Bacteria 2 - What Is SIBO? Is It Giving You Digestive Woes?

What Is SIBO? Is It Giving You Digestive Woes?

Bacteria 2 300x212 - What Is SIBO? Is It Giving You Digestive Woes?

Updated July 2019


Bacteria have been part of the human experience since the very beginning.


Ever since the germ theory of disease was accepted, we’ve been fighting bacteria in the hopes of ridding ourselves of every ailment known to humankind.


Bacteria have always been seen as something negative, but we now know better.


Fast forward to today and we now appreciate the essential role bacteria and other microorganisms play in our health and well-being. It’s estimated that we host about 100 trillion of them in, on and around us. In every nook and cranny and of course, loads of them are found in our digestive tract where they perform vital roles.


This includes protecting us from other microorganisms that can make us sick, stimulating our immune system, and helping to digest food while synthesizing various nutrients to name a few (1).


Even though we live in harmony with our bacteria most of the time, there are situations where bacteria that are normally helpful, can be a problem. When that happens, our health can take a turn for the worse as is the case with Small Intestinal Bacterial Overgrowth or SIBO.

Keeping gut bacteria balanced

We have bacteria along the entire length of our digestive tract, from ‘snout to tail’ as they say.


The mouth, stomach and small intestines have relatively few bacteria compared to the large intestine or bowel.


For example, the first 90% of the small intestine has between 1,000 and 10,000 organisms per one milliliter (one-fifth of a teaspoon) of intestinal fluid.


GI bacterial distribution - What Is SIBO? Is It Giving You Digestive Woes?

Photo credit


That number increases towards the end of the small intestine; where it connects to the colon. The bacterial count in the last one-third or so of the small bowel, called the ileum, is home to some 10,000,000 (10 million) organisms per one milliliter of fluid.


Things REALLY take off in the colon; some 1, 000, 000,000,000 (one trillion) organisms are jam-packed in every milliliter of fluid in the large intestine. A number that is basically unimaginable.


There are more microorganisms in your digestive tract than there are stars in the Milky Way galaxy – amazing!


Your defenses against bacterial imbalance

Your body is built to withstand unnecessary imbalances where gut bacterial real estate is concerned but, like anything, your gut can run into trouble.


In a healthy gut, bacteria in the lower part of your small intestines are prevented from over-growing AND other micro-organisms from the bowel are normally barred entry.


Keeping bacteria in check is achieved with several defenses (2, 3):

  • Primary defense is the hydrochloric acid in your stomach. With a very low pH, stomach acid kills most of the bacteria that enter your mouth (food, drink, utensils, fingers etc).
  • Pancreatic enzymes & bile which are used to digest food also destroy any bacteria/microorganisms that survived the acid bath in your stomach.
  • The resident bacteria that live in your gut and the cells that line your digestive tract also secrete antimicrobial chemicals that kill off foreign bacteria.
  • 80% of your immune system is found in your digestive tract, loads of immune cells keep unwanted bacteria in check.
  • A series of contractions in the intestines (peristalsis and the migrating motor complex) help to ‘sweep’ bacteria along towards their final destination [poop and the toilet].
  • A valve or sphincter, called the ileocecal valve, acts as a one-way gate between the very end of the small intestines and colon. This valve prevents colonic bacteria/microorganisms from sneaking back into the small intestines.

What is SIBO?

Under normal circumstances, the proportions of our gut bacteria are maintained within a normal physiological range and health thrives via the defenses listed above.


But there are times when these defenses can go awry and the amount, and type, of bacteria in the small intestine can increase in number leading to bacterial overgrowth , a.k.a. ‘SIBO’.


It’s important to note that SIBO isn’t about an overgrowth of some kind of foreign bacterial strain or invader. SIBO is not an “infection”. It’s not something you catch/acquire like the bacteria that cause food poisoning.


