Are these bad boys trashing your gut?


Small intestinal bacterial overgrowth (SIBO) is exactly what it sounds like, an overgrowth of pathogenic or harmful bacteria in the small intestine, and I think a lot of people are walking around with this medical condition but have no idea they have it. Partly because most people have never heard of it and partly because many doctors don’t screen for it when someone comes to their office complaining of GI issues. I certainly wasn’t screened for it when I was diagnosed with IBS and I’m sure this is not unusual.

As I’ll discuss in the next post, a number of diseases like irritable bowel syndrome, various inflammatory bowel diseases, gluten intolerance, celiac disease, alcoholic and non-alcoholic fatty liver disease, fibromyalgia, rheumatoid arthritis, restless leg syndrome, rosacea and interstitial cystitis (bladder pain syndrome) have all been associated with SIBO. In reality, however, given the inflammation caused both in and outside the gut, the list of diseases associated or caused by this disorder is quite lengthy.

Let me just say that I’m not a big fan of the term small intestinal bacteria overgrowth. Not because there isn’t an overgrowth of pathogenic bacteria in this part of the digestive tract, but because I think it’s highly unlikely that unfriendly bacteria are the only type of organism causing trouble.

Yeast is a normal constituent of our digestive tract and normally kept in check by our friendly gut flora. Once commensal gut flora are disturbed for whatever reason, their ability to keep this yeast in check is also compromised. This is a major reason so many people develop yeast overgrowth issues after a course of antibiotics. I find it implausible that anyone presenting with SIBO doesn’t also have this issue. I sure as hell did.

Perhaps this is the reason some patients don’t respond to a course of antibiotics when being treated. It could be they also need an antifungal to control a Candida albicans overgrowth. I’ll talk more about this when I post on treatment options.

 So what exactly is SIBO?

SIBO is defined as an overgrowth of bacteria either originating from the mouth/upper respiratory tract or colon that has taken up residence in your small intestine where they don’t belong. Once this occurs all sorts of nasty things begin to happen.

As noted in my earlier post on beneficial gut flora, the small intestine has relatively few native bacteria when compared to your colon. SIBO is usually diagnosed when colony-forming units exceed 105 units per millimeter in fluid removed from the small intestine (a procedure known as aspiration), although some controversy surrounding this medical definition exists. Some researchers and physicians think the diagnoses should be made at even lower concentrations as long as tests find bacteria that don’t normally live in this part of the digestive tract and I fully agree.

Although aspiration is considered the “gold standard”, it isn’t perfect, but hey, what is? There’s the possibility of contamination with bacteria from your mouth or throat. Who’s to say that the bacteria in the aspirate fluid didn’t actually come from these areas?

And SIBO, like celiac disease, is often patchy meaning that one area of your small intestine could have an overgrowth but be clear of pathogens just a short distance away. Finally, there are a lot of bacteria that can’t be cultured so while you may actually have a pathogenic overgrowth, the test may come back negative.

Because aspiration is invasive, another test is normally used that measures levels of hydrogen in the breath after ingesting a non-digestible carbohydrate, usually lactulose. The theory behind this is that if the test detects hydrogen in your breath before lactulose reaches your colon, then the small intestine is colonized by bacteria fermenting what should only be fermented in the colon.

I won’t go into the particulars of this test, but I do want to mention that it isn’t always accurate. There are many false negatives, especially in someone whose malabsorption of carbohydrates is seriously advanced. For these folks lactulose just sails right through the small intestine and enters the colon giving the clinician no hint that anything is wrong. Previous antibiotic therapy or diarrhea could also return a false negative. Finally, just over 25% of the population produces methane instead of hydrogen so if the test doesn’t also measure methane, you’ll be told all’s fine when in reality it isn’t.

For all these reasons, a good clinician will rely on other tests and symptoms to determine the presence of SIBO. Many use stool tests to look for the presence of pathogenic bacteria, yeast and undigested fat and protein.

If the infection is from the mouth/respiratory tract, the pathogenic bacteria that overgrow in the small intestine are usually of the gram-positive variety. If, however, the infection is from the colon, the predominant bacterial types are gram-negative and more apt to result in malabsorption issues. Nevertheless, there are exceptions to this general rule. I’ll have a bit more to say about the difference between these two types of bacteria in a future post.

SIBO symptoms

Common symptoms of SIBO are gas, bloating, diarrhea, constipation, fat in the stool, anemia, B12 deficiencies and increased intestinal permeability. Do these symptoms strike any of you IBS (or gluten) sufferers as vaguely familiar? Yeah I thought so.

