ISB Treatment: Addressing an Irritable Bowel Naturally

IBS, or Irritable Bowel Syndrome, is a digestive disorder which affects more than 10 percent of the world’s population. This article explores traditional and functional medicine approaches to treatment of IBS; testing; and the relationship between IBS, SIBO and IBD. And if those initials don’t mean anything to you, don’t sweat it, they’re all covered in this article.

So… what is IBS?
IBS is a cluster of symptoms that include abdominal pain, cramping or bloating that may be alleviated by a bowel movement; excess gas; diarrhea, soft stool, constipation or alternating diarrhea and constipation; and mucus in the stool. Other symptoms of IBS might include changes in texture and color of stools, nausea, acid reflux, easily feeling full or loss of appetite.

There are also non-digestive symptoms of IBS, which people might be less aware of. These can include anxiety or depression, difficultly sleeping, fatigue, headaches, an unpleasant taste in the mouth, muscle aches, sexual problems, body image issues or heart palpitations.

For most people who suffer from IBS, symptoms are worse at certain times, improve at other times, and even disappear altogether for periods of time. For some people, IBS symptoms are not severe, and can be managed with diet, lifestyle and stress management; but for many others, they can significantly impact their quality of life, make it hard to leave the house because of urgent runs to the bathroom with diarrhea, may involve accidents necessitating a change of clothes, and may impact people’s ability to work or be seen as reliable at work or in their social life. And unfortunately, many suffer in silence and don’t get the help they need because of the stigma or embarrassment.

IBS presents itself differently in different people. Clinicians organize the syndrome into three basic types: constipation-predominant (called IBS-C), diarrhea-predominant (IBS-D), or alternating constipation and diarrhea or mixed (IBS-M). According to Dr.Jockers.com, as much as 12 percent of the U.S. population suffers from IBS, or nearly 40 million people, and women and people under the age of 45 are more prone to IBS.

What’s the difference between IBS and SIBO?
SIBO, or Small Intestinal Bacterial Overgrowth, is believed to be the most common cause of IBS, with some experts citing the figure of approximately 60-70% of IBS being caused by SIBO. And the symptoms of SIBO (bloating, constipation, diarrhea, flatulence and abdominal pain) overlap with IBS, so in some sense, one could reasonably say that they’re basically the same thing, but IBS is more of a traditional or allopathic diagnosis, while SIBO is used more in the functional medicine world, although more and more gastroenterologists are using the term SIBO, the American College of Gastroenterology has put out clinical guidelines for treating SIBO, and some gastroenterologists are now using some of the same testing methods as functional medicine practitioners. And like with IBS, SIBO has traditionally been divided up into SIBO-D, SIBO-C and SIBO-M.

However, the nomenclature of SIBO and the issue of whether symptoms are coming from general bacterial overgrowth has been called into question because the testing that has been used to diagnose it, that is hydrogen and methane breath testing, has neither been shown to be terribly reliable, in particular with the hydrogen part (meaning that if you test at one time, do no treatment, and test two weeks later, you get different results), nor has it been shown to be valid in at least two recent studies (Cangemi et al., 2020), (Saffouri et al., 2019), meaning that if you compare aspirates (or suctioning of) bacteria in the small intestine, it doesn’t correlate with what’s showing up on breath testing or with patients’ symptoms. And an article published out of Dr. Mark Pimintel’s lab out of Cedars-Sinai Hospital (a leading SIBO researcher), seems to validate the lack of validity of the hydrogen breath tests in the abstract, where it says that at the 90-minute time point on the lactulose breath test (which is considered the cutoff time for measuring gases coming from the small intestine), 4/7 SIBO subjects had a rise in hydrogen (H2) ≥ 20 ppm above baseline, which would mean they had SIBO, as compared to 2/13 non-SIBO subjects. So first, those are small sample sizes so it’s difficult to call these results definitive, but at least in this study, the hydrogen breath test only correctly identified SIBO 57% of the time, and 15% of the time gave a false positive for SIBO in someone without it as compared to the results of the duodenal aspirates (or sampling of cells in the first part of the small intestine, or duodenum). This is one of the main reasons I never recommend breath testing to my clients.

