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The Facts On SIBO And Gut Microbiome Testing

The Facts On SIBO And Gut Microbiome Testing

Small Intestinal Bacterial Overgrowth (SIBO) is a hot topic but there's a lot of confusion. This article explains what SIBO is and why gut microbiome testing doesn’t work for it.

The human body is a host to bacteria that perform essential functions for our health. They live on the skin, in the mouth, colon, armpits, and even in the nose. Sometimes, these bacteria can grow out of control, and when they do, it can cause health problems.

SIBO is one of such conditions, and it happens in the small intestine. For this reason, it’s not uncommon for people to think SIBO happens in the gut microbiome, an ecosystem of bacteria that inhabits the colon (a nearby part of the intestines).

This article by Zora DeGrandpre, Doctor of Naturopathic Medicine and author for, a website dedicated to science-based information on this condition, explains some important differences and facts about SIBO testing and gut microbiome DNA sequencing (like our Microbiome Test).

What is SIBO?

Small Intestinal Bacterial Overgrowth (SIBO) describes a condition where, for reasons that are not very clear, bacteria begin to grow and overpopulate the small intestine.

Normally, few bacteria are found in the small intestine. When you hear people talking about gut bacteria (gut flora), they are talking about bacteria found in the large intestine, which is also known as the colon.

The small intestine connects the stomach to the large intestine, and it carries out most of the digestion of food and nutrient absorption we need to survive.

The function(s) of the large intestine are somewhat different - we’ll discuss this later on - and this helps explain the difference in the numbers of bacteria.

Photo by Johnny Brown / Unsplash
There are 1,000,000,000 bacterial cells for each mL of fluid in the colon

For many years, SIBO was thought to be rare and mainly associated with either an anatomic abnormality, or some condition that interfered with movement of partially digested foods through the small intestine (dysmotility).

Now, scientists are finding that SIBO is more common than originally thought. While DNA sequencing methods (like the ones used by Atlas Biomed) can give you important information, they won’t help diagnose SIBO.

Currently, there is not a single completely valid and reliable test for SIBO. To find out why, read on.

☝️DISCLAIMER☝️ This article is for informational purposes only. It should not be used to diagnose, treat, prevent, or cure any disease or condition.

What are the signs and symptoms of SIBO?

SIBO is defined by the presence of higher-than-normal numbers of bacteria in the small intestine that can lead to a variety of signs and symptoms:

A sense of bloating Increased gas
Diarrhoea (sometimes constipation too) Nausea
Abdominal pain or discomfort Fatigue
Malnutrition, vitamin and mineral deficiencies Unintended weight loss

SIBO interferes with the digestion and absorption of vital nutrients. If left untreated, SIBO can lead to some significant problems, including malnutrition, various vitamin deficiencies (especially deficiencies in Vitamins A, D, E and B12), mineral deficiencies (Iron), bone disorders, anemias, and nerve disorders.

☝️Atlas Biomed says☝️ These symptoms are present in a wide range of digestive conditions and diseases which is why it’s important to consult a doctor who can conduct diagnostic testing to exclude other potential causes.

Risk factors for SIBO

SIBO is more likely to be diagnosed in women and older adults, and is often associated with a disorder known as Irritable Bowel Syndrome (IBS). It is associated with several risk factors:

Low stomach acid Gastric acid is important for breaking down food and preventing bacteria from travelling into the intestines.
PPI medication Long-term use of proton pump inhibitors, these medications decrease stomach acid to prevent gastroesophageal reflux.
Weak immune system The immune system is designed to fight off pathogens, preventing infections and unwanted bacterial overgrowth.
Dysmotility Changes in the speed, strength, or coordination of the muscles of the digestive tract interfere with the movement and digestion of food by the body.

Certain diseases have been linked to increased risk of developing SIBO. Some of them affect the digestive system, like coeliac disease (gluten intolerance), Crohn’s disease (an inflammatory bowel disease), and irritable bowel syndrome (IBS).

However, other illnesses can also heighten a person’s risk for SIBO: liver disease (specifically, cirrhosis), diabetes, HIV/AIDs, fibromyalgia, and scleroderma.

What about the gut microbiome?

The gut microbiome refers to the ecosystem of bacteria that are mostly located in your large intestine, which is a bit further south of your small intestine where SIBO occurs.

The specific pattern of the types of bacteria (and other microorganisms) in your gut can be as unique as your fingerprints. In fact, a healthy digestive tract contains about 100 trillion organisms.

The specific composition of these important microbes depends on your diet, your environment, family history and ethnic background, and your lifestyle habits. It can also be influenced to some degree by your particular history.

For example, were you breastfed as an infant? Did you live in a rural or urban setting? Do you have a longer or shorter history of healthy eating? Do you have a history of antibiotic use? These and other factors can influence your gut microbiome.

I wanted to take some photos of the mountains and invited my girlfriend to go with me. She turned a normal photo day in a very romantic day
Photo by Willian Justen de Vasconcellos / Unsplash
Your microbiome is shaped by your lifestyle and early childhood factors

The relationship between gut bacteria and the human host (that means YOU!) is both commensal (non-harmful, peaceful co-existence) and mutualistic. A mutualistic relationship means that both the bacteria and you benefit from the relationship.

For your part, you provide the bacteria with a safe place to live and food to eat. They provide you with protection against other disease-causing bacteria, support and educate your immune system, produce nutrients such as biotin, Vitamin K and short-chain fatty acids, and help you digest your food.

☝️Atlas Biomed says☝️A healthy gut microbiome performs essential functions for human health. They help maintain the integrity of the gut lining, protect from several diseases, prevent chronic inflammation, and fight off pathogens that can make you sick.