Malabsorption affects all macronutrients: carbohydrate, fat and protein.

Carbohydrate malabsorption is due to both fermentation of carbs in the small intestine and the damage done to the intestinal brush border caused by the byproducts generated by these same bacteria. Fermentation will contribute to diarrhea as the production of fatty acids is a result. Fats tend to speed up the plumbing if you know what I mean.

Another way carbohydrate malabsorption causes diarrhea is because undigested carbohydrates enter the colon. This pulls water rapidly from the body leading to that oh-so-awful and potentially embarrassing dash to the nearest toilet.

Pathogenic bacteria in the small intestine will inhibit bile from properly breaking down fat (in medical jargon this is called bile deconjugation) leading to fat malabsorption and fat in the stool or steatorrhea. Stool will be especially foul smelling, gray in color and appear greasy. If after you flush, lots of fecal matter is still adhering to the side of the toilet bowl, this is also a good sign that you’re not absorbing fat properly.

Fat malabsorption will inevitably lead to malabsorption of all fat-soluble vitamins (A, D, E and K) and most minerals as both fat-soluble vitamins and minerals rely on proper fat digestion to pass through the intestinal wall and enter the portal vein leading to your liver.

The deconjugation of bile will also lead to the production of a substance called lithocholic acid that can be directly toxic to the cells (enterocytes) lining your digestive tract. Toxicity equals inflammation, and inflammation equals the very real possibility of developing an inflammatory bowel disorder if this goes on long enough.

Inflammed enterocytes in turn will contribute to increased intestinal permeability or “leaky gut” and all the negative consequences resulting from this. Increased intestinal permeability leads to more inflammation, which attracts more pathogenic bacteria resulting in a vicious feedback loop that can be difficult to resolve. Throw in Candida overgrowth for good measure and you’ll soon wonder who you pissed off in a past life.

Protein malabsorption can lead to loss of muscle mass and low albumin levels in your blood as your body becomes protein starved. Normal repair and recovery of protein structures in your body are therefore impaired. Finally, maldigested protein will result in potentially toxic amounts of ammonia as ammonia is a byproduct of protein degradation caused by bacteria adding even more insult to already damaged enterocytes.

Abundant amounts of gas are produced by all this fermentation of food in the small intestine and by the increased amounts of undigested carbohydrate, fat and protein that now enter the colon. Here, colonic bacteria try to break it down adding further to the gas produced in the small intestine. You’ll be producing so much gas Goodyear® could use you to fill their blimps!

If you’re lucky, you’ll pass plenty of wind, although those unfortunate enough to be near you will feel anything but fortunate. If you’re unlucky, (and boy was I ever) the ability to fart and move things along will be impaired as many of these pathogenic organisms negatively affect intestinal movement. Gas continues to build up but has no where to go resulting in painful bloating and the “sexy” profile of a six-month pregnant woman. Fun times!

I do want to mention that gluten opioids will also slow intestinal movement so it can be hard to tell whether it’s gluten or toxic bacterial metabolites causing the paralysis of the gut. For me, cutting gluten out of the diet resolved the bloating and constipation but did not resolve yeast and bacterial overgrowth. A very good case can be made that it’s a combination of both leading to the inability to pass gas.

These pathogenic bacteria eat and guess where they get their food? Yep, that food you just ate gets eaten by the pathogenic organisms residing in your small intestine and will often have first shot at any nutrients contained therein.

Pathogenic bacteria also love, love, love iron so don’t be surprised when your doctor tells you you’re anemic even though there isn’t any hint of bleeding anywhere, and you eat plenty of iron-rich food. Vitamin B12 deficiencies are also a big problem in those with SIBO.

In the next post, I’ll cover some diseases that can result from all this intestinal mayhem…



Unlike earlier blog posts, I’m not including a full reference section anymore. This is a blog, not a term paper, and citing a reference for each statement of fact is getting very old, very fast. So from this point on I’ll just include references to overview articles, and you can delve deeper by viewing the references they cite.


Bures J., Cyrany J., Kohoutova D., et al. (2010) Small intestinal bacterial overgrowth syndrome. World Journal of Gastroenterology, 16(24): 2978-90.

Parodi A., Lauritano E.C., Nardone G., Fontana L., Savarino V., Gasbarrini A. (2009). Small intestinal bacterial overgrowth. Digestive and Liver Disease, (3), 44-49.

Quigley E. M. M., Quera R. (2006). Small Intestinal Bacterial Overgrowth: Roles of Antibiotics, Prebiotics and Probiotics. Gastroenterology, 130: S78-S90.

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