Recurrent SIBO : Symptoms, Causes, Testing and Treatment

Recurrent SIBO: Symptoms, Causes, Testing and Treatment

Adapted from episode 83 of The Perfect Stool podcast hosted by Lindsey Parsons, EdD and edited for readability.

What is SIBO (Small Intestine Bacterial Overgrowth) and how does it relate to IBS?

There are 1-10 trillion bacteria in our intestinal tract and most of them can be found in the colon or large intestine. These bacteria take care of the final breakdown of food into a form where it can be absorbed into the body for nutrients or discarded as waste. These bacteria play a critical role in maintaining health throughout the body.

The small intestine normally contains far less bacteria compared to the large intestine. SIBO (small intestine bacterial overgrowth) occurs when the bacteria in your small intestine become unbalanced and overgrow. SIBO can damage the intestinal lining, leading to leaky gut, which can cause further health complications. For example, an imbalance in bacteria could lead to nutrient malabsorption, which causes you to get sick from a lack of vital nutrients, or histamine reactions, which surface as food sensitivities. If untreated, SIBO has the potential to snowball into even worse health conditions.

Typical SIBO symptoms include bloating, gas, diarrhea, soft stool, constipation or a mix of diarrhea and constipation, burping, abdominal pain or cramps, food intolerances, B12 and iron deficiencies, fat malabsorption, and if left untreated long enough, autoimmune diseases, skin disorders or systemic diseases like fibromyalgia or chronic fatigue syndrome. SIBO is broken into three types – SIBO-D or diarrhea, which is not exclusively diarrhea, it can just be soft, messy stool, which may or may not be very frequent. This is caused by either excess hydrogen or hydrogen sulfide producing bacteria. Then SIBO-C for constipation, also known now as IMO or intestinal methanogen overgrowth, which is not necessarily in the small intestine but can be throughout and may be more a question of dysbiosis, or an imbalance of bacteria and methanogens, which are archaea, a different kingdom of microorganisms, rather than an overgrowth, per se. Methanobrevibacter smithii is the primary and most well-known methanogen, meaning methane producer. And then SIBO-M or mixed, which may have some constipation and diarrhea, sometimes because you have breakthrough diarrhea when constipated, or because as your diet, eating habits or underlying root causes change, things shift back and forth in your intestines. About 70-80% of what’s called Irritable Bowel Syndrome, basically a diagnosis of exclusion, is caused by SIBO, so I think of them almost synonymously.

What causes SIBO or IBS?

There are a range of possible root causes of SIBO/IBS, some of which can lead to recurrent SIBO if not addressed. Some relate to impaired digestion – such as low stomach acid or hypochlorhydria, which is important for breaking proteins into amino acids, or a lack of pancreatic or brush border enzymes (which can come from celiac disease). Enzymes help digest all types of foods so undigested food can serve as fuel for bacterial overgrowth.  Other potential causes are low secretory IgA, your gut immune defense system (which can follow from chronic stress) or poor bile flow, which is essential for digesting fats. Of course if you’ve had your gallbladder taken out, which stores the bile produced by your liver, then you can assume you have insufficient bile. Medications such as opiates, narcotics, antidepressants, proton pump inhibitors, cholestyramine, antibiotics and antispasmodics can also cause SIBO or IBS-like symptoms. Then there are physical issues like Ehlers-Danlos Syndrome, adhesions from abdominal surgery, endometriosis, and ileocecal value dysfunction that can cause SIBO. Then there are environmental causes like mold toxicity and other health conditions like diabetes, pre-diabetes, hypothyroidism and traumatic brain injuries that can be at the root of SIBO symptoms. Then what I suspect is the most common cause – an autoimmune dysfunction caused by an episode of food poisoning that impacts the migrating motor complex is the final cause, and this one will definitely cause recurrent SIBO. This is what’s called post-infectious IBS and is the reason I personally have recurrent SIBO.

