My question is, if I have SIBO-D, with never a hint of constipation, is it still a motility issue that responds to the same treatment as someone with SIBO-C? Thanks.

Casey | August 30, 2016

Angela Pifer

Talk with your doctor about this - they are the same ones that are well studied for peripheral nerve regeneration with diabetes, like alpha lipoic acid.


Angela Pifer | August 11, 2016

Thanks for the reply! Are there any particular nerve-regenerating supplements you'd recommend? I've heard lion's mane can help. Also, re-emphasizing that I tested positive for CdtB and NOT vinculin antibodies - just read elsewhere in the comments that you distinguish between these when considering SIBO truly "autoimmune." That's very encouraging for me to hear, as I've regarded my ibschek results as a bit of a death sentence for the past year. It's nice to think there's hope :)

Melody | August 9, 2016

Angela Pifer

Hi Melody,

Over time, the body will produce less antibodies and this will reduce the destruction of vinculin. Vinculin will begin to regenerate on it own. There are supplements that we use to support this process along and these are the same nerve regeneration supplements that one would use for peripheral neuropathy (as would be seen with diabetes - and there are plenty of studies on this). Addressing SIBO, utilize visceral manipulation (there should be a lot of home self care on the IC valve, which is heavily innervated by the ICC and vinculin and its integrity will likely be affected). The timeline will be different for each person - with all the variable factors that are in play, but this can and will recover. I see this clinically, all the time.


Angela Pifer | July 29, 2016

Hi Angela,

Are there any studies you can point to that suggest nerve regeneration is even possible while an autoimmune response is still going on in post-infectious SIBO (i.e. someone has anti-vinculin or anti-cdtb antibodies)? I saw you recommended this in a comment below, but it's my understanding that the nerves cannot recover while the body continues to mount an attack on vinculin via continuous autoimmune response (I tested positive for anti-Cdtb antibodies on IBSChek).


Melody | July 27, 2016

Angela Pifer

Hi Genevieve,
A prokinetic is used to support the movement (frequency, duration and intensity) of the migrating motor complex in the small intestine. You might need a prokinetic and additional bowel motility support (like magnesium). For herbals, ginger, motilpro and sometimes iberogast or bitters work. If more on the constipative side, I much prefer Resolor (through a Canadian Pharmacy). I would also discuss LDN with your doctor (low dose naltrexone). Though, you might need to also take Iberogast or Motilpro with it.

Angela Pifer | July 23, 2016

Any recommendations of prokinetic? Tried Iberogast and Motilpro but it doesn't seems to do that much moving...

Thank you for your help!

Genevieve | July 22, 2016

Angela Pifer

Hi Sandra,

Pregnancy is not a risk factor for SIBO. It definitely will not cause SIBO. There is something else going on here that needs to be figured out. During pregnancy, the body modifies its immunological immunity from a TH1 to Th2 pathway. It may be that there is an underlying issue that is going on, that once highlighted by the Th2 pathway becoming dominant, that this effected motility more. I recommend gently modifying your diet to manage symptoms (still getting in plenty of nutrition for the baby) and then see if your symptoms recover after birth (waiting 3 months for the shift to return to TH1 dominance). Then see if you still have symptoms, if you still have a positive breath test, etc. then decide to treat, if needed. This study explains the shift: http://www.ncbi.nlm.nih.gov/pubmed/9588218

I have seen false positive SIBO breath tests with gastritis, inflammatory bowel disease and with Celiac. I would continue to investigate this before jumping into treatment. It may be that something else is going on here.


Angela Pifer | July 23, 2016

Hi Angela,
Curious if you have ever seen pregnancy in and of itself as an underlying cause of SIBO? I had perfect digestion before my first pregnancy 3 years ago and starting in my first trimester already started dealing with bloating, and over time, developed new food sensitivities, both of which have not gone away since. I read a study about how gut motility slows down significantly during pregnancy, and am wondering if that could be an underlying cause by itself. I did eat constantly during my pregnancy (about every hour), which I'm guessing did not help the MMC do its job. I am working with an ND at the moment on an herbal protocol, but just wanted to get your thoughts if you think pregnancy could be the one and only underlying cause (secretly hoping you say yes so that I have hope of beating this thing in one round :-) ) I saw you mentioned in another comment to a post that once SIBO is there, supporting motility is not enough on its own to knock it out, so my logic is that even if motility returned to normal after pregnancy (and it did because my BM's are normal), the SIBO was already present at that point and needs to be treated. Am I way off? Thanks!

