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AutoImmune & Chronic Disease

What is SIBO?

Causes and Symptoms of SIBO

It’s safe to say most of us are familiar with the experience of having a tummy ache or getting a serious bout of bloating. But what happens when your belly pain becomes so severe you have to cancel plans? Or your bloating gets so bad you can hardly fit into your pants?

Unfortunately, this is the frustrating and life-hindering reality for a growing number of people grappling with a condition known as small intestinal bacterial overgrowth or SIBO. 

Today we’re going to explore exactly what small intestinal bacterial overgrowth is, do a deep dive on what causes SIBO, and touch on some of the common misunderstandings that have made this condition difficult to treat. And most importantly, we’ll cover some steps you can take to begin addressing and reversing the root cause of small intestine bacterial overgrowth.

Small Intestinal Bacterial Overgrowth Explained

Small intestinal bacterial overgrowth, more commonly referred to as SIBO, occurs when you have an overgrowth of bacteria residing in your small intestine. While your digestive tract is indeed designed to house trillions of different microbes that collectively make up your gut microbiome, the majority of these microbes are meant to live in your large intestine and colon. 

In a healthy balanced small intestine, you’ll typically find small populations of gram-positive bacteria. These are species of bacteria that have a cell wall and are generally considered “good” or friendly bacteria. But in SIBO, there’s a shift from a small population of gram-positive bacteria, to an excessive overgrowth of gram-negative bacteria.

Gram-negative bacteria are species of bacteria that only have a cell membrane and no cellular wall. And these gram-negative bacteria contain compounds known as lipopolysaccharides or LPS – a potent inflammation-promoting toxin. Now let’s take a look at some of the symptoms that can be triggered when bacterial populations begin overgrowing in your small intestine.

Signs and Symptoms of SIBO

Some cardinal SIBO symptoms include: [1]

  • Abdominal pain and/or discomfort
  • Bloating and abdominal distention
  • Excessive gas – flatulence and/or belching
  • Diarrhea
  • Constipation
  • Indigestion and heartburn
  • Nausea
  • Feelings of fullness or loss of appetite

If left unaddressed, SIBO can interfere with your ability to digest food and absorb nutrients leading to complications such as: [1]

  • Weight loss
  • Vitamin and mineral deficiencies
  • Malabsorption 
  • Kidney stones
  • Weakened bones
  • Leaky gut syndrome

So aside from experiencing these troublesome digestive symptoms, how do you know if you have SIBO?

How Is SIBO Diagnosed?

SIBO can be tricky to diagnose primarily because there is often confusion surrounding the underlying mechanisms that drive SIBO. There is a significant overlap in the symptoms seen in SIBO and irritable bowel syndrome or IBS. And because there is often a lack of understanding surrounding the underlying root cause of these dysfunctions of the gut, these diagnoses are often haphazardly slapped on in an attempt to label what’s happening. 

This leads to some inaccurate SIBO testing, diagnostic techniques, and treatment strategies. For example, a breath test that measures the presence of gasses emitted by these gram-negative bacteria is often used to diagnose SIBO. But the problem is, studies have shown that breath tests are only accurate about 50% of the time. 

The only way to truly and accurately diagnose SIBO is through an aspirate test in which a tube is inserted into the small intestine and a sample is extracted in order to examine the amount and types of microbes present.2 SIBO is technically defined as an increase in bacteria greater than or equal to 105 colony-forming units per 1 milliliter of upper gut aspirate.

So exactly what causes overgrowth of bacteria in the small intestines? Before we dive into the root causes of SIBO, let’s review how a healthy, well-functioning digestive tract is designed to run.

How A Healthy, Well-Functioning Gut Is Designed to Prevent SIBO

To understand the underlying “upstream” issue that’s causing the perplexing “downstream” issues seen in SIBO, it’s important to first have an understanding of how the gut is designed to function. You see, your small intestine is actually an ideal place for bacteria to grow – it’s warm, moist, and has lots of nutrients continuously flowing in. So why do some people develop SIBO while others don’t?

It’s because despite being an ideal environment for bacteria to grow, your body is designed to function in a way that shields your small intestine from bacterial growth. Your gut has natural built-in protective mechanisms that prevent small intestine bacterial overgrowth that goes something like this:

Your Mouth

Your mouth is the gateway to your gastrointestinal tract. And you inevitably come into contact with countless microbes that set up camp in your mouth. It’s perfectly normal to find an abundance of gram-negative bacteria such as E. coli, Klebsiella, Staphylococcus, and Enterococcus in your mouth. [3]  

And as these microbes colonize your mouth, they inevitably are washed down into the rest of your digestive tract as you swallow gallons of saliva each day.