There is some interesting information coming from that study, however, including that subjects with bloating had a relatively higher abundance of bacteria from the family Enterobacteriaceae, while people experiencing urgency with bowel movements had a relatively higher abundance of bacteria from the family Aeromonadaceae. Also, the subjects with what they were calling SIBO (based on the quantity of the bacteria in their small intestine) had a 4.31-fold higher relative abundance of the phylum Proteobacteria (averaging around 37%) and a 1.64-fold lower relative abundance of the phylum Firmicutes. They also reported that subjects with SIBO also exhibited greater urgency with bowel movement than non-SIBO subjects (P = 0.022), which was the only symptom they seemed to be able to correlate to overgrowth, which again in my opinion calls into question the definition of SIBO as a state of general bacterial overgrowth. And, a brief aside for people who have studied statistics, the p value on that last item was only. 0.022, versus 0.0001 for the relative abundances by family and phylum. So clearly the more statistically significant issue shown in that study is the predominance of proteobacteria, and in particular, Enterobacteriaceae and Aeromonadaceae. And further, they also found that SIBO subjects had relatively more bacteria from the genera (which is the plural of genus by the way) Klebsiella, Escherichia/Shigella, Acinetobacter and a couple more unknown genera.

As a result, “SIBO” may not be the right word. Rather, the term “dysbiosis,” which typically implies that there is an overgrowth of a particular kind of bacteria (but maybe not bacteria in general) may be more accurate. Dysbiosis may be bacterial overgrowth in both the small and large intestines, or an overgrowth of yeast in your intestines (also known as SIFO, or Small Intestine Fungal Overgrowth), an infection with a parasite, a general lack of diversity, or underrepresentation of certain important species. However, in my experience looking at lab results of tests like the GI Map and Organic Acids Test, typically all three things are happening at once when you have symptoms of IBS. But that being said, I have a client now who has an IBS diagnosis and symptoms, and when we did her labs, there were no overgrowths of pathogenic bacteria, no yeast overgrowth, and it seems like the amino acids I educated her about to help bring up her dopamine and serotonin levels have already positively impacted her IBS, which points to anxiety and stress as a likely root cause in her case. So you never know what you’re going to find out until you test. That, by the way, is one of the benefits of doing an Organic Acids Test – it helps identify when things are going wrong with your neurotransmitters, which impact your mental health, which is often impacted when you have gut issues.

As I mentioned above, IBS is divided up by whether it involves diarrhea, constipation or both. For people with constipation, it’s usually caused by an overgrowth of methanogens, or methane-producing microbes. Rather than grouping that under SIBO-C or IBS-C, the newest term being used is IMO or Intestinal Methanogen Overgrowth, because the methanogens may be located in both the small and large intestines, plus the term SIBO has the word bacteria in it, and archaea are not bacteria. [All organisms on earth are separated into three domains: eukarya (which is where you find animals, including humans), bacteria and archaea]. Anyway, IMO can be another cause of IBS, especially if it involves ongoing constipation. 

Now some good news for people who have been suffering and can’t figure out exactly why: breath testing that includes a third type of gas in your small intestine, hydrogen sulfide, has just come online for commercial use. Prior breath testing was for hydrogen and methane, with hydrogen typically being associated with diarrhea and methane with constipation. But up until now, you couldn’t test for hydrogen sulfide in a commercial setting; it was only used in a research setting. This new test was developed by Dr. Pimintel. It’s called trio-smart™ and it’s is available from Gemelli Biotech. It looks like an overgrowth of hydrogen sulfide-producing bacteria is also typically associated with diarrhea. Breath tests can be done in a lab or using a home kit, which is what the trio-smart is. If you drink glucose and do any type of SIBO breath test, which involves breathing into a tube and saving the results, it covers the first part of your small intestine. If you drink lactulose and do the test, it covers the lower part of your small intestine. Dr. Pimintel also developed a test called ibs-smart™, which tests for autoimmune markers which impact your intestinal motility, which can be a root cause of IBS, originally brought on by food poisoning, which likely is the primary root cause of IBS.

But the long and short of it is, what you’ll find out by doing an ibssmart test is whether you have an autoimmune issue, which you’ll need to address after killing any dysbiotic micro-organisms, by using something called a prokinetic. That’s a drug or natural substance, like ginger, that helps the intestines to move. Some of the prescription medicines used as prokinetics are low dose erythromycin, low dose prucalopride and lose dose naltrexone and one neutraceutical one is called Iberogast*. So if you seem to have recurring problems even after SIBO or IBS treatment, try taking a ginger pill before bed, or have a cup of ginger tea in the evening after dinner to stimulate the migrating motor complex as you sleep. Or if those don’t work, you may need something by prescription to deal with your motility issues. Or you can skip the test, cure your IBS, wait and see if it comes back quickly, and if it does, you’ll probably need to take a prokinetic. And at minimum, once you’ve cleared up your IBS or dysbiosis, you should make sure you don’t eat more frequently than every 4-6 hours, you don’t eat at least 2 hours before bed, and you go at least 12 hours at night without eating, to allow your intestines to clear out and let the migrating motor complex do its job.

