What is SIBO?

There are somewhere between 1-10 trillion (with a “T”) microbes living in our intestines.  Most of them call the colon (or large intestine) home. 

Small intestinal bacterial overgrowth (SIBO) is a state in which too many microorganisms make their way into the small intestine.  When there is overgrowth, some bacteria (both good and bad strains) can migrate into the small intestine, and can lead to a variety of different health problems, both acute and chronic. 

SIBO damages the small intestinal cell wall, and can create leaky gut syndrome in the area, resulting in food allergies, sensitivities, and chronic inflammatory processes.  Symptoms can range from mild to severe, depending on the damage.  Some other symptoms can include: gas, bloating, diarrhea or constipation, abdominal pain/cramping, skin disorders, IBS, fibromyalgia, autoimmune conditions, diabetes, neuromuscular disorders, and fat malabsorption.  Luckily, functional nutrition providers can be of great help in these cases.

But before we get to that, let’s break down how and where bacteria are supposed to be normally.  The first two parts of the small intestine (the duodenum and jejunum) normally contain very small amounts of bacteria.  The final part of the small intestine, the ileum, does not contain a lot of bacteria either (more than the ileum and jejunum, however), but tends to be affected the most when it comes to SIBO.  There is a valve, known as the ileocecal valve that separates the small intestine from the colon.  When microbes are able to traverse the valve and inhabit the ileum in large numbers, SIBO occurs.  This increase and imbalance of bacteria are what eventually cause the symptoms associated with the condition.

SIBO can lead to maldigestion and malabsorption, as the bacteria interfere with the enzymes and normal metabolism of the food we eat.  Maldigestion refers to our inability to properly break down the food we eat, while malabsorption is our inability to absorb the nutrients we need efficiently.  Nutrients like iron and vitamin B12 are absorbed in the small intestine and can be affected by SIBO; if they are not properly absorbed, it can lead to microcytic anemia or macrocytic anemia, respectively.

In addition to this, the bacteria that invade the small intestine are also associated with endotoxin formation, as well as other compounds the stimulate the production of pro-inflammatory mediators known as cytokines.

The sheer amount of microorganisms and the metabolic waste they produce can have quite a burden on the body.  Additionally, the number of microbes that make it to the ileum are not the only factor that plays a role in dictating the symptoms and signs of SIBO.  The types of microbes are just as important.  For example, if the invading bacteria break down bile salts, it can lead to fat malabsorption and diarrhea. On the other hand, certain organisms metabolize carbohydrates to short-chain fatty acids and gas, producing bloating.  Other microbes produce toxins harming the intestinal wall, causing leaky gut syndrome.

How do we even get SIBO in the first place?

We have multiple mechanism in place which, when healthy, keep our intestinal bacteria in check.  When these homeostatic mechanisms are disrupted, it increases the chances of an overgrowth.  The two most common are low stomach acid levels and poor intestinal motility. 

The stomach cannot function properly when we do not have enough stomach acid.  Stomach acid is needed to properly break down protein and reduce bacteria levels in the food we eat. When stomach acid levels are low, the stomach cannot digest food adequately n and larger bacterial loads get into the small intestine.

When the stomach is compromised, large protein molecules make their way into the small intestine.  This puts an incredible amount of strain on the pancreas, because it then has to generate massive amounts of enzymes in an effort to break down the larger food particles.  If this continues over long periods of time, it can lead to pancreatic insufficiency.

Proton pump inhibitors, H2 blockers, and antacids taken for acid reflux create a more basic environment in the stomach.  This leads to less stomach acid, meaning poor digestion and influencing the cycle mentioned above.  Additionally, antibiotics can alter gut flora, resulting in gut issues and potential infections.

When it comes to poor intestinal motility, our gut relies on a harmony of different muscles, nerves, enzymes, and neurotransmitters working in concert to digest food properly.  Enzymes are largely responsible for breaking our food down, but the muscles, nerves, and neurotransmitters need to physically move our food through the entire digestive tract. 

In healthy individuals, microbes get passed through the digestive tract along with the food to its final destination: the colon.  When the pace is slowed down, problems can occur.  Food can get stuck in portions of the large and small intestines.  If it gets stuck, it can then ferment and create the ideal breeding grounds for bacteria and the development of SIBO.

Additionally, when motility is slow, the ileocecal valve, which separates the large and small intestines, can weaken of be held open by feces.  This allows bacteria to move from the colon into the small intestine.  When addressing SIBO, it is crucial to correct any gut motility issues.

Other causes include:

  • Physical obstructions, like scarring (usually from surgery, Crohn’s Disease, or even the buildup of the bacteria themselves)
  • Diverticuli, or tiny pouches that can form in the wall of the small intestine, can also collect bacteria instead of passing it on to the colon
  • Intestinal Neuropathy.  When the nerves or muscles that line the gut are damages, bacteria end up never making it to colon, leading to a buildup in the small intestine.  This can be caused by diabetes or trauma. 

How to Test for SIBO

As always, no one knows your body better than yourself.  History and symptomatology are crucial when making a diagnosis.