Sandra | June 20, 2016

Angela Pifer

Hi Paloma,

It is more common to recover from the food poisoning reaction and then have symptoms start to rear their head about 3 months later (once vinculin is reduced enough the start to interfere with gut motility and SIBO is set up to a degree that it causes symptoms).

It sounds like you have some further complications with tropical sprue and villi blunting that may have already been an issue and then the food poisoning event really tipped the balance for you, from the start.

I do still recommend the IBS Check test. There is further support for nerve regeneration that can be added to the treatment protocol that will help speed the healing process.


Angela Pifer | July 23, 2016

Hi Angela,

Thank you for this very informative post! This is the first time I have heard any mention of the anti-vinculin + SIBO connection being related to a delayed onset, and I am very interested!

My SIBO/digestive woes began with an episode of salmonella poisoning, but my symptoms came on immediately and were very evidently linked to the gastrointestinal episode, as I had never had any digestive troubles before. I have put off taking the IBSChek test (as recommended after a visit with Dr. Sandberg-Lewis in Portland) to see if I can treat the overgrowth and prevent recurrence first (and also because I don't think I could stomach--pun unintentional--a positive anti-vinculin diagnosis!). I was also diagnosed as having "tropical sprue", as my endoscopy showed mild villous blunting and my fecal biomarkers were quite elevated, indicating a pathogenic infection as opposed to normal SIBO.

It is very interesting to hear you say that many SIBO patients with the antibodies actually do not begin experiencing symptoms until three months after their episode of food poisoning. Is this something that you have noticed across the board in patients who have tested positive for the IBSChek test? And have you had any success in using various prokinetics for treating this specific type of SIBO?

Thank you so much!


Paloma | June 4, 2016

Hello Camilla!During a flu I spent more time than usual on my computer and dug into the blog-world. I very much enoyejd reading your blog,I like the atmosphere, your eye for detail, the swedish flavour, your art, your dog (you could make a book about him) and decided to start a blog myself!!!I am looking forward to discover your Rome (I was there 3 years ago).

Jack | February 27, 2016

Angela Pifer

Hi Jeff,

I hope at this time, you are under the direct care of your doctor as you work through a fast. Resting your gut may help calm inflammation and reduce the triggering of an autoimmune condition, but this is inaccurate information: "Every cycle I do purges old immune cells and creates new ones. It is the new ones that seem to be less likely to attack our own body."


Angela Pifer | July 23, 2016

I have just seen some encouraging research that fasting cycles can resolve autoimmune issues. I am embarking on a 3-day water only fast once a month to see how this affects my gut. This is also from research showing huge immune benefits from 3-4 day water fast. I am not sure how many cycles to try. Every cycle I do purges old immune cells and creates new ones. It is the new ones that seem to be less likely to attack our own body. I am thinking around 5 fasting cycles should be enough for the body to correct an immune issue. I'm just breaking my first cycle which was 75hrs water only. I'm on light vegetable juice for another day, then will slowly re-introduce food for 2 more days. At the moment my stomach is flat as a board and feels great. If I notice any slight improvements it will certainly encourage me to do another cycle in 30 days. I am also gearing up for another DIY fecal transplant which ended my constipation issues for 2 months the last time I did it. I wish I could just be normal and not have to deal with all this but oh well..

jeffg | December 6, 2015

Angela Pifer

Hi Shyma,

Mixing all the ingredients in the smoothies didn't cause this. It could be that they were stored a bit too long and/ or, there was some cross contamination happening and you inadvertently gave yourself food poisoning. I would have the IBS Check test done to see if you have post infectious IBS (SIBO from a food poisoning event that is effecting your bowel motility).

If you are still that sensitive to eating foods 'off plan' then SIBO wasn't fully addressed, or there is an underlying issue that is still present, or you have a motility issue that hasn't recovered or you have more gut healing to do. I realize that this can all be quite complicated. I do recommend that you work directly with someone on this. There are a few of us who work long distance with patients, so if you don't have someone in your area, then you might consider this.

I would have stool parasite testing done with your doctor as well. This will be covered by insurance.