Differences between SIBO and the gut microbiome

Here are a few key differences between bacteria in the small intestine and those in the gut microbiome, as well as SIBO and testing for SIBO.

Most of the gut bacteria are found in the large intestine, about 1,000,000,000 for each mL of fluid. In the small intestine there should be relatively few bacteria present (less than 1,000 per mL).

Bacterial growth in the small intestine is suppressed by an acidic environment, high levels of oxygen, and the fact that they don’t get to spend much time in the small intestine - the food is digested and “pushed through” pretty quickly!

In SIBO, the number of bacteria present in the small intestine is increased, but there are still many fewer bacteria compared to the large intestine. In addition to that, the bacteria that cause SIBO are not necessarily abundant in the large intestine.

The most common genera of bacteria (a classification of bacteria) in the healthy large intestine are Bacteroides, Clostridium, Faecalibacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, Bifidobacterium, and Lactobacillus.

But when there is an overgrowth of bacteria where they do not belong (like the small intestine), only the bacteria benefit. Humans don’t.

Types of SIBO

There are different types of SIBO depending on what gases are produced by the bacterial overgrowth.

When bacteria break down food particles, they can produce lots of things, including various gases. When there is bacterial overgrowth in the small intestine, these gases can make their way upwards to be exhaled in a person’s breath.

The two recognised types of SIBO are determined by the dominant gas produced by these bacteria:

  • Hydrogen: SIBO can be caused by bacteria that produce hydrogen gas, and may include bacteria that are somewhat similar to those found in the large intestine.

  • Methane: SIBO can be caused by bacteria that produce methane gas, mostly Methanobrevibacter smithii (referred to as M. smithii for short).

It has recently been found that there may be yet another variant of SIBO. Bacteria in the intestines can also produce hydrogen sulfide gas. These are primarily Pseudomonas, Citrobacter, Aeromonas, Salmonella, and Escherichia coli.

Recent evidence suggests that hydrogen-type SIBO might go undiagnosed if a patient’s breath test results don't show high levels of hydrogen. This may happen if the hydrogen is used for fuel by other bacteria in the small intestine before it escapes.

In this case, the hydrogen sulfide-producing bacteria in a person’s small intestine may obscure the fact that there are hydrogen-producing bacteria there too. Researchers describe SIBO patients in this situation as hydrogen non-producers.

More evidence is showing that many people have more bacteria in the small intestine, but don’t show any symptoms. Even more experience one or more SIBO symptoms.

☝️REMEMBER☝️ The fact that these bacteria produce either hydrogen, methane, or hydrogen sulfide gases gives us the main tool that is used for diagnosis (breath testing), but it is a tool with many problems and is not universally accepted.

Testing for SIBO

Stool tests and gut microbiome tests can tell you important information about your health, but they don’t work for SIBO.

DNA sequencing of the gut microbiome using a stool sample, like at Atlas Biomed, can reveal significant information about your health and protection from certain diseases.

It can tell you how well you are digesting fiber, what nutrients your microbes produce, and how to achieve a healthy and diverse microbiome. What it won’t give you much information about, however, is the state of your small intestine. Why? There are a few reasons for this.

First, remember that the small intestine connects the stomach with the large intestine (colon). The small intestine is about 20-feet long, whereas the large intestine is just about 5-feet long. Bacteria in the small intestine have a long, long, REALLY long way to go to become part of the stool.

Also, if the bacteria in the small intestine have formed what is known as a biofilm (which they often do, especially in digestive disorders), they are going to be using that biofilm to anchor themselves in the small intestine.

Secondly, the sheer number of bacteria in the large intestine is likely to, essentially, overwhelm any bacteria arriving in the stool from the small intestine. Remember, the large intestine has 1,000,000,000 for each mL of fluid, while the small intestine normally has about 1,000 per mL.

Estimated bacteria per mL of fluid Location/condition
1,000/mL Bacterial cells in a healthy small intestine
100,000/mL and over Diagnostic level of bacterial cells in the small intestine for SIBO diagnosis
100,000,000/mL Average number of bacterial cells in the gut microbiome (large intestine)

One set of diagnostic criteria for SIBO is the presence of more than 100,000 bacteria per mL. That’s still about 10,000 times more bacteria in the colon than in the small intestine: it’s a bacterial needle in a haystack!

The types of bacteria found in the small and large intestine overlap, and there is no reliable way to tell where that bacteria originally started their journey.

One possible exception would be if an individual had a large population of M. smithii and a positive breath test (see below) for methane, but this result would not necessarily constitute a diagnosis.

So how is SIBO diagnosed?

There are no universally accepted diagnostic criteria for SIBO. We are not even certain of how often it occurs, but it’s more common than we previously thought.

Some studies suggest that it is present in more than a third of patients with IBS. Others have suggested higher numbers, with up to 40% of healthy people showing some indications of SIBO.

Part of the reason for these results is that the test most commonly used to help diagnose SIBO (a breath test) is problematic itself. The current “gold standard” is to take a sample of the contents of the small intestine and culture them.

But this is invasive because it requires an endoscopy, in which a scope with a miniature camera is inserted into the digestive tract. The test is also costly.

The breath test is not invasive and is relatively inexpensive, but can have false positives and false negatives. Therefore, the results have to be combined with other criteria to make a diagnosis.

The test is performed after an individual consumes a liquid containing a sugar solution. After 90 minutes, the person’s breath is tested for the presence of hydrogen, methane, and hydrogen-sulfide gas. However, there is no universal agreement on what constitutes a positive or negative result.

☝️REMEMBER☝️ Only a trained medical professional can make a diagnosis of SIBO. Always consult a doctor if you are concerned about chronic digestive symptoms. Created by Josh, a SIBO survivor himself, this website is a resource for people seeking information about this condition based on scientific evidence, written and reviewed by medical experts.
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