Hands down, one of the top things I see in my practice is gut problems with bacterial overgrowth in the bowel. Often in the small bowel.
People usually don't come in and say "I have SIBO, please fix me". No, they come in with abdominal bloating, cramping, gas, diarrhea, constipation, or food sensitivities. The symptoms of IBS and SIBO.
They have often been told they have IBS or fibromyalgia. Sometimes they are concerned about Candida overgrowth.
Sometimes they are down to only a handful or two of foods they can eat due to food sensitivity or food intolerance symptoms.
Bacterial overgrowth can happen in the large bowel or the small bowel. And it can involve fungal or "Candida" overgrowth as well.
Let's talk about the overgrowth of bacteria in the small bowel, because the small bowel is different than the large bowel.
Small intestinal bowel overgrowth is called SIBO for short [1,2]. If it involves fungal overgrowth, it is called SIFO, or small intestine fungal overgrowth .
Small Intestinal Bowel Overgrowth vs. Large Bowel Microbial Overgrowth
In a nutshell, the small bowel is the part of the bowel that comes right after the stomach. The small bowel section of the intestine is where you absorb the nutrients from your food.
If you had to point to where the small intestine is on your body, you might be surprised. The small bowel goes all the way down the middle of your abdomen, from just under your ribs down to the pubic bone. Then it veers off to the right, where it meets the large bowel. That junction is where your appendix is.
The small bowel is supposed to be relatively free of bacteria.
When you eat, food goes into the stomach where it is broken down by stomach acids and enzymes. That process does a pretty good job of killing off most bacteria and fungus that might be on food. Obviously it is not perfect, as anyone who has had any type of food poisoning will tell you.
The large bowel makes a big loop around the small bowel, going up the right side, then traveling across to the left side right under the lower ribs, then down the left side and then veers to the middle.
The large bowel is where many many bacteria live. All these bacteria do what bacteria do, which is to ferment things. Fungus can do this too.
When things are working as they should, fermentation is done in the large bowel on what is left of your food after the nutrients are absorbed in the small bowel. This works best if there is a fair amount of fiber present. Some foods are more fermentable than others.
The end product of all of this fermentation is various fatty acids that are used as energy to keep the gut wall healthy, such as butyrate.
Problems arise, such as IBS, gas, bloating, cramping, diarrhea or constipation, when you have either too many bacteria in general, too many bacteria in the small bowel (SIBO), or the wrong balance of bacteria. The same goes for fungus.
Too few of the good bacteria can be problematic as well. Probiotics and fermented foods can be consumed to increase good bacteria, which is sometimes a good idea and sometimes not.
Now let's go back to the small bowel.
SIBO, or Small Intestinal Bacterial Overgrowth
When there are too many bacteria in the small bowel, where, as you recall, they are not supposed to be, that can cause IBS symptoms.
Remember that one of the major roles of bacteria is to ferment. That is exactly what they do when they get up in the small bowel.
As we said before, the small bowel is where you absorb nutrients. The small bowel is not at all happy when bacteria colonize in the small bowel and start fermenting. This can cause a lot of bloating, gas pain, cramping, belching, diarrhea and constipation, which are classic SIBO symptoms.
Since the small bowel goes all the way down the middle of the abdomen, you can have bloating symptoms in what seems like the lower bowel, but it is really the small bowel.
How Do Bacteria Get Into The Small Bowel?
Left to our ancestral eating patterns, we would eat some food that is not overly carbohydrate, and certainly not sweetened with sugar or processed, and that would get broken down by stomach acid and digestive enzymes.
We wouldn't be taking any stomach acid blocker medications to reduce stomach acid.
In most cases, this process would wipe out most of the bacteria and fungus on food. Then it would go on to the small bowel, in a fairly sterile state, where it would be acted on by more enzymes and nutrients would be extracted.
But in these modern days, when we tend to repeatedly eat overly starchy foods, sweetened foods, and overly processed foods, it is easy for microbes to not be neutralized as they should be. Instead, these bacteria and yeasts, or fungus, which love fermentable sugars, can start fermenting food while it is still in the small bowel.
Adding to this is the problem of slow stomach and small bowel emptying and slow gut motility. One of the hallmarks of diabetes is slow stomach emptying.
Low thyroid, even while taking thyroid medicine, can also contribute to a slow moving intestine . So can a fiber poor diet.
In addition, we have bacteria that make their way up from the large bowel into the small bowel.
Anything that disturbs the forward movement of food through the digestive tract can allow food to stick around longer in the small bowel than it should. That contributes to small bowel bacterial (or fungal) overgrowth.
