Small Intestinal Bacterial Overgrowth (SIBO): What is SIBO, What Causes It, and Can HMO Prebiotics Benefit SIBO?

August 10, 2022 13 min read

Small Intestinal Bacterial Overgrowth (SIBO), what to do?

Once thought to be a rare occurrence solely in those with anatomical abnormalities of the intestines, small intestinal bacterial overgrowth (SIBO) is now known to affect many more subgroups of people. 

While SIBO’s prevalence is unknown mainly because it cannot be diagnosed via symptoms alone, this condition commonly overlaps with other gastrointestinal disorders, like irritable bowel syndrome (IBS) and celiac disease. 

As SIBO is a challenging condition that often recurs and requires multiple rounds of treatment, many patients and practitioners alike are searching for new, natural ways to manage the condition. 

In this article, we’ll take a deep dive into what SIBO is, the symptoms, causes, and currently available treatments for SIBO, and how HMO prebiotics may be able to benefit people with SIBO.

What Is SIBO?

Small intestinal bacterial overgrowth (SIBO) is defined as the presence of excessive bacteria in the small intestine of the gastrointestinal tract — sometimes referred to as the smallintestines/bowel. 

While it’s normal — and necessary — to have plentiful bacteria in the large intestine, relatively few bacteria should be found in the small intestine. The large intestine, or colon, typically contains an astonishing 1,000,000,000 bacteria per milliliter of fluid. Conversely, the small bowel should only hold less than 10,000 bacteria per milliliter of fluid. 

We have several defense mechanisms that prevent bacteria from entering or growing in the small bowel, including:

  • High acidity kills bacteria in the stomach
  • Bile and pancreatic enzymes destroy bacteria that made it through the stomach
  • Small intestine epithelial cells release infection-fighting compounds called antimicrobial peptides
  • Intestinal mucus creates a physical barrier that traps bacteria
  • Peristalsis, or intestinal contractions, transport trapped bacteria out of the small intestine
  • Gastrointestinal immune cells kill off harmful bacteria
  • A specialized valve connecting the small intestine and the large intestine called the ileocecal valve stops colonic bacteria from migrating back into the small intestine. 

When some or all of these defense mechanisms break down, bacteria can grow and multiply in the small intestine instead of the colon, leading to SIBO. 

As we know that having diverse and plentiful bacteria in our colon is beneficial to gut, immune, metabolic, and cognitive health, you may wonder why the same is not true for bacteria in the small intestine. The short answer is that small intestinal bacteria produce incredibly uncomfortable and unpleasant symptoms when they come in contact with dietary carbohydrates from certain foods we eat — let’s take a closer look at what happens.

What Are the Symptoms of SIBO?

The symptoms of SIBO can vary from person to person, but most experience gastrointestinal (GI) discomfort or pain in some way. The most common GI-related symptoms include:

  • Abdominal pain or cramping
  • Belching
  • Constipation
  • Diarrhea
  • Extreme bloating
  • Fat malabsorption
  • Food sensitivities or intolerances
  • Gas
  • Gastroparesis — slow motility of gastric emptying after a meal
  • Heartburn
  • Nausea 

SIBO is also associated with some non-gastrointestinal symptoms, such as:

  • Anxiety
  • Brain fog
  • Depression
  • Fatigue
  • Headaches
  • Joint pain
  • Nutrient deficiencies
  • Restless Leg Syndrome
  • Rosacea or other skin manifestations
  • Weight loss 

Nutrient deficiencies and weight loss can occur because many people avoid or limit eating regularly due to painful and uncomfortable symptoms. Scientists aren’t entirely sure why some of the other symptoms arise, like brain fog, anxiety, and depression, but they likely have to do with the gut-brain axis — a bidirectional communication system linking the gastrointestinal tract and gut microbiome with the central nervous system.

What Are the Leading Causes of SIBO? 

  • Hypochlorhydria (Low stomach acid)

Reduced levels of hydrochloric acid (HCl) in the stomach lower the gut’s ability to regulate bacterial growth. This condition of hypochlorhydria can be caused by an H. pylori infection, chronic use of antacids or medications like proton pump inhibitors, and gastric bypass surgery. 