Testing for SIBO

You can get tested for SIBO either using a breath test, there are a number of hydrogen or methane breath tests out there for SIBO, or test for all three possible gases, including hydrogen sulfide, with the triosmart test, the only one that includes hydrogen sulfide currently. Or stool tests like the GI Map or GI Effects can also point to the presence of SIBO in conjunction with symptoms, when you see many elevated opportunistic bacterial markers or even elevated commensal or good bacteria markers. And you can also see whether certain bacteria associated with different types of SIBO are present or elevated, such as Desulfibrio piger, Bilophila wadsworthia or Fusobacteria for Hydrogen sulfide SIBO or Methanobrevibacter smithii for IMO.

Treating SIBO

So the first round treatments for SIBO are either herbal antimicrobials or rifaximin (the generic name of Xifaxan®),  a very expensive antibiotic that only impacts the gastrointestinal tract. And for people with methane-dominant SIBO, the antibiotic neomycin is often prescribed as well. I ended up taking a round of rifiximin, which was 2 weeks long at 3 pills a day after I didn’t feel that herbal antimicrobials had done the trick for me (this was years ago and I have since taken different herbal antimicrobials that have worked better for me). The main drawback to rifaximin is that it will only kill bacteria. And many people I see have an overgrowth of candida (a yeast that’s a normal part of our digestive system) as well from a history of antibiotic use, or from the same root causes that caused SIBO. And while the herbals kill both yeast and bacteria, rifaximin only kills bacteria, which then offers yeast an opportunity to overgrow or overgrow even further.

I should also mention elemental and semi-elemental diets. When all else fails, this is another route for dealing with SIBO that has shown good success. These are liquid diets of predigested nutrients, which seem to work equally well, with the semi-elemental being a bit more palatable than the elemental diet. One study in 2004 of a prescription elemental diet on 93 patients showed a SIBO lactulose breath test normalizing after 2 weeks for 80% of subjects, and 85% by three weeks, with a 65% improvement of IBS symptoms at 2 weeks. But since this requires you eating no real food for 2-3 weeks, I don’t think of it as a first line option, as that doesn’t sound like much fun to most people.

There is also good evidence supporting the use of probiotics in SIBO, but since this is controversial and debated, I’m not going to go too far into the topic right now.

Lifestyle Factors in Preventing SIBO Recurrence

If you’re going the route of antimicrobials, in conjunction with taking them, there are other things you can do to ensure success and prevent recurrence. First, making sure that you’re observing good meal hygiene: trying to eat in a relaxed parasympathetic, or rest and digest state, not while stressed out, working, at the computer, on the run, etc. This will help your body produce the stomach acid and enzymes it needs to digest properly. A minute of 5-5-7 breaths (5 in, hold for 5, 7 out) can help bring you into this state prior to eating if you sense you’re in a stressed state. And then maintaining this parasympathetic state while digesting, which can range from 30 minutes to 4 hours, depending on the size or your meal. Then chewing each bite very well, like 25 times well. And they say not drinking too much liquid with meals, but this is something I struggle with, but you can experiment with that and see if it’s helpful.

Second, not snacking between meals, and spacing your meals out to every 4 to 6 hours. The migrating motor complex stimulates peristalsis, which is how your body moves food and bacteria through your digestive system. When you’re in a fasted state, specifically, when there is no more food in the duodenum, or the first section of the small intestine, it secretes motilin, which starts off the peristaltic wave, emptying out your intestines. This helps clean out bacteria and move them towards the large intestine. This happens generally around 90 minutes after eating but up to 2-3 hours after eating, and lasts around 2 hours. If you’ve heard your stomach gurgling when hungry, what you’re hearing is the migrating motor complex, which is a good thing. If you never hear stomach gurgles, it’s either because you’re eating too frequently, or you have had some disruption to your migrating motor complex.

And then third, trying to have a solid overnight fast of 12, even better 13 hours. Or even longer if you’re trying to lose weight (in 14-16 hour range). This will give your body a good chance to clean out the intestines.

How does my diet impact my SIBO?