The 3 Keys to Addressing Small Intestinal Bacterial Overgrowth Syndrome (SIBO)
So now, we have the convergence of three factors coming together to create and perpetuate the small bowel overgrowth syndrome.
• Diet - We have a diet that is high in starches, sugars and fermentable sugars. And we have bacteria and fungus remaining on food or coming up from the large bowel that is fermenting in the wrong place, the small bowel.
• Motility - These food and bacteria are not moving along as fast as they should into the large bowel. And they are doing what bacteria do. They are fermenting. This slowness can be easily apparent when there is IBS constipation. But motility can be low even when there is not obvious constipation.
Too often, factors such as slow motility due to diabetes or hypothyroidism are not addressed.
Hyperthyroidism or different bacteria can also cause too fast of movement through the bowel, resulting in diarrhea, referred to as IBS-D or IBS diarrhea.
• Recognition - And lastly, as a whole, conventional medicine does not recognize SIBO (or SIFO) as being a potential problem.
Diagnosis and treatment are postponed and the problem continues without help. Furthermore, the role of diet is not appreciated.
Let's talk a little more about these three factors
1) Diet - A lot of us tend to eat a highly fermentable diet: high starch, high processed carbs, high sugar, and simply too much of those things over and over. This diet is a perfect setup for SIBO and general bacterial imbalance.
Also, the result of this diet is often heart burn, or GERD, which then leads to a prescription for acid blockers, which reduces the very acid that is needed to help with food digestion and microbial killing.
This high sugar diet all too often also leads to diabetes or insulin resistance.
But diet is something we can actively take steps to change.
2) Motility - We don't pay as much attention as we should to problems that cause low gut motility. Two big reasons for low motility are diabetes and hypothyroidism, even with thyroid medication treatment.
But there are step we can take with diet, supplements, and sometimes medications, that can help reduce those conditions and help improve the ability of the intestines to move food through.
3) Recognition - Conventional medicine tends to avoid thinking about diet and intestinal microbial overgrowth as being behind problems like IBS, GERD and "functional" bowel problems such as bloating, diarrhea, constipation, and even fibromyalgia and chronic fatigue syndrome.
Instead, there is a trend to use medications for symptom control, which allows the root problem to continue on unaddressed.
But diet, repairing healthy microbial balance, and testing and treating for SIBO and fungal overgrowth are things we can do something about.
What To Do To Diagnose and Treat SIBO (and Fungal Overgrowth)
In medical school, training, and even in practice, I was taught repeatedly that small bowel bacterial overgrowth was a pretty uncommon problem. I was taught that fungal overgrowth was nonexistent. But they are not. And, when combined with general bowel overgrowth, they are very common.
Fourteen percent of the population has IBS, which we now know is often associated with SIBO, and can be treated, as I talked about in this post.
In fact, the idea that the gut microbiome is important in many aspects of health is becoming more and more apparent.
Everybody is different. Some people will have underlying diabetes. Some will have hypothyroidism. Some will have autoimmune issues or food sensitivities. Some will have bacterial overgrowth problems, while others will have fungal overgrowth, or Candida, problems, or both.
So what to do is not one size fits all. There are some basics though that are a general roadmap to identifying and resolving small bowel overgrowth. and general bowel overgrowth syndromes.
The basic approach to IBS treatment and SIBO treatment is fairly straightforward:
1) Test with a hydrogen and methane breath test (SIBO breath test), and a stool test.
In many cases it is important to do testing to rule out Celiac disease as well. The breath test only tests for whether or not bacteria are making hydrogen or methane gasses in the small bowel due to their fermentation process.
Bacteria can make hydrogen sulfide gas as well. At this time, the breath testing technology available can not detect hydrogen sulfide. However, stool testing does detect the main bacteria that makes hydrogen sulfide.
It does not tell you anything about bacteria or fungus that are in the small bowel that do not make hydrogen or methane gases.
The stool test only tells about the small bowel indirectly, but it is useful for the large bowel as well and for seeing what actual bacteria, fungus or parasites are present. It also gives information about digestion.
Neither test is perfect but they are the best we have. If suspicion is high, it can be reasonable to go ahead with a "cleanse" type of plan that goes straight to diet and supplements.
There is also now a test that can be used to determine if chronic diarrhea is due to diarrhea predominant IBS, the IBSCheck test . The test is designed to determine if the diarrhea is a chronic response to a previous episode of gut infection. This is often called post-infection IBS.
If this test is positive, then you would still go ahead with testing for SIBO but could often avoid other invasive testing with colonoscopy or endoscopy.
2) Remove the offending bacteria.
There are several ways to reduce bacteria. You can do it with a combination of dietary change and either antibiotics or herbals that have antibiotic properties.