Angela Pifer | July 23, 2016

Hi Angela,

I apologize for the long post, but I am looking for some insight and want to provide sufficient background. Reading Dr. Pimental's work has been illuminating, as I think it may be relevant to my health issues. Despite being a graduate student myself, I did something quite foolish 6 months ago that caused my various ongoing gastrointestinal problems (I now know better). Six months ago I tried to start making "healthy" smoothies with nuts, fruits, vegetables, quinoa, parsley, and raw garlic. It was something new and I made many mistakes - first, I mixed way too many things together, second, I drank these in large quantities daily despite it being a completely new diet experiment, and third, I stored these drinks improperly in the refrigerator for up to 7 days at a time (great way to produce toxins). I drank these over the course of a month. I was likely digesting it improperly as well since I was drinking a lot of water at the same time (diluting my stomach acids most likely). I was also making and drinking homemade kefir during this time (also a new addition to my diet). I started getting stomach/intestinal pains which progressed from dull to severe. I recall vomiting once, though I do not recall if I had diarrhea or not. I believe I likely poisoned myself to some degree with toxins or bacteria. When I ceased making smoothies, I felt improvement in symptoms, though I noticed over time certain foods would increasingly trigger stomach aches. Over the months that followed I developed symptoms such as high gas production upon eating certain foods, stomach pains, heartburn, indigestion, etc. Occasionally I would get constipation. I had a lot of stomach gas, which would fill my stomach and cause a lot of discomfort and heartburn, etc. Eventually I could barely eat anything without getting severe pain lasting for hours about 1-2 hours after eating (especially after eating carbs). I had an endoscopy and colonoscopy done which showed I had gastritis but no ulcers (my stomach and colon looked otherwise normal). My blood and urine tests at the time were normal (I'm still waiting for stool test results, but these are mostly looking at white blood cells or parasites). I then developed some diarrhea and some foul smelling stool/flatulence. I had two incidents with yellowish stool. I went from my usual 110 llbs to 96.4 llbs. I tried a number of things, like fermented cabbage juice, but anything seemed to help only for a little while.

After doing quite a bit of research and educating myself on these issues, I learned a lot about SIBO, SIYO, gastritis, etc. The stomach gas issue (I'm guessing it's really a small intestine issue) was a major symptom. I began a protocol of berberine HCL 200 mg 2-3 times per day, monolaurin 550mg 2 times per day, and lactoferrin 150 mg 1 per day. I also took a daily probiotic (Renew Life Ultimate Flora, Colon Care, 80 billion, with higher bifido bacteria). After 2.5 weeks I finished the berberine HCL dose. I am taking 2 DGL chewables before meals. Finally, I changed my diet to greatly reduce carbs, dairy, sugar, and exclude wheat/gluten. For the most part I eat green leafy vegetables (a lot of kale, some spinach), cucumbers, green beans, 2 eggs a day, chicken, fish, turkey, only use coconut or olive oil. I still eat rice but a much lower quantity and only jasmine rice, which has a low fermentation potential. I drink some tea maybe 1-2 times per day, mostly digestive bitters, green tea with lemongrass, or some peppermint tea. The only fruit I have is melon and papaya, which don't seem to trigger my symptoms, and I drink 1 teaspoon of manuka honey with black seed oil (Nigella sativa) every morning with a glass of water on an empty stomach. I find that I can occasionally eat a little bit of almonds, but haven't dared eat too much. I haven't found a good source of calcium yet, since dairy seems to trigger the gas.

I'm not sure if these are the right things to do, but I was desperately looking for a solution. My symptoms have reduced greatly, I no longer have pain at all and I can eat more and very comfortably. Unfortunately, I do notice that if I eat anything outside those items above, I start to feel the gas production immediately, which makes my stomach feel discomfort or nausea. So I feel that rather than this being "healed", the symptoms are simply controlled due to being strict with diet. I am trying to figure out how to get back to my normal self. Prior to 6 months ago, I was healthy and did not have symptoms like these at all. I never had issues with eating any foods really (I'm well traveled and always prided myself on a hardy stomach!). I did not drink, smoke, and I ate fairly clean, mostly organic, many fruits and vegetables, not significant amounts of wheat/flour, no red meats, not many processed foods. I was always thin, though I definitely need to exercise more. I'm a 30 yr old hispanic female. I do have a bit of history of some constipation though, and there is family history of gastrointestinal issues. But my current problems largely started 6 months ago.