SIBO is a condition in which the bacteria that normally reside in the lower part of the small intestine overgrow. This leads to an excessive amount of ‘normal’ bacteria which is problematic. Think of it as a nightclub that is WAY over capacity; far too many people are packed in. It’s not the individuals themselves but when they’re that packed, trouble often follows.


SIBO also occurs when bacteria that normally resides in the bowel migrate up into the small intestine where they encroach on their newly found territory. The bacteria and microorganisms that live in your large intestines are never given permission to leave under normal circumstances. When they end up where they don’t belong, they also become trouble-makers.


The location and concentration of bacteria throughout the digestive tract is very important when it comes to maintaining health. There are relatively few throughout the length of the tract until the large intestine/bowel where there is a nearly incomprehensible amount of them: 1 trillion per ml or 5 trillion per teaspoon!!


With SIBO however, the ideal location and quantity of bacteria is anything but.


Bloated - What Is SIBO? Is It Giving You Digestive Woes?


Why is SIBO a concern?

SIBO is more than just the inconvenience of a handful of symptoms. If it was just a case of uncomplicated bloating, gas or occasional belching, it could be managed painlessly. The problem with SIBO is the impact on the digestive tract both in terms of the digestive tract’s structure and function.


SIBO causes a lot of digestive woes by damaging the gut.


Bacteria produce metabolic waste that irritates the gut lining leading to inflammation. The inflamed gut tissue damages enzymes that normally line the digestive tract (brush boarder enzymes) (4, 5). They help to digest the foods you eat. An inflamed gut lining with fewer digestive enzymes leads to the maldigestion of protein, fat and carbohydrate.


Carbohydrate maldigestion is particularly problematic with SIBO (2, 3).


When carbohydrates become a problem

Undigested carbohydrates [sugars, starches, fibers] become a food source for the bacteria. As they feed, they populate rapidly leading to the overgrowth.


Remember, SIBO is nothing more than having too many bacteria in an area where they don’t normally exist in large numbers. Too many “normal” bacteria = increased bacterial activity. They eat, produce their own waste, secrete their own digestive enzymes, and die off like all living things. Increased bacterial death leads to increased bacterial decay all of which takes its toll on your digestive tract.


Colonic bacteria produce a lot of gas (CO2, methane and hydrogen) under normal circumstances. But, when those bacteria have taken up residency in your lower small bowel, excess gas increases internal pressure which can lead to reflux. This gas is also the source bloating and pain that comes with SIBO.

Carbs and gas. What’s the connection?

Bacteria ‘exhale’ gas as they eat. If there’s loads of bacteria at an all you can eat carbohydrate buffet (the food you eat), they gonna produce lots of gas, but how much really?


Anyone wondering if enough gas could be produced to cause enough pressure leading to excruciating pain, or even reflux consider this: just 30 g of carbohydrate (the amount found in an apple and a slice of bread or the weight of 6 nickels) is enough carbohydrate for bacteria to produce 10 liters (about 2 1/2 gallons) of gas!!!


The impact of this makes sense when you consider the volume of the small intestines which is about 1 L. As they say, you do the mass; 1 liter of available space to hold 10x as much gas?!?! The increased volume of gas cause the intestines to expand, and that stretching strains the nerves causing pain.


This excess gas has to go somewhere so it makes its way up upstream.

Bloated word cloud - What Is SIBO? Is It Giving You Digestive Woes?

SIBO symptoms

Symptoms can vary from person to person, and within those who have recurrent SIBO episodes but some of the more common ones are (2, 3):

  • Post-prandial bloating (usually extreme) specifically bloating up under the ribs
  • Gas/flatulence and belching
  • Brain fog
  • Unintended weight loss
  • Intestinal pains/cramping
  • Diarrhea, constipation or both
  • Depression and anxiety
  • Indigestion
  • Heartburn/reflux
  • Nutrient deficiencies
  • Nausea
  • Weight loss
  • Fatigue
  • Joint pain

Of course, symptoms alone are not enough to diagnose SIBO despite loads of information and other self-stylized practitioners on line who insist otherwise. SIBO testing should be part of a comprehensive assessment and be seen as another tool for diagnosis.