  • Structural changes to the small intestine

Structural intestinal problems can arise from surgery, digestive disease, or trauma, leading to inhibited gut motility. Slow stomach-to-small-intestine motility means that residual bacteria will not be cleared out of the small bowel as effectively, causing a bacterial accumulation. Examples of intestinal structural changes include abdominal adhesions, small bowel obstructions, and small bowel diverticulosis. 

  • Poor small intestine motility

Dysregulated motility from the small to large intestines means that waste products — including bacteria — remain in the small bowel for too long, allowing the bacteria to multiply. 

This is related to dysfunction of the migrating motor complex, a housekeeping-like way that our intestines sweep food particles from the small intestine into the colon. The migrating motor complex — which only gets to work between meals — is necessary to keep bacteria levels low in the small intestine and prevent SIBO. 

  • Medications

​​Overuse of certain medications can disrupt normal gut microbiome and acid balance, including antibiotics, narcotics, and gastric acid suppressants (antacids like Tums). 

  • Poor bile flow and enzyme production

We need adequate bile and proteolytic (protein-breaking) enzymes to digest food; they also provide anti-bacterial activity to the gut. Without enough enzymes, food isn’t entirely broken down and can become fuel for small intestinal bacteria to consume and thrive on. 

  • Chronic stress

Stress can indirectly lead to SIBO by affecting several of these previously mentioned causes, including reducing stomach acid production, bile secretion, and enzyme release. Chronic stress can also slow down gut motility and weaken the immune system, allowing harmful bacteria to take over.

What Are the Top Risk Factors For SIBO?

There are strong links between SIBO and irritable bowel syndrome (IBS), and these two conditions have many overlapping symptoms. 

A meta-analysis that compiled data from 50 studies found that IBS patients were almost five times as likely to have SIBO than people without IBS. In one of those studies, up to 78% of people with IBS were also diagnosed with SIBO.  

Scientists have also found robust associations between SIBO and inflammatory bowel disease (IBD), which includes Crohn’s disease and ulcerative colitis. In a meta-analysis of 11 studies, the average rate of SIBO in people with inflammatory bowel disease was 22%. 

Similarly, studies have found that up to 20% of people with celiac disease — a severe immune reaction to eating gluten — are also at increased risk of developing SIBO. 

Other factors that increase the risk of developing SIBO include:

  • Increased age
  • Medication use (antibiotics, narcotics, proton pump inhibitors, antacids)
  • Any digestive surgery, injury, or trauma
  • The presence of other health problems, including ​​gastroesophageal reflux disease (GERD), diabetes, HIV/AIDS, scleroderma, Parkinson's disease, hypothyroidism, pancreatitis, lupus, and liver cirrhosis.

How to Test and Diagnose SIBO

SIBO is often underdiagnosed because its symptoms closely mimic other gastrointestinal disorders — especially IBS, which overlaps significantly with SIBO. The main difference between the two is that SIBO can be clinically diagnosed and treated, while IBS treatment and diagnosis are murkier. 

SIBO testing involves measuring bacterial amounts in the small intestine, which can be done using a small intestine aspirate and culture or breath testing.

  • Small Intestine Aspirate and Culture

While this method is considered the “gold standard” for diagnosing SIBO, it’s not as commonly used because it is a costly and highly invasive procedure. 

The small intestine aspirate and culture procedure involves taking a fluid sample from multiple sites in the small intestine using an endoscope. The samples are then cultured in a lab where the bacteria can be measured. A SIBO diagnosis must show bacterial levels greater than 100,000 CFU (colony-forming units) per milliliter of fluid. 

However, some clinicians prefer an even lower cut-off of only 1,000 CFU per mL of fluid. Researchers also disagree about the validity of using small intestine cultures to diagnose SIBO because samples could be contaminated by other gastrointestinal bacteria.

  • Breath Testing

Most health practitioners prefer to use the less expensive, less invasive breath test to diagnose SIBO. The mechanism behind breath testing is based on the fact that gut bacteria produce gases when they break down and ferment certain carbohydrates. (This is also why SIBO produces such unpleasant digestive symptoms.) 

The primary gas produced is hydrogen, but some gut bacteria also convert hydrogen into methane or hydrogen sulfide — the classic “rotten egg” smell. When our guts produce gas, the majority (80%) of it leaves the digestive system in the traditional, room-clearing kind of way. But the other 20% of gas makes its way into the bloodstream and travels to the lungs, where the gas is exhaled and can be measured in the breath. 