And I should mention that with particular types of SIBO, a diet change may be in order. So methane dominant SIBO, or SIBO-C or IMO, tends to occur more in vegetarians and vegans, as the archaea that are dominant in this condition, like Methanobrevibacter smithii, feed on carboyhydrates. And protein sources in vegetarians and vegans, like tofu, beans, lentils, etc. are pretty much all high in carbohydrates. Moving more towards an animal-based diet with higher fats and low in fermentable carbohydrates, like a low fermentation diet or low FODMAP diet is in order. It is possible to do a vegetarian low FODMAP diet, but in my experience, its people on vegan diets who have the most stubborn cases of IMO.

SIBO-D, which is characterized by an excess of hydrogen-producing bacteria, typically responds well to a low FODMAP diet or if you want to get really fancy, a biphasic diet.

And then Hydrogen Sulfide SIBO, which is characterized by an overgrowth of hydrogen sulfide producing bacteria, also presents as diarrhea but with the added benefit of it smelling like sulfur, and often accompanied by visceral sensitivity, which is a lower threshold for pain in your internal organs and excessive flatulence. This is more likely to occur in someone who is on a ketogenic or primarily animal-based diet. So moving more towards a plant-based, low-fat, Mediterranean diet with no dairy but avoiding sulfur-containing vegetables like garlic, leeks, onions, scallions, and shallots and cruciferous vegetables, if they bother you, is recommended in this case.

And sometimes of course there is overlap, because methanogens eat hydrogen, and hydrogen sulfide producers eat hydrogen, so killing off all types of bacteria and/or archaea and their food source (the hydrogen producing bacteria) at once may be necessary to quell the overgrowth.

But note that diet alone will not likely get rid of your SIBO, and all of these diets will result in nutritional deficiencies if followed in the long-term, so doing some other primary treatment while using diet as an adjunct or for symptom relief is generally how I view SIBO diets.

Is my SIBO/IBS autoimmune?

So if you have a history of food poisoning, meaning you’ve ever had unexplained diarrhea, the stomach flu, Montezuma’s revenge or the like, and you’re dealing with ongoing bloating and or diarrhea, you may want to check if your SIBO is autoimmune. And mind you, if you have persistent diarrhea or soft, messy stool, this is also abnormal, it doesn’t have to be full on diarrhea. Autoimmune SIBO almost always tends towards the diarrhea type, rather than the constipation type. It starts because your body starts attacking its own protein, vinculin, that helps with the migrating motor complex, because it ressembles the toxin produced by the offending bacteria – CdtB – Cytolethal Distending Toxin B. So if you’ve succeeded in fixing your problem at least once using antimicrobials, prescription or herbal, and it’s come back, it’s time to determine whether your underlying cause may be autoimmune.

If you are constipated, you should also double check that your constipation is not from H pylori, a bacteria that can cause ulcers and stomach cancer, if you have the virulence factors, because it can also cause bloating and constipation. I like the H Pylori profile from Diagnostic Solutions as a simple H pylori test, although the full GI Map is a more thorough test that includes the H pylori profile and the virulence factors. And don’t assume you don’t have H pylori because your doctor tested you on an endoscopy. They miss it all the time.

So to check for autoimmune SIBO/IBS, there is a test called the ibssmart test that will tell you. It’s $199 and you can order it yourself online from the US. They even show some international distribution of it now as well on their web site but that may require a doctor’s prescription. It will show if your antibodies to vinculin and cdtB are elevated. If vinculin is elevated, you’ll probably have a lifetime battle with SIBO. Then the steps above I mentioned regarding meal hygiene and timing are especially important for you. In addition, you will likely want to start trying prokinetic, or small intestine motility agents, to help your migrating motor complex do its job. I’ll go into those more in a moment.