SIBO causes

  • Scarring/strictures in digestive system
  • Digestive tract structural abnormalities
  • Immunodeficiency
  • Hypochlorhydria
  • Low stomach acid (especially in the aging population)
  • PPIs [Nexium, Pantaloc], acid reducers [Zantac],  antacid use
  • Frequent use of antibiotics
  • Frequent steroid use
  • High stress lifestyle
  • Motility problems
  • Poor diet (high sugar, high carbohydrate)
  • Enzyme & bile acid insufficiency/deficiencies
  • Carbohydrate malabsorption/maldigestion
    • Lactose, fructose, sugars, resistance starch


Diabetes self blood sugar testing - What Is SIBO? Is It Giving You Digestive Woes?

Conditions associated with SIBO

Most gastrointestinal symptoms resolve with a little detective work; getting to the root cause is crucial. However, for any symptoms mentioned above that do not resolve with the usual medical or dietary interventions, SIBO should be considered.


Those who should be tested for SIBO are those with any of the symptoms listed above AND who have any of the following conditions that track with SIBO (2, 6).

  • Diabetes (7)
  • Liver or pancreas disease (8, 9, 10)
  • Celiac disease (11, 12)
  • Non celiac gluten sensitivity
  • Inflammatory bowel disease (13, 14).
  • Hypothyroidism (15)
  • H. pylori infection (16)
  • Gastroparesis (17)
  • Gallstones & gallbladder removal (18, 19)
  • Compromised immunity (HIV, IgA deficiency, stress, functional deficiencies) (20, 21)
  • Rheumatoid Arthritis (22)
  • Irritable bowel syndrome (23)
  • Short bowel syndrome (24, 25)
  • Chronic fatigue syndrome (26)
  • Chronic constipation (27)
  • Rosacea (28)
  • Overweight & obesity (29, 30)
  • Scleroderma (31, 32)
  • Restless leg syndrome (33)
  • Interstitial cystitis (34)
  • Liver cirrhosis (35, 36)
  • Fibromylagia (37)
  • Parkinson’s disease (38, 39)

As with any health-related issues or conditions, not everyone at risk for something will in fact have that condition. The same goes with SIBO. Not everyone who has classic symptoms, who also has an associated condition will have SIBO.

Nutritional Implications

Another common problem with SIBO is the risk for clinical and functional micro-nutrient deficiencies (7).


Nutrients needed for health are preferentially used by the bacteria themselves. This reduces the amount of nutrients available for  absorption for the person with SIBO leading to decreased nutrient absorption. As well, any gut inflammation or damage and result in micronutrient malabsorption.


Functional and/or clinical nutrient deficiencies can include:

  • Vitamin B12
  • Vitamin A
  • Vitamin D
  • Vitamin E
  • Iron
  • B-vitamins

Nutrients spheres - What Is SIBO? Is It Giving You Digestive Woes?Testing for SIBO

Testing for SIBO is not perfect (but then a lot of tests in medicine aren’t), and this one of the main criticisms of testing. The two types of testing are small intestine aspirate and culture (to count how much bacteria are present in intestinal fluid) or breath testing (to test for the presence of hydrogen and methane).


What is the best SIBO test? The reality is, they both have their strengths and weaknesses. The aspirate test is expensive and invasive so most choose the breath test.


Over the years, I’ve heard from countless clients and patients that their gastroenterologists have dismissed the notion of SIBO. Other MDs who are aware of SIBO won’t do breath testing. Perhaps it’s because testing is not perfect and if the doctors aren’t confident with a diagnosis, they’ll choose not to treat and figure there’s not point in testing.


Other health practitioners such as naturopathic doctors or functional nutritionists will typically use SIBO breath testing .