For this simple procedure, you will first provide a baseline breath sample. Then, you’ll drink a liquid carbohydrate made of either glucose or lactulose and continue to provide breath samples every 15 minutes for two to three hours. 

If you breathe out any hydrogen, hydrogen sulfide, or methane gas, they’ll know that it is a byproduct of gut bacterial fermentation. Unlike the small intestine aspirate and culture, this method can only determine whether or not you have SIBO — not how many bacteria are present or the magnitude of the overgrowth. 

While many practitioners only measure hydrogen gas, it would be best to measure all three because you’ll better understand which types of bacteria are colonizing the small intestine to guide treatment recommendations.

What Are the Current Treatments For SIBO?

The primary goal of SIBO treatment is to kill off unwanted small intestinal bacteria while also preventing them from recolonizing. Unfortunately, many people with SIBO will have recurring bouts of this overgrowth. There are three currently available avenues of treatment:

1.   Prescription Antibiotics

Antibiotics are designed to kill bacteria. Standard antibiotic treatment for SIBO involves a 2-4 week schedule, depending on symptom severity. The most commonly used antibiotic for SIBO is rifaximin (brand name Xifaxan). The antibiotic neomycin may also be given concurrently if methane gas is detected in the breath. 

Research has found that Xifaxan eliminates SIBO and normalizes breath test results in 50-70% of people. However, ​​​​the rate of SIBO recurrence after antibiotic treatment is typically high, especially if the root cause of the bacterial overgrowth is not addressed. 

Further, some antibiotics are not selective for “bad” bacteria — they can also kill off healthy, normal gut flora and create dysbiosis. Interestingly, studies have found that Xifaxan does not significantly disrupt the colonic microflora.

2.   Herbal Antimicrobials

Herbal antimicrobials are essentially natural, non-prescription herbs and spices that act similarly to antibiotics and kill off bacteria. 

Most herbal antimicrobial courses are about four weeks, and research has shown that they can be as effective as prescription SIBO antibiotics. Many people choose these because they prefer to go a more natural route or do not want the potential adverse effects of prescription antibiotics. 

The composition of herbal antimicrobials can vary widely. Commonly used herbs and spices include thyme, oregano, lemon balm, berberine, Chinese skullcap, ginger, Chinese licorice root, bilberry extract, milk thistle, echinacea, goldenseal, white willow bark, garlic, grapeseed extract, and tea tree oil. 

A downside of herbal antibiotics is that they have not been widely studied; more research is needed to determine the most effective doses and herbal combinations for treating SIBO.

3.   Elemental Diet

People who don’t respond to antibiotics or herbal antimicrobials may need to go on a restrictive plan known as an elemental diet. While the elemental diet is effective, it’s not typically enjoyed by patients because it involves solely drinking nutrient-dense meal replacement shakes for two to four weeks — nothing else! 

The shakes are mixed with water and contain the simplest — most “elemental” — forms of macronutrients, like glucose for carbohydrates, amino acids for protein, and fatty acids for fats. These broken-down macronutrients would get absorbed at the top end of the small intestine, which will starve the overgrowth of bacteria in the lower end of the small bowel. 

The elemental diet has a higher success rate than antibiotics — about 85% recovery from SIBO compared to 70% — but is challenging to follow because it is restrictive, expensive, and not very appetizing.

HMO 101: Benefits of HMOs to Gut Health

HMOs are a type of non-digestible sugar abundant in human breast milk that can travel to the large intestine and benefit gut, immune, and cognitive health. Although HMOs are only naturally present in breast milk, they can also be created through a scientific process involving enzymes and fermentation. 

HMOs benefit the gut in several ways. HMOs are not digested or absorbed in the gut, so they migrate to the large intestine, where they interact with bacteria. These gut bacteria ferment and digest the HMOs, leading to the production of healthy metabolites like short-chain fatty acids (SCFAs) that benefit both the gut and overall health by preventing the development of leaky gut, or increased intestinal permeability.

Can HMOs Help With SIBO?

As one of the causes of SIBO is low stomach acid, HMOs may help with SIBO because these prebiotic carbohydrates help to regulate intestinal pH. HMOs can also help support healthier gut bacterial makeups, which may help with SIBO. 

HMOs select preferentially for Bifidobacteria, a healthy type of bacteria, and strengthen the intestinal barrier to keep out pathogens. 