Stomach Acid

As these microbes migrate from your mouth down to your stomach, they encounter the first defense mechanism designed to protect your small intestine from bacterial overgrowth – stomach acid.[4] These harsh, acidic gastric juices circulate throughout your stomach and are leaked into your duodenum (the section of the small intestine connected to your stomach). This gastric barrier acidifies microbes, killing them off and drastically reducing the number of microbes that survive the journey to your small intestine.


Any microbes that do survive your harsh stomach acid, then have to contend with your bile. Bile is a substance secreted by your liver that helps you absorb fat-based nutrients. With each meal, your body continuously releases and cycles bile through your small bowel. Bile is important for nutrient absorption, but it also serves as a natural antimicrobial – binding to microbes and toxins and circulating them back through the liver where they are neutralized and packaged up for excretion. [5] 

The Nuclear FXR Receptor

Bile also plays another important role in preventing bacterial overgrowth in your small intestine. Before bile is reabsorbed at the ileum (the final portion of your small intestine), it activates something called the nuclear FXR receptor. Once activated, the nuclear FXR receptor stimulates the cells that line your intestines to release a cocktail of antimicrobial compounds to kill off any bacteria that may have survived the journey thus far. [6]


Bacteria have what’s known as a lag phase and a log phase. In the lag phase, the bacteria grow and multiply slowly and during the log phase, they begin growing and replicating rhythmically – multiplying exponentially. [7] This is why you can leave food out on the counter for a couple of days and it will appear fine, and then boom – all of a sudden it’s spoiled.

There were already microbes on the food, but they just needed some time to ferment and grow. Well, the same thing happens in your gut. If food and bacteria are left in place for too long, bacterial populations will begin to explode and overgrow. To circumvent this, your small bowel is designed to empty rather quickly and regularly through a motion known as peristalsis.

Think of peristalsis like squeezing toothpaste through a tube. The rhythmic muscle contractions push food and bacteria out of your small intestine before there’s a chance for bacteria to enter their log phase and begin taking over. 

Migrating Motor Complex

Your final built-in protective mechanism to shield against bacterial growth in your small intestine is what’s known as the migrating motor complex. The migrating motor complex is a type of sweeping mechanism that’s designed to help shake loose and clear out any remaining debris that may have been left behind in your stomach and small intestine. This cleaning mechanism is only triggered when your stomach is empty and is intended as a final sweep to prevent any food or bacteria from hiding out and creating overgrowth. [8] 

So now that you have an understanding of how your small intestines are intended to work, you can better understand SIBO causes and exactly what goes wrong when bacteria begin overpopulating your small intestine.

Check out our Deep Dive Training Webinar on SIBO with Kiran Krishnan, Microbiologist & Chief Scientific Officer of Microbiome Labs. We cover the symptoms, root causes, & effective strategies to treat SIBO naturally.

Root Causes of SIBO

Because SIBO is known to affect people from all walks of life and it’s impossible to pinpoint a singular common trend among those suffering from SIBO, the underlying root cause is likely a complex combination of factors. You see, SIBO itself isn’t the actual problem. An overgrowth of bacteria in the small intestine is just the end result of a bigger-picture dysfunction of the gut. 

It’s likely that more than one imbalance leads to a shift that causes an overall dysfunction – resulting in bacteria overpopulating the small intestine. Some of the factors that can potentially contribute to this disruption and gut malfunction include:

Insufficient Stomach Acid: 

Without adequate amounts of stomach acid, a much larger volume of microbes will inevitably survive digestion and make their way into your small intestine. Things that can impair stomach acid secretion include:

  • Proton pump inhibitors (PPI’s): Over-the-counter medications designed to inhibit the release of stomach acid.
  • Antihistamines: Over-the-counter medications used to control allergy symptoms that can stifle stomach acid production by blocking histamine from binding to H2 histamine receptors in your stomach.
  • Magnesium deficiency:  There is a direct link between low magnesium levels and low stomach acid.

Anything that puts a damper on acid production hinders your first and most important defense mechanism against SIBO.

Decreased Bile Flow:

Your bile acts as a potent natural antimicrobial that neutralizes any bacteria that survive your stomach. Factors that can slow or stop the flow of bile include:

  • Gallbladder removal
  • Bile duct obstruction
  • Liver dysfunction
  • Dysbiosis

Without adequate bile, your small intestines are much more vulnerable to invasive bacteria.

Impaired Peristalsis and Migrating Motor Complex

If your gastric movement is impaired and significantly slowed, bacteria will simply have more time to grow and proliferate. Conditions that can contribute to slow gastric movements include:

  • Gastroparesis
  • Celiac disease
  • Enteropathy
  • Diabetes
  • Hypochlorhydria

Even a slight impairment in gastric movement can have a major impact on bacterial growth.