How to interpret hydrogen breath tests. Journal of Gastroenterology & Motility


Regarding interpretation, there is no universally accepted standard (40). As mentioned, breath tests are not perfect but they can help provide more information than simply going on symptoms alone.

How is the breath test done?

It’s based on the same principle of the low FODMAP diet. Testing relies on the fact that bacteria produce gases when the ferment (consume/expire gas) carbohydrate. The main gases produce by gut bacteria are hydrogen, which some bacteria consume and convert into methane, and hydrogen sulfide (41, 42).


In a nutshell, you would prepare for the SIBO test as instructed, drink a carbohydrate solution such as glucose, lactulose or both, and have breath samples taken every 20 minutes or so. Depending on what is collected (hydrogen, methane), when (at which time interval) and how much, a positive or negative diagnosis is made.

Potential problems with SIBO testing

When preparing for a breath test, strict adherence to the pre-test steps is crucial to minimize problems. That’s because many different things can alter your gut, gut bacteria and any potential gas production produced by your microbiota. You need to do everything you can to avoid a false negative or positive (43).


The following needs to be considered:

  • Antibiotic and antifungal use prior to the test. These can kill off some of the problematic bacteria, but not fully eradicate them. This will reduce the amount of hydrogen and/or methane production leading to a false negative (43, 44, 45, 46)
    • Recommendations are to wait 2 to 4 weeks after using any antibiotics before testing
  • Laxatives can also interfere with test results. This includes anything with a laxative effect such as magnesium and high dose vitamin C. More potent laxatives can ‘wash out’ some of the bacteria (temporarily reducing the amount in your gut) which can lead to a false negative (47).
    • Wait at least 4 to 7 days after using a laxative product before testing
  • Fermentable carbohydrates such as high FODMAPs, prebiotic fibers or commonly problematic sugars like lactose, fructose or resistant starch. These may promote the growth of bacteria which can lead to methane/hydrogen production above your typical level leading to a false positive
  • Avoid heavy exercise prior to the test. Increased respiration rate can lead to a decrease in breath hydrogen. You can literally ‘blow off’ the excess hydrogen leading to a false negative (48). Also. exercise can alter the overall response to lactulose (if using lactulose as the test sugar), interfering with the breath test results (49).
  • Unless otherwise directed by your doctor or health care provider, avoid PPIs one week prior to testing.

SIBO treatment

Forward thinking gastroenterologists who understand what SIBO is and its impact on patients will often treat with antibiotics without testing.


Treatment is complex and must be individualized. Treatment is always informed by a comprehensive assessment of symptoms, risk factors and predisposing conditions that puts someone at risk for SIBO.


A thorough assessment should include a breath test to measure the gases expelled by the bacteria, despite some of the limitations of testing.


Some conventional and integrative/functional medicine practitioners will treat based on risk factors and symptoms alone after ruling out other more likely causes of symptoms (Celiac, IBD etc). This is referred to as “treating empirically”; treatment based on clinical experience and using clinical judgment.


The ideal approach to treating SIBO is to treat the underlying disease, manage comorbidities and risk factors that increase the risk for SIBO, eradicate or reduce the overgrowth of bacteria, and address nutritional deficiencies that may be associated with, and/or result from SIBO itself (42).


Despite best efforts to address risk factors and to manage conditions that increase the risk for SIBO, some kind of anti-microbial treatment is required whether that’s with antibiotics or antimicrobial herbs.


Antibiotics typically used in the treatment of SIBO are:

  • Rifaximin (43)
  • Ciprofloxacin (44)
  • Norflaoxacin (45)
  • Amoxicillin/clavulanate (46)
  • Metronidazole & trimethoprin/sulfamethoxazole (47)
  • Metronidazole & cephalexin (47)
  • Rifaximin & neomycin (48)

You’ll read lots of stuff on the internet about how ineffective antibiotics are when it comes to treating SIBO. The reality is, SIBO often requires more than one round of antibiotics. This can depend on several factors but suffice it to say, while not impossible to treat, SIBO does require a thoughtful approach to treatment.


