One of the most common questions I’m asked is “what are the best probiotics for SIBO?” You might be surprised to learn that if you have SIBO (Small Intestinal Bacterial Overgrowth), your regular probiotic for gut health could actually exacerbate the problem. For this reason, you want to take a specialized approach in your probiotic regime with a soil-based probiotic that will provide the support you need.

In this article, I’ll explain what soil-based probiotics are, and why soil-based probiotics for SIBO are the best probiotics to for SIBO.

You can also check out my video on SIBO and probiotics below:

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What is SIBO?

Small Intestinal Bacterial Overgrowth (SIBO) occurs when the bacteria in your GI tract, particularly your small intestine, get out of balance and overgrow. As I always say, “Too much of a good thing can be a bad thing,” and this is true of SIBO.

Too much good or bad bacterial flora in the small intestine produces a number of gastrointestinal symptoms that interfere with your normal digestive process, including gas, bloating, and diarrhea. SIBO often goes undiagnosed because of the way its symptoms manifest in different people. Sometimes there are no physical signs whatsoever. In fact, an estimated 6-15% of healthy, asymptomatic people and roughly 80% of people with IBS are actually suffering from SIBO.1

SIBO risk factors include:

  • Diets high in sugar, alcohol, and refined carbohydrates
  • Damage to nerve or muscles in the gut resulting in dysmotility
  • Physical obstructions in the gut, such as scarring from surgeries or Crohn’s disease
  • Medications that influence or disrupt the normal gut flora, such as antibiotics, acid-blocking drugs, and steroids

The SIBO, Leaky Gut, and Autoimmune Connection

Having SIBO can damage your mucosal lining and lead to intestinal permeability or leaky gut. In fact, besides Candida overgrowth, SIBO is one of the main causes of leaky gut I saw in my clinic.

Once your gut is leaky, toxins, viruses, bacteria, and food particles flood your bloodstream. As your gut remains leaky and more and more particles escape into your bloodstream, your immune system sends out wave after wave of inflammation. Eventually, it becomes over-stressed and begins firing less accurately. 

What’s more, many particles that are now flooding your bloodstream look like your body’s own tissues. Your immune system then creates antibodies against these substances which mistakenly attack your tissues in a phenomenon called molecular mimicry.

Probiotics: Adding Fuel to the Fire

Treating SIBO is a 3-step approach. The first step is to remove the foods that feed it. A SIBO diet eliminates sugar, alcohol, and many carbohydrates. In addition, probiotic foods containing strains of lactobacillus or bifidobacterium including kombucha and dairy products such as kefir, can add fuel to the fire. 

Second, attack the bad bacteria. Depending on the type of gas produced by your gut organisms (hydrogen or methane), the primary antibiotics used for treating SIBO are Xifaxan and Neomycin. I recommend Microb-Clear™ to anyone working to overcome SIBO. This cutting edge blend of botanical extracts, minerals, and fatty acids works to create an inhospitable environment for parasitic microorganisms while promoting the ideal environment for beneficial probiotic bacteria.

Third, restore the beneficial bacteria with SIBO probiotics. The problem with many probiotics available on the market is that they simply don’t work for SIBO. Many probiotics can actually make the problem worse. 

Here’s why: Your small intestine is not meant to have much bacteria in it. It interferes with digestion and nutrient absorption. Some bacteria are necessary for these functions. You want your bacteria levels to be just right for optimal digestion and absorption.

When bacteria are present in the small intestine, they are often of the lactobacillus or bifidobacterium species. The majority of probiotic supplements contain lactobacillus or bifidobacterium, so using this type of probiotic increases the bacteria in your small intestine and adds fuel to the fire. For this reason, I believe soil-based probiotics for SIBO are the best probiotic for SIBO.

The Dirt on Soil-Based Probiotics

Back in the day, we grew all our own food and pulled it straight from the ground, eating it right there without washing it. The earth is full of bacteria, and it’s where we used to get most of our probiotics. Essentially, most of our probiotics were soil-based probiotics, such as spore forming probiotics.

In our hyper-hygienic modern lives, we are so far removed from the dirt that grows our food that we’re missing out on some of the crucial microorganisms and probiotics that populate our soil which used to populate our own microbiomes. I believe this is one of the reasons digestive health issues are more common today than they once were. That’s where soil-based probiotics come in.

Soil-based probiotics for SIBO do not contain lactobacillus or bifidobacterium strains, yet they still provide all the benefits of a probiotic.

Soil-based probiotics have a natural, seed-like structure that makes them hardier than lacto-based probiotics. Therefore, soil-based probiotics survive the journey through the stomach with the help of far fewer colony-forming units (CFUs) than lactobacillus-based supplements. This is due to the formation of endospores, which can withstand stomach acid, bile salts, and pancreatic enzymes that would normally destroy the bacteria.2

These characteristics of soil-based probiotics are also what make them the best probiotics for SIBO.