So if dysbiosis is a root cause of IBS, maybe even covering 60-70% of it, what about the rest? IBS can be related to other things, like adhesions or bands of scar tissue from a surgery, inflammation or an injury that’s keeping your intestines from moving properly. Or it could be from Ehlers-Danlos syndrome, which is a hyperflexibility condition that can impact your intestines. Or it could be from hypothyroidism, blood sugar issues, type 2 diabetes, drugs you’re taking or took, Lyme disease or various autoimmune diseases like scleroderma or rheumatoid arthritis. Or it can be from a traumatic brain injury, which can also impact your migrating motor complex.

What’s the difference between IBS and IBD?
Now just a brief interlude to address the difference between IBS and IBD, or Irritable Bowel Disease. IBD is an umbrella term which describes digestive disorders caused by inflammation of the bowel, and autoimmune issues that affect the gut and intestines, including Crohn’s disease, ulcerative colitis and microscopic colitis. IBD symptoms are typically more serious and less common than IBS symptoms. These might include: loss of appetite, blood in the stool and nutrient deficiencies brought on by malabsorption.

How is IBS diagnosed and treated?
Typically doctors will give a diagnosis of IBS once they’ve excluded everything else, including IBD, which usually involves an endoscopy (or where they put a camera down your throat to look at your esophagus, stomach, and the upper part of the small intestine), and a sigmoidoscopy or colonoscopy (where they put a camera through your rectum to look at your colon, or for a sigmoidoscopy further into your small intestine). That’s one of the reasons Dr. Pimintel has developed the tests mentioned above, to spare you having to have the entire length of your intestines scoped. But typically, if the endoscopy and colonoscopy are negative and gut symptoms continue, including abdominal pain for at least 12 non-consecutive weeks out of the precious year, characterized by a change in how often you have a bowel movement, and your bowel movements are not normal, then a diagnosis of IBS may be indicated.

If you see a functional medicine practitioner with an IBS diagnosis or symptoms, depending on your symptoms, you will likely either be asked to do a PCR-based stool test like Diagnostic Solutions’ GI Map or Doctor’s Data’s Comprehensive Stool Analysis with Parasitology, a SIBO breath test and/or an Organic Acids Test. The results of those tests will give your practitioner a lot more data about what’s actually at the root of your issues.

In terms of treatments, if you see a traditional gastroenterologist and have a positive breath test or just based on symptoms alone, you may be prescribed antibiotics, in particular one called Rifaximin or xifaxin, an antibiotic that only impacts bacteria in the intestinal tract. It’s super expensive though – last I checked it was about $1750 for a two-week course – so if your insurance won’t cover it or your doctor isn’t in the know, you may want to go the herbal antimicrobial route. There are also some other antibiotics that may be helpful, including neomycin, metronidazole, augmentin, bactrim and nitazoxanide. However, although antibiotics may reduce your symptoms in the short-term, many times they may further stress the gut lining and microbiome or cause an incidence or increase in fungal overgrowth, which will cause a relapse or even a worsening of symptoms in the long-term. Rather than an antibiotic approach, many naturopaths, functional medicine practitioners and experts in the field prefer antimicrobial nutraceuticals because they simultaneous address both bacterial and fungal overgrowths. Typical antimicrobial herbs used for dysbiosis include Berberine, Allicin from garlic, Oregano Oil, Thyme Oil and Uva Ursi. And hydrosol silver and bismuth are also used. One of my favorite protocols that kills both bacteria and yeast is using the Candibactin BR* and AR* products. But you’ll want to get help using them because the die-off or Herxiemer reaction can be unpleasant or even dangerous if you have severe overgrowths of bacteria or yeast. That’s when you have flu-like symptoms as you begin to kill stuff in your intestines. And then once you have dislodged the bacteria and yeast, you want to use prebiotics and probiotics strategically to help reset your microbiome in an effective manner.