Many gastroenterologists will simply prescribe standing antibiotic treatments. For example, at one hospital here in Toronto, a GI doc prescribes 1 week of Flagyl (Metronidazole) every month or so in a maintenance fashion. Other approaches include prescribing a course of antibiotics and wait to see if symptoms return. Often, because no other changes have been made by the patient, recurrent treatments are necessary.


Oregano fresh leaves - What Is SIBO? Is It Giving You Digestive Woes?


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Antimicrobial herbs

Rifaximin (Zaxine in Canada) is the most commonly prescribed antibiotic treatment for SIBO. Antibiotics do have a time and place but they’re not without their issues which is beyond the scope of this post. As such, herbs with antimicrobial properties provide an additional choice and are appealing to people for a few reasons.


Herbs have fewer unintended effects (so-called “side effects”) and have a wider range of antimicrobial properties. As well, there’s virtually no meaningful risk for resistance. Understandably, there’s a lot of suspicion about the effectiveness of herbs but many, such as berberine, olive leaf extract, garlic and oil of oregano, for example, have well documented antimicrobial effects (49, 50, 51, 52, 53, 54).


Herbal therapy is equivalent to rifaximin for the treatment of Small Intestinal Bacterial Overgrowth


A randomized controlled trial looked at specific standardized herbal supplements in various combinations and found that they performed as well, and even better, than standard antibiotic treatment (55). The study used two products by Biotics Research FC-Cidal* and Dysbiocide*, as well as, two products by Metagenics Candibactin-AR* and Candibactin-BR*. Other protocols will often include an emulsified oil of oregano such as ADP* from Biotics Research and a standardized garlic extract such as Allimax*.


Regardless, SIBO can be tricky to get rid of and any treatment needs to include addressing underlying risk factors to help prevent it from recurring. A simple round of antibiotics a few times a year has not been shown to help, a more integrative and holistic approach is needed.

Nutrition support

In addition to either antibiotic or herbal treatment, nutritional support includes dietary modifications to help address the bacterial overgrowth and its symptoms. There are several approaches that can be leveraged such as a low FODMAP diet, Specific Carbohydrate Diet or a lower-carbohydrate, higher-fat variation.


The concurrent use of evidence-informed supplements are typically part of the healing protocol. They help to address any gut inflammation, as well as, address any functional and/or clinical nutrient deficiencies (Multi Basics 3, Ortho Core, B-Right Optimized B-Complex, D3 & K2).


Does this sound like you or someone you know? Yes! Then grab a  free introductory call to learn more about my SIBO treatment protocol

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Bottom line

Once a highly contested diagnosis, small intestinal bacterial overgrowth – SIBO – has gained traction as a legit explanation for a variety of gastrointestinal symptoms. This interest is supported by ongoing empirical evidence.


There are now several documented risk factors for SIBO including medical conditions, so-called lifestyle factors and issues of the the gastrointestinal tract itself. Because symptoms can overlap with many other conditions, it’s important to rule them out first and not diagnosis SIBO by symptoms alone.


Left unchecked, SIBO does have negative health consequences. Testing for SIBO is possible and the most popular choice is breath testing. While not without its limits, breath testing can help to provide clarity to the source of your symptoms so that proper treatment can be started.


Antibiotic treatment, along with dietary modifications and nutritional support are needed to eradicate the excess bacteria that are causing symptoms while getting to the root cause of SIBO itself. For those who want a non-pharmacological option, the use of evidenced-based antimicrobial herbs is an option.


Doug Cook RDN is a Toronto based integrative and functional nutritionist and dietitian with a focus on digestive, gut, mental health.  Follow me on FacebookInstagram and Twitter.