The Benefits of Soil-based Probiotics – Infographics – Amy Myers MD®The Benefits of Soil-based Probiotics - Infographics - Amy Myers MD® Benefits of Soil-based Probiotics – Infographics – Amy Myers MD®

Soil-Based: The Best Probiotics for SIBO

Soil-based probiotics do not exacerbate symptoms of SIBO in the way other types of probiotics can. In fact, one clue that you may have SIBO is that when you take a probiotic containing lactobacillus or bifidobacterium you have an exacerbation of your symptoms such as more gas, bloating, constipation, diarrhea or other digestive symptoms. If you are currently dealing with SIBO, a probiotic containing lactobacillus or bifidobacterium probiotic strains is not recommended until you eliminate your bacterial overgrowth and repair your gut microbiome.

When it comes to SIBO and probiotics that won’t exacerbate your symptoms, soil-based probiotics don’t colonize in the small intestine or feed the bacteria already growing there. 

What’s more, the soil-based organisms in soil-based probiotics know to stay in their spore state until their environment is safe. This makes soil-based probiotics a great option for SIBO because they don’t populate the small intestine. Instead, these probiotics head straight to the large intestine and colon where they can support vibrant health benefits.

A 2-week double-blind clinical study of patients diagnosed with IBS (irritable bowel syndrome) demonstrated a significant reduction in symptoms when treated with a soil-based probiotic.3 About 80% of IBS patients are likely dealing with SIBO, so soil-based probiotics are an effective way to alleviate any SIBO-related symptoms.

Soil-Based Probiotics for Autoimmunity

Because SIBO and autoimmunity are so closely linked, soil-based probiotics for SIBO can benefit those with autoimmune conditions as well. One specific strain of bacteria found in soil-based probiotics helps with the production of immunoglobulin A (IgA). These immunoglobulins, or antibodies, play a key role in your immune system.

Many of my autoimmune patients were low in IgA. When their IgA levels were optimized, I saw a positive impact on inflammatory and autoimmune markers. Additionally, IgA supports your gut repair pathways, helping to restore your gut lining so that toxins, microbes, and food particles are no longer able to escape via your bloodstream and trigger an immune response.4

Soil-Based Probiotics: Superstar Strains

The unique benefits of soil-based probiotics come from the combination of organisms they contain. The three, well-studied bacterial strains found in soil-based probiotic Primal Earth are Bacillus clausi, Bacillus coagulans, and Bacillus subtilis.

1. Bacillus Clausii (B. Clausii):

  1. Helps modulate your immune response
  2. Assists in IgA synthesis
  3. Antibiotic resistant for use with antibiotic treatment of SIBO
  4. Produces bactarin, a weapon against pathogens5

2. Bacillus Coagulans (B. Coagulans):

  1. Helps the good bacteria successfully colonize in your gut
  2. Potent immune stimulator
  3. Long history of studied use in IBS, Crohn’s, and ulcerative colitis6

3. Bacillus Subtilis (B. Subtilis):

  1. Supports gut repair by increasing IgA and butyrate
  2. Produces over 12 antibiotics
  3. Ferments Vitamin K in your gut, which is essential for growth and repair
  4. Has a positive impact on inflammatory and autoimmune markers
  5. Widely used, safe, and effective

In addition to these specialized skills, the superior seed-like structure of soil-based SIBO probiotics makes them resistant to heat, light, oxygen, and the harsh conditions of your digestive tract. This means that Primal Earth soil-based probiotics will make it through to your gut alive and ready to work! Members of my community with SIBO tell me all the time they experience better results with soil-based probiotics. Plus, these probiotics don’t need to be kept in the fridge and travel well.

With a great soil-based probiotic such as Primal Earth, a healthy diet, and the goal to achieve optimal wellness, you can eliminate SIBO and take back your health.

Bottle of Primal Earth Probiotic

Soil-Based Probiotics FAQs

What are soil-based probiotics?

Soil-based probiotics contain bacteria that are naturally found in our soil. Soil-based probiotics get us back to our roots (literally!) by giving us the same bacteria that we consumed with our food before sterilizing farming techniques.

What are the best probiotics for SIBO?

Because soil-based probiotics don’t colonize in your small intestine or feed the bacteria already growing there, soil-based probiotics are the best probiotics for SIBO.

Which types of probiotics are found in soil?

There are over 100 types of soil-based probiotics. My Primal Earth Probiotic contains three of the most well-studied strains: Bacillus Clausii, Bacillus Coagulans, and Bacillus Subtilis.

Article Sources

  1. Small Intestinal Bacteriall Overgrowth: A Comprehensive Review. Andrew C Dukowicz, Brian E Lacy, Gary M Levine. NCBI. 2007.
  2. Bacterial Endospores. Cornell Department of Microbiology. 2021.
  3. Prescript--Assists Probiotic--Prebiotic Treatment for Irritable Bowel Syndrome: A Methodologically Oriented, 2-Week, Randomized, Placebo-Controlled, Double-Blind Clinical Study. Alvah C Bittner, Robert M Croffut, Mary C Stranahan. NCBI. 2005.
  4. Intestinal IgA Production and It's Role in Host-Microbe Interaction. Cindy Gutzeit, Giuliana Magri, Andrea Cerutti. NCBI. 2014.