Plus, HMOs strengthen the immune system. The gut microbiome and the immune system are intricately linked by a secondary lymphatic organ called gut-associated lymphoid tissue (GALT), which protects the body from pathogens but allows tolerance to healthy bacteria. 

HMOs may directly modulate immune responses by preventing the adhesion of pathogens to the intestinal lining or indirectly by inhibiting the activity of pro-inflammatory molecules called cytokines. HMOs prevent pathogenic adhesion by acting as a “decoy” receptor for unhealthy bacteria, like E.coli.The functions of these receptors suggest that HMOs are involved in regulating the innate immune system against infections or bad bacteria.

But I Thought Prebiotics Were Bad For SIBO?!

Many people think that prebiotics or prebiotic foods make SIBO worse because they will cause the small intestinal bacteria to ferment the carbohydrates and cause GI symptoms — and this could be true for some types of prebiotics (for example, inulin) or prebiotic foods, especially FODMAP foods, which could potentially worsen the symptoms of SIBO.

Ways to Help SIBO

Unfortunately, SIBO is notoriously challenging to treat, and recurrence rates are high. But there are some things you can do to hopefully prevent a SIBO relapse, including taking prebiotics and probiotics and changing your diet.

1.   HMO Prebiotics

Regularly supplementing with HMO prebiotics can selectively increase Bifidobacteria, strengthen intestinal barriers, improve immune system functioning to fight off pathogenic bacteria, and promote the growth of healthy gut flora.


2.   Probiotics

Probiotic supplements containing healthy bacteria may also help to prevent SIBO from recurring. 

In a study of 30 people with SIBO, researchers looked at people who took a probiotic called Lactol (​​Lactobacillus sporogenes)in addition to a regular SIBO antibiotic course. Six months later, 93% of those in the probiotic group had negative hydrogen breath tests, compared to 66% in the antibiotic control group. The probiotic group also experienced a complete disappearance of abdominal pain, gas, belching, and diarrhea. 

3.   SIBO Diet

The most commonly used SIBO diets are the low-FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet and the Specific Carbohydrate Diet (SCD). 

These are both diets low in fermentable carbohydrates, which may help reduce digestive symptoms and limit the available “food” for small intestinal bacteria to survive on. However, some researchers argue that some bacteria need to remain active in the small intestine in order for antimicrobials to do their job. Otherwise, the bacteria can “go into hiding” in the intestinal mucus and become challenging to kill off. 

One study supports this theory, finding that SIBO patients who took both antibiotics and a guar gum prebiotichad more effective SIBO eradication than antibiotics alone. This suggests that people with SIBO should continue to consume fermentable carbohydrates unless they develop gastrointestinal symptoms. 

Plus, diets low in fermentable carbohydrates will reduce the number of healthy gut bacteria in the colon, which may be detrimental to both gut and overall health in the long term. 

Certain foods may worsen SIBO symptoms, including onions, garlic, beans, high-fructose corn syrup, and apples. However, everyone is different, so some trial and error may be necessary to find the proper diet for you.

Key Takeaway:

  • ​​Small intestinal bacterial overgrowth (SIBO) is the presence of excessive bacteria in the small intestine of the gastrointestinal tract.
  • SIBO symptoms are similar to irritable bowel syndrome symptoms, including abdominal pain, bloating, gas, abnormal bowel movements, cramping, and non-GI symptoms like anxiety, brain fog, and fatigue.
  • The two ways to test for and diagnose SIBO are a small intestine aspirate and culture or a hydrogen breath test.
  • Current treatments for SIBO include antibiotics, natural antimicrobial compounds, or an elemental diet.
  • HMOs (human milk oligosaccharides) may help with SIBO. HMO prebiotics are naturally found in breastmilk and support gut health by strengthening the intestinal barrier, boosting healthy bacteria growth, improving immune function to fight pathogenic bacteria, and preventing leaky gut.
  • Other ways to prevent or treat SIBO include taking supplemental probiotics and limiting your consumption of some fermentable carbohydrates, like onions, apples, and garlic.


Written By: 

Cambria Glosz, Registered Dietitian 


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1 Response


March 19, 2023

Thank you. A lot of important information and explanation. I will talk to my Dr about this. Nothing seems to help my IBS bouts.

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