This brings me to really think about Dr. Pimental's work. My questions are - am I currently doing/taking the right things to address my health issues, in your opinion? If this could really be an autoimmune response stemming from a food poisoning incident, what can I do now to treat it and get my gut back to normal? Are there any tests you recommend me to do? Insurance rarely covers these things, so I also have to take finances into account. Unfortunately there aren't too many NDs where I live. Thank you for your great work, and thanks for reading this long post!

Shyma | November 27, 2015

Angela Pifer

Hi Nikki,

Unfortunately, I do not have a good referral in Los Angeles. I'll be sure to follow up with you if I find a name to share.

Angela Pifer | February 15, 2016

I would like a gastrointestinal doctor referral in Los Angeles, please. I had a food poisoning event and within months had a full blown auto immune response. I'm seeing so many doctors now, but still have constipation.

Nikki | November 19, 2015

Angela Pifer

Hi Mia,
Each patient is going to be different in the approach that is used to help support motility. The first goal is to figure out why motility has been effected and then a plan is put together to help address this. There are quite a few supplements that will help stimulate motility, serotonin support, bile acid/ motilin, meal timing (fasting), vagus nerve toning... stress reduction, assess thyroid health. There is a lot to consider. Medications may very well help for a period of time AND there is more to do and assess.

In the studies, the medications help lengthen the time in between SIBO recurrence. This is not a cure, but a helpful aid.


Angela Pifer | November 2, 2015

So do you normally use meds for motilty?

Mia | September 13, 2015

Have you dealt with people with multiple autoimmune issues? I have celiac and hashimotos. I am autoimmune to gluten,dairy, soy, chocolate and cellulose. I also have problems with eggs. And I have problems digesting protein and fat. The only protein i eat is tiny bit of fish daily. Became a veggie 30 years ago bc had sever gastro issues. Stopped eating meat and symptoms went away. These issues came back when Dr tried to put me on SCD for SIBO. Treatment for 6 months with herbals. SIBO went from medium to sever (but cleared up for a few weeks i believe!). Part of issue is my auto immune reaction to cellulose in herbs and low stomach acid. Specialist has now put me on xifaxan and said i had to basically suck up the auto immune reaction for 2 weeks (all antibiotics have cellulose.) I have had side effects, but don't feel reduction in SIBO symptoms. I'm on day 9 of antibiotics. I have a UGI scheduled in 2 weeks. All probiotics also have cellulose so been eating probiotic veggies, which may be making my SIBO worse. Have had all the other tests you recommend. Am getting B12 shots and taking powdered herbs and minerals (My Dr could only find one brand without cellulose!) When SIBO is diminished as it was for about 3 weeks on herbs, by Hashimoto symptoms improve. And as SIBO gets worse, so do Hashimoto symptoms. One thing that has improved is i don't think i have leaky gut anymore. Previously everything i ate made me sick. Now, not so. Was wondering if you've dealt with anyone like me before.

lee | August 6, 2015

Hi Angela,

Angela:Unless you are exposed to the Cdt-B toxin again, the antibody levels will decline over time and they won't keep targeting vinculin to the same degree. .

Dont you think that people with SIBO are constantly exposed to the toxin because they still have this bacteria: E. coli, Salmonella, Shigella or Campylobacter

peter | August 5, 2015

Angela Pifer

Hi Peter,

If you are exposed to the toxin and your body produces antibodies to that toxin... then there is a cross reaction that will occur, where these same antibodies attack vinculin. Though you will always have a trace amount of these antibodies, this causes damage acutely and then starts to recede. You can, over time, regain some of the vinculin links as the body start to regenerate. This takes months and months to happen. In the meantime the damage has been done and this is when SIBO is set up...

Unless you are exposed to the Cdt-B toxin again, the antibody levels will decline over time and they won't keep targeting vinculin to the same degree.


Angela Pifer | July 31, 2015

Hi Angela,

Do you mean that vinculin was damaged once /after food poisoning/ or that antibodies damage it again and again?

peter | July 31, 2015

Angela Pifer

Thank you Kristina! I hope that you are on the road to recovery!


Angela Pifer | July 31, 2015

So crazy! I see an amazing gastro doctor in LA, CA. I was one of the first to get this test and of course, I was positive! Dealing with SIBO and stomach issues for over a year now. Found out may have possible lyme. The story never ends. You're detail is amazing! This made total sense. Just hoping that one day I will get my body back :(

Kristina | July 19, 2015

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