Some additional supplements that may be effective in addressing IBS symptoms or root causes include Betaine HCl* and digestive enzymes*, especially if there is evidence of a lack of stomach acid or pancreatic enzymes, respectively, on the GI Map test. And if there’s evidence of leaky gut, like food intolerances, or low gut immunity (indicated by low secretory IgA on the GI Map) l-glutamine powder* and an IgG product like MegaIgG* or Megamucosa* can be helpful. And then there are some supplements that help soothe and lubricate or reinforce the mucus lining of the digestive tract, like aloe vera*, which also helps with constipation, as well as marshmallow root, DGL and slippery elm (which can be found in combination products like this one*). And Atrantil (find in my Fullscript Dispensary) is a great over the counter medication that’s very helpful with constipation and actually consists of various plant polyphenols. And another really good one for help with bloating is peppermint oil*, which is good to take prior to meals.

One of my mentors, Lucy Mailing, PhD, believes that treatment shouldn’t focus on quelling bacterial overgrowth by antibiotic means. Rather, she focuses on the depletion of the short chain fatty acid butyrate, which is the food for the cells lining the colon (while glutamine, by the way, is the food for the cells lining the small intestine). Antibiotics, gut infections, low-fiber intake, and stress are all factors that can deplete gut butyrate, causing oxygen leakage into the gut. This encourages gut dysbiosis characterized by an overgrowth of faculatative anaerobes like proteobacteria, which can survive in the presence of oxygen. Therefore, she recommends avoiding antibiotics, treating fungal gut infections, eating plenty of fiber, managing stress and getting plenty of regular exercise. Speaking of which, a study published in the American Journal of Gastroenterology in 2011 found that increased physical activity improves GI symptoms associated with IBS, and improves quality of life to such a great extent, that exercise should be utilized as a primary treatment for symptoms associated with an irritable bowel. If you’re thinking of supplementing with butyrate and some more advanced interventions that Lucy recommends, I’d suggest you do it under the care of an expert gut health practitioner, such as myself. I’ve personally found supplemental butyrate to be one of the most helpful things for me in keeping my bloating in check and my stool at a nice Bristol #3. In case you’re not familiar with it, the Bristol stool chart rates stool from 1 to 7. A 3 or 4 is considered normal, but I’d much rather a 3 than a 4, personally.  

In terms of diet, one of the most commonly recommended for IBS is a low FODMAPs diet (which stands for fermentable oligosaccharides, disaccharides, monosaccharides and polyols), which, along with eliminating gluten, dairy, and a wide selection of fruits and vegetables, eliminates the omnipresent ingredients garlic and onion and their powders. The low FODMAPs diet should not be used long-term or it may result in the extinction of vital gut microbes. Rather, it’s best used to precede treatment to reduce symptoms, as a self-diagnostic tool (if you do better on it, you know your issue is at least partially bacterial) and to temporarily deplete the microbes that cause problems, so your killing regime will be more successful. Or it can be used as an elimination and reintroduction diet to see which of those foodstuffs most affect you. There are also other diets out there that are even more restrictive like the specific carbohydrate diet or the biphasic diet, but honestly, I think low FODMAPs is already a lot to ask of people, so I generally go the route of treating the underlying cause of IBS symptoms quickly rather than playing out a difficult diet like FODMAPs. But honestly, by the time most of my clients find me, they’re usually reduced to a diet consisting mostly of vegetables, meat and fat in their desperation to find a solution to their problems, so I’m not inclined to ask them to restrict their diet even further. 

Could my gut issues cause or be the cause of my autoimmunity?
So if you have a mild case of what seems like IBS, you may just be toughing it out thinking the symptoms are tolerable, but be careful. My gut issues preceded my autoimmune issues, and I know they’re related. Dr. Alessio Fasano, a pediatric gastroenterologist, research scientist, and founder of the University of Maryland Center for Celiac Research, believes three factors are at the center of all autoimmunity issues. They are genetic susceptibility, antigen exposure and increased intestinal permeability. Given that you find increased intestinal permeability in IBS and dysbiosis, it is not surprising to find that they are common underlying causes and precede many autoimmune conditions. Although that association isn’t entirely clear, what it clear is that with its high likelihood of generating leaky gut, it is important to address IBS for the prevention and treatment of autoimmunity.

And if you’re struggling with a IBS, another gut issue, autoimmune disease or a mystery health issue, please feel free to set up a free, 30-minute breakthrough session with Lindsey to talk about what’s been going on and hear about how health coaching could help.

Listen to episode 36 of The Perfect Stool: Understanding and Healing the Gut Microbiome podcast.

*Product links in this article are affiliate links on Amazon. Thanks for your support of the podcast and blog by using my links!

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