If your ibssmart test is negative, but are seeing SIBO recur, you may have some other underlying condition that’s at the root of it your symptoms. Some obvious ones are your prescription medications – check their list of side effects and wean off them as directed by your doctor to see if that will impact you. Another is hypothyroidism that isn’t properly addressed with thyroid medications and/or autoimmune reversal protocols for Hashimoto’s thyroiditis. Another common one, blood sugar dysregulation can cause IBS symptoms. If you know that you’re prediabetic or diabetic and do not have your blood sugar under control, then getting completely off sugar and simple carbs, reducing carb intake to 100 grams/day, including protein and healthy fats at every meal and if you’re having any snacks, and including some intermittent fasting in your days or weeks are first steps to reversing that and getting things under control. And of course seeing your doctor and getting prescription medications as necessary. Or a traumatic brain injury or a mental health trauma that’s causing vagus nerve dysfunction could be at the root. If you have a traumatic brain injury or history of concussion, check out my episode 73 with Dr. Corey Deacon, Head Injuries, IBS, SIBO and the Gut-Brain Connection. If you have a serious history of trauma and also experience depression, I’d check out the book Accessing the Healing Power of the Vagus Nerve by Stanley Rosenberg. And if you have endometriosis, or adhesions from abdominal surgery, visceral massage, hormone based treatment, or surgery may be necessary to address it.

Prokinetics for Recurrent SIBO

If you determine that your SIBO is or will be recurrent, one of the best things you can do is take a prokinetic before bed or possible between meals as well. There are some prescription ones, which would require a very SIBO-informed gastroenterologist to prescribe. These include Prucalipride which is the generic name of Motegrity at ½ mg/day, which you get by cutting a pill in half, low dose erythromycin, which is 50 mg, or low dose Naltrexone, which is also often used for autoimmune conditions in doses ranging from 2.5 mg to 5 mg, usually more for constipation. There are actually services online for prescribing low dose Naltrexone where you can talk to a doctor virtually and then get a prescription.

Then in terms of over the counter prokinetics, there’s Iberogast*, which is used before bed, 30-60 drops. It’s a combo herbal product. And then there’s GI Motility Complex (find in my Fullscript Dispensary*), which contains a formulation called ProDigest, which is a combo of ginger that’s formulated to not produce that ginger burn effect but helps with small intestinal motility and artichoke extract, which helps with stomach emptying) and apple cider vinegar powder. Then there are a few more formulations like Motility Activator, MotilPro, Prokine, SIBO MCC (find all in my Fullscript Dispensary*) and Bio.Revive Kinetic. Some of these have 5-HTP which is not just good for your intestinal motility, because it’s a precursor to serotonin, most of which is made in your gut and helps move the intestines, but also good for your mental health, because serotonin is your feel good neurotransmitter which helps for anxiety and depression. These may be more helpful for people with IMO or SIBO-C. And the last one I mentioned, Bio.Revive Kinetic is sold in the UK, not sure about the U.S. has some of the ingredients of the ayurvedic preparation triphala, which is known to be good for constipation in particular.

What to do when my SIBO comes back?

So say you’ve gotten rid of your SIBO and you’re taking your prokinetic but then you notice the telltale bloating, soft stool, diarrhea, or constipation coming back. What to do?

Well you might start by increasing the dose or frequency of your prokinetic. I take mine before bed, but you could also take it between meals. Or you could try a different prokinetic. But if things get back to where they were, then you will probably want to take another course of antimicrobials. I have also seen clients who just give themselves ongoing small doses of antimicrobials on a daily or every 2-3 day basis. For this I’ve heard of them using products like oregano oil or Biocidin drops (find in my Fullscript Dispensary*). Of course the danger with any single agent like oregano oil, is that the bacteria could become resistant to it, as I know that this can happen when treating yeast with oregano oil.

But recurrent SIBO has been my story for years now since I am positive for the antibody to vinculin, which is a protein essential to the functioning of the migrating motor complex, which is what the ibssmart test tests for, so I pretty much have gone the route of just taking another course of antimicrobials whenever things get bad again. But before I do that, I try to curtail snacking, eat a clean diet, stop eating dessert before bed (yeah, I know you probably think because I’m a gut health coach I’d follow my own advice but we’re human right, and I get lazy and self-indulgent like everyone else). But if that doesn’t work, then I know it’s just time to kill off more bacteria.

So if you’re struggling with ongoing bloating, constipation, diarrhea, soft stool, etc. and want to get to the bottom of it, that’s what I help my clients with. You’re welcome to set up a free, 30-minute breakthrough session if you think you might like to sign up for a 3 or 5-session package. Or I offer individual consultations as well.

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