In terms of tests, the best test out there is the SIBO Breath Test.  Unfortunately, this is not the easiest test perform.  After fasting for 12 hours, you are to consume a glucose-containing liquid, breathe into a small balloon, and place the sample into a vial.  This process is repeated between 10-15 times over a 3+ hour span.

A stool analysis can also of help.  Stool analyses are useful when looking at the flora inhabit the colon.  Stool analyses are not definitive for SIBO Specifically, however.  Stool analyses are great for looking for overgrowth of pathogenic bacteria and parasites such as H. Pylori, Klebsiella, Candida, Blastocystis, and others.  This is usually done to back up or confirm a SIBO breath test.

Finally, an organic acid test could be a useful option.  Organic acid samples are collected via urine, and can uncover a variety of potential health concerns, including neurotransmitter disruptions, B vitamin deficiencies, mitochondrial issues, oxalate malabsorption, toxicity issues, as well as yeast and bacterial overgrowths.  This is a useful, simple test, but not necessarily diagnostic of SIBO on its own, like the breath test.

How to Treat Small Intestinal Bacterial Overgrowth

  1. The 4R Protocol for SIBO (and the Gut) 

The 4R protocol is a powerful tool that can help with SIBO and other gut issues. For more information about this, check out this blog post: 4 Steps to Repairing the Gut (The 4 R’s).

Also, check out more in-depth analysis of Phase 1 & Phase 2 of this protocol via our podcast, The Art of Eating.

2. A Low FODMAPS Diet

FODMAPS is an acronym Fermentable Oligo, Di- and Monosaccharides and Polyols.  These are all types of sugar based carbohydrates that are found in certain foods and are challenging on the bowel.  These foods have three common functional properties:

1. Poorly absorbed in the small intestine due to:

a) slow, low-capacity transport mechanisms across the epithelium(fructose)

b) reduced activity of brush border hydrolases (lactose)

c) lack of hydrolases (fructans, galactans)

d) molecules being too large for simple diff usion (polyols).

2. Small and therefore osmotically-active molecules. Lactulose is a synthetic FODMAP increases the liquidity of luminal contents and subsequently affecting gut motility

3. Rapidly fermented by bacteria. Fermentation by bacteria is dictated by the chain length of the carbohydrate; oligosaccharides and sugars are very rapidly fermented compared with polysaccharides such as soluble dietary fiber.

Examples of High FODMAP Foods include:

• Fruits

– apples, pears, peaches, cherries, plums, prunes

• Grains

– wheat, rye

• Legumes

– lentils, beans

• Sweeteners

– fructose products, sugar alcohols

• Dairy

• Vegetables

– artichokes, asparagus

– avocado, beets, broccoli

– Brussels sprouts, cabbage

– cauliflower, garlic (with large consumption)

– fennel, leeks, mushrooms

– okra, onions, peas

– radicchio lettuce, scallions (white parts), shallots

– sugar snap peas

– snow peas

A low FODMAPS Diet should last for roughly a month.  You can then slowly introduce higher FODMAP foods.  You can do this in a similar way you would perform an elimination diet.  Take one food (like beans) and add it back for 3 days and see if you notice more gas, cramping and other digestive issues.  If so, eliminate that food again.  Then, wait 2-3 days and try another food higher FODMAP food (like fennel).

3. Stay Hydrated

Proper hydration is crucial during the treatment period.  Your goal should be to consume at least half your body weight in ounces of water.  Proper hydration helps flush out bad bacteria.  It is also important to get the proper electrolytes you need during this time period.  Adding sea salt to water (1/4tsp. per 8oz. glass) is a great way to get the minerals you need.

4. Intermittent Fasting

Intermittent fasting can be helpful, and those with SIBO tend to respond well to it.  The fasting window gives some bacteria the opportunity to starve and reduce their numbers in the small intestine.  It also helps improve the healing and repairing rates of the affected gut lining.  If you are new to intermittent fasting, you simply want to restrict your eating window to a 6-8 hour timeframe each day.

5. Acidify the Stomach

There are natural remedies out there to help add acid to the stomach and improve digestion overall.  Adding apple cider vinegar or lemon juice to water and teas are fantastic ways to do this at home.  In terms of ratios, you are looking for 1 tbsp. of ACV or ½ juiced lemon per 8oz. of water prior to having a meal.

These acids help kill bacteria in the stomach and stimulate digestive processes like hydrochloric acid (stomach acid) production and regulate the release of bile salts and pancreatic enzymes in the small intestine.

6. Getting Sunlight and Exercise

Sun exposure provides us with vitamin D3, which aids in proper gut health, mineral absorption, and healing processes.  Regular exercise helps improve bowel transit times and reduce inflammation in the body as whole.


Though based in research, personal, and clinical experience, the opinions in this article should not be taken as medical advice. The information is designed for educational purposes only and is not designed to diagnose, treat, or cure disease.  Botanical medicine and nutraceuticals should be treated with the same caution and care as pharmaceuticals, as both have the potential for strong, potentially adverse effects and allergic reactions. Please consult a trained, licensed health care practitioner before proceeding.  Neither the publisher nor the author takes responsibility for possible health consequences of any person reading or following the information in this book. All readers, especially those taking prescription or over-the-counter medications, should consult their physicians before beginning any nutrition or supplement program.

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