Some SIBO diet methods that are helpful are elimination diets, low carbohydrate Paleo or Primal/Ancestral diets, a low FODMAPS diet, GAPS diet, and sometimes an elemental diet.
Common antibiotics used are Xifaxan, Neomycin and Nystatan as well as herbal regiments that can include berberine, garlic, oregano, neem and other herbs .
3) Restore a more normal bacterial microbiome.
Restoring the microbiome is more complex than just taking probiotics. Restoring bacterial balance involves the right diet, the right balance of probiotics or fermented foods, and taking steps to keep the gut motility optimized.
While some people benefit from higher doses of probiotics, others will have problems with almost any probiotics. Some people do better with fermented foods. Others will have problems with fermented foods as well as probiotics.
And some people can have a dangerous build up of D-lactate, either from the bacteria they started out with, or from common probiotics or fermented foods that produce D-lactate [7,8], such as acidophilus.
It is not necessarily as easy as just taking a bunch of probiotics.
4) Rejuvenate the normal bowel.
Many people have developed leaky gut, food sensitivities and other problems due to long standing SIBO or fungal overgrowth. Taking steps to heal the intestinal mucosa and sustain a healthy intestinal microbiome for the long term is the last step.
Depending on the person, different IBS or SIBO diets can be used to address individual problems. A low carbohydrate Paleo or Ancestral type diet is very useful, but other diets such as low FODMAPS, GAPS, and the AIP diet can help as well. High nutritional value, low sugar, inflammation quenching, and food sensitivity calming, are what they all share.
Finding the right diet, the right way to keep proper motility going, the best way to keep bacteria balanced, whether it be with diet, fermented foods, or probiotics, and the use of appropriate supplements, is important.
1) Lin, H. C. (2004). Small Intestinal Bacterial Overgrowth. JAMA, 292(7), 852. https://doi.org/10.1001/jama.292.7.852
2) Pimentel, M., Chow, E. J., & Lin, H. C. (2003). Normalization of lactulose breath testing correlates with symptom improvement in irritable bowel syndrome: a double-blind, randomized, placebo-controlled study. The American Journal of Gastroenterology, 98(2), 412–419. https://doi.org/10.1111/j.1572-0241.2003.07234.x
3) Erdogan, A., & Rao, S. S. C. (2015). Small Intestinal Fungal Overgrowth. Current Gastroenterology Reports, 17(4), 16. https://doi.org/10.1007/s11894-015-0436-2572-0241.2003.07234.x
4) Brechmann, T., Sperlbaum, A., & Schmiegel, W. (2017). Levothyroxine therapy and impaired clearance are the strongest contributors to small intestinal bacterial overgrowth: Results of a retrospective cohort study. World Journal of Gastroenterology, 23(5), 842–852. https://doi.org/10.3748/wjg.v23.i5.842
5) Pimentel, M., Purdy, C., Magar, R., & Rezaie, A. (2016). A Predictive Model to Estimate Cost Savings of a Novel Diagnostic Blood Panel for Diagnosis of Diarrhea-predominant Irritable Bowel Syndrome. Clinical Therapeutics, 38(7), 1638–1652.e9. https://doi.org/10.1016/j.clinthera.2016.05.003
6) Chedid, V., Dhalla, S., Clarke, J. O., Roland, B. C., Dunbar, K. B., Koh, J., … Mullin, G. E. (2014). Herbal Therapy is Equivalent to Rifaximin for the Treatment of Small Intestinal Bacterial Overgrowth. Global Advances in Health and Medicine, 3(3), 16–24. https://doi.org/10.7453/gahmj.2014.019
7) White, L. (n.d.). NUTRITION ISSUES IN GASTROENTEROLOGY, SERIES #145 D-Lactic Acidosis: More Prevalent Than We Think? Retrieved from https://med.virginia.edu/ginutrition/wp-content/uploads/sites/199/2014/06/Parrish-September-15.pdf
8) Kowlgi, N. G., & Chhabra, L. (2015). D-lactic acidosis: an underrecognized complication of short bowel syndrome. Gastroenterology Research and Practice, 2015, 476215. https://doi.org/10.1155/2015/476215
Dr Ann Haiden DO is an internal medicine physician and functional medicine specialist, two time breast cancer survivor, multiple other things survivor, and advocate of a low carb, plentiful produce, Paleo Ancestral eating and living lifestyle.
If you would like to work with Dr Haiden for personalized medical care, we invite you to find out more about her clinic and how to become a patient.
Dr. Haiden's clinic is in Los Gatos, California, in the greater San Jose and San Francisco Silicon Valley area.
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