Dysbiosis, or an imbalance in the organisms that reside in your gut, can create a vicious cycle that exacerbates SIBO. If your microbiomes ecosystem shifts, allowing for the overgrowth of “bad” bacteria that crowd out good bacteria, it has a ripple effect that causes an increase in LPS which can:

  • Skyrocket inflammation
  • Damage the membrane that serves as a protective barrier between your digestive tract and your bloodstream – creating what’s known as leaky gut syndrome
  • Trigger the release of TNF alpha which stifles peristalsis and the migrating motor complex
  • Disrupt the release and circulation of bile

So as you can see, these factors combined can significantly contribute to the dysfunction seen in SIBO. And while we’ve made great strides in understanding SIBO, we are often still missing the mark when it comes to treating this imbalance of the gut. 

The Functional Medicine Approach

The trouble with both conventional medical approaches and functional medicine approaches to SIBO, is that they both typically end up treating the symptoms rather than the root cause of dysfunction. In conventional medicine, doctors typically prescribe antibiotics. And in functional medicine, practitioners typically prescribe all-natural antimicrobial agents. While one may be more natural than the other, the end result is still essentially just “carpet-bombing” the gut and decimating bacterial populations – good or bad.

While this works in the short term and can provide temporary relief, it doesn’t address the underlying dysfunction that led to SIBO in the first place. So is it possible to reverse SIBO naturally?

How to Treat SIBO Naturally

The good news is, there are some strategies that can provide relief and actually work to heal the root cause of the dysfunction that causes SIBO and cure SIBO naturally. It requires a big-picture approach that may encompass things like:

  • Boosting stomach acid production: By avoiding acid-suppressing medications and incorporating stomach acid-supporting supplements like HCL Guard or MegaGuard.  
  • Enhancing bile production and flow: By supporting liver health, addressing exposure to environmental toxins, assisting the body in detoxing accumulated toxins, and incorporating supplements like artichoke leaf extract or ox bile to stimulate bile production.
  • Balancing the microbiome: Resetting the microbiome in both the mouth and stomach by minimizing inflammation, reinoculating with beneficial bacteria (especially HU58 which blocks the growth of opportunistic pathogens), increasing microbial diversity with MegaSporeBiotic and MegaPre to fuel good bacteria, and healing leaky gut syndrome with MegaMucosa to beef up the intestinal barrier and prevent LPS leakage.
  • Accelerate gastric emptying: By incorporating supplements like ginger root extract and/or licorice flavonoids and trying intermittent fasting to reset your gut.

There are two other things that are important to touch on when it comes to SIBO natural treatment strategies – the low FODMAP diet for SIBO and digestive enzymes.


Many people diagnosed with SIBO are advised to follow a SIBO diet, also known as a low FODMAP diet that restricts the consumption of fermentable carbohydrates. While this can offer temporary relief, it’s also not a long-term solution. Following a low FODMAP diet for an extended period of time can actually contribute to dysbiosis because your beneficial bacteria thrive on these fermentable carbs as well.

So part of addressing SIBO includes supporting a healthy diverse microbiome and slowly increasing the types of foods you’re able to tolerate. And one of the most potent ways to do that is by incorporating digestive enzymes.

SIBO and Digestive Enzymes

Digestive enzymes can be particularly helpful when it comes to addressing SIBO thanks to their ability to help break down food particles into more easily digested molecules. Products like FODMATE are specifically designed to help address the consumption of foods that contain FODMAPs while supplements like Holozyme are a little more broad-spectrum. 

Because insufficient or ineffective stomach acid is one of the primary drivers of SIBO, taking digestive supplements with each meal can go a long way in boosting your digestion and shifting the balance to help your body heal from SIBO. To really give your body an edge on healing and treat SIBO naturally, you can try our SIBO Ultimate Bundle. It contains:

  • FODMATE digestive enzymes for SIBO
  • HoloZyme digestive enzymes for gut health
  • HCL Guard and MegaGuard to support stomach acid
  • MegaMucosa to bolster your gut lining
  • And MegaSporeBiotic to help balance your microbiome

You can find the SIBO Ultimate Bundle and more through our online store. And you can even snag 10% off your first order by clicking right here.

Are You Struggling With SIBO?

If you’ve been diagnosed with SIBO or are struggling with unexplained digestive problems, it might be time to dig a little deeper into what’s going on. If you want to dive even deeper into the underlying root cause of SIBO and how to reverse SIBO, you’ve got to head over and check out our webinar with Kiran Krishnan, Microbiologist & Chief Scientific Officer of Microbiome Labs where we chat all about the science behind what really causes SIBO

And if you’re ready to start taking steps to heal the underlying cause of SIBO or any other digestive challenges you’re grappling with, we’ve got you covered with tons of value-packed and easy-to-understand resources that you can find on the blog, on our podcast, and over in the Wellness Vault.

RHT Gut Repair & Microbiome Optimization Guide

10 Steps to Repair Your Gut, Optimize Your Digestion, and Build a Healthy Microbiome!


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