Soil with seedings and parent with child's hand by The Healthy RD

Soil Based Probiotics: Do They Help Your Gut Health?

What are Soil-Based Probiotics? Soil based probiotics, as they name implies, are tiny microbial species which reside in the rich dirt of garden beds, forest floors and other earthy, natural environments.

As humans, why should we care about these?

Our digestive tract holds the key to so many aspects of our health, so finding out how to best improve digestion is key for ALL of us.

Probiotics, the tiny, beneficial microorganisms in our body, are always a cornerstone to digestive health.

This post is written by Kasey Hutchinson, RD, a colleague of mine that focuses on sustainable food choices, soil ecology, and evidenced-based health solutions.

Soil-Based Probiotics Overview

Soil based probiotics help plants by mining minerals in the soil and delivering these nutrients to plant roots.

In this way, soil probiotics help plants grow and increase the mineral content of foods.

In recent years, researchers discovered that many of these soil based probiotics also inhabit the human gut.

In our gut, they complete a vast number of tasks which help the human body.

In particular, soil based organisms help [R, R, R, R]:

  • Restore gut health
  • Reduce symptoms of IBS
  • Send mind-calming signals along the gut-brain axis
  • Form disease-fighting molecules.
  • Reduce leaky gut


Soil-Based Probiotics Are Native to the Human Gut

Soil based probiotics are normal inhabitants of the human GI tract.

Most popular are the Bacillus strains-they are generally recognized as safe, according to the FDA.

Historically, soil-based probiotics would hitch hike into the digestive tract on the foods we eat [R].

What happened to our Gut Probiotics?

Humans of the modern age are much more sanitary than they used to be [R].

Handwashing, pesticides, antimicrobial cleaners and triple washed vegetables have created a separation between us and microbes.

While greatly reducing risk of infection, sanitation has also abridged our exposure to good bacteria, too. Some experts even think that the loss of beneficial bacteria increases some kinds of infection.

Researchers speculate that this hyper-sanitation, along with several genetic, dietary, and lifestyle factors, has led to numerous unintended consequences, such as a rise in immune and gut-related disorders.


Soil-Based Probiotics Promote Symbiosis and Help Restore Gut Health

The human gut microbiome operates as an ecosystem.

Certain keystone species perform necessary functions which support other colonies of beneficial bacteria.

What is Symbiosis?

Symbiosis is a beneficial interaction between two things.

Here is an example of how soil based probiotics give us symbiosis.

Lactic acid producing bacteria can increase the acidity of the gut.

This creates an environment where pathogens cannot thrive and promotes the production of anti-inflammatory molecules such as butyrate.

This delicate symbiosis is also why numerous inflammatory and pathogenic species also bloom simultaneously.

Which Kind of Soil Probiotics to Choose?

Soil-based Bacillus species that are the most researched include [R].­:

  • B. coagulans
  • B. subtilis
  • B. clausii
  • B. lichenformis
  • B. indicus

All of these Bacillus species are shown to increase the abundance of lactobacillus and bifidobacteria [R]. These families of bacteria improve digestion, modulate immunity and lower inflammation.

Lactobacillus and Bifidobacteria are the most popular probiotics found in many supplements.

Interestingly, soil-based probiotics such as Bacillus subtilis and Bacillus clausii also work in synergy with more recently discovered strains.

How do they work?

Bacillus species metabolize resistant dietary starches.

This produces acetate, lactate and oligosaccharides as a byproduct. Another name for these is called postbiotics.

These postbiotics are then fed to other gut friendly species like F. prausnitzii and Akkermansia muciniphila [R, R].­­

These friendly bacteria prevent leaky gut and boost metabolism.

However, F. prausnitzii and Akkermansia muciniphila cannot be taken as a probiotic at this time.

So using soil based probiotics plus prebiotics is a recommended method for improving their abundance in the gut.

The Honest Company

What is the Research Behind Soil-Based Probiotics?

Research on soil-based probiotics is still in its infancy, yet studies are coming out every day regarding their benefits.

Leaky Gut

One recent study found that daily supplementation with a 5-strain bacillus spore probiotic for 30 days led to a significant reduction in leaky gut.  What is leaky gut?

According to the journal of Nutrients, substances called endotoxins are formed when harmful bacteria like Gram-negative bacteria cause systemic inflammation.

They do this by increasing endotoxins, such as lipopolysaccharides  [R].  The gut  is considered the main natural reservoir of pro-inflammatory endotoxins in the body.

As these endotoxins are released when harmful bacteria die, they cross the gastro-intestinal barrier and end up throughout your body.  This is known as leaky gut and endotoxemia.

Where do soil-based probiotics come in? They reduce these toxic effects and may reduce leaky gut as well.

Bonus: these soil probiotics lowered blood triglycerides and inflammatory biomarkers in individuals consuming ultra-processed, high fat meals [R].

Respiratory Benefits

Benefits of soil bacteria may extend to the lungs as well.

Another double blind, placebo-controlled study assessed the effects of intermittent Bacillus subtilis supplementation on 100 elderly people.

The goal was to see how this treatment effected incidence of respiratory and gastrointestinal illness. Results indicated that B. subtilis activated the immune system and significantly reduced incidence of respiratory infection [R].


Soil-based probiotics may also be useful in the treatment of acne [R]. Acne patients have altered intestinal bacteria [R].

Doctors as far back as the 1930’s were recognizing the potential benefits of probiotics for skin.

To support these theories, diets of hunter-gatherer societies that are still in touch with soil culture have little to no acne [R]. Meanwhile, acne rates in Westernized cultures continue to soar.

Gut bacteria influences body fat profiles.  It is possible that they affect skin sebum production and fat within the sebum [R].


Do you need a soil-based probiotic supplement?

Soil-based probiotic supplements can be part of a protocol to restore gut health in those with gut dysbiosis and/or leaky gut.

They also can help treat secondary conditions such as acne leaky gut.  Leaky gut can lead to metabolic endotoxemia.

The most exciting part is that soil based bacillus species is that they are spore formers.

Spore formers are:

  • Highly resistant to stomach acid
  • Can have long time period on the shelf
  • resistant to heat and other factors

Therefore they are able to survive digestion and arrive safely to the gut, where they are reactivated and begin to work their magic.

Natural Soil Based Probiotics

These beneficial bacteria exist in other natural places as well.

  • spending time outside
  • gardening
  • purchasing foods from local, organic farms

Spending time doing these activities may also increase your chances of picking up these hitchhikers on the food we eat.

There are also some fermented foods that contain the same bacillus species as found in many supplements.

For example natto, a Japanese dish made with fermented soybeans, contain Bacillus subtilis.

Probiotic supplementation is therefore not necessary for most healthy adults, but may be beneficial for more potent interventions.

Soil Probiotics Brands

Many brands contain some strains of soil based probiotics.

I don’t get paid to endorse this brand and no personal gain from recommending it, but my colleagues use and love it too.

A very high quality brand is from Microbiome Labs.  It is called Mega Spore.  At this point, you need a practitioner to prescribe this kind of probiotic.

Because this brand is spore-based, it is shelf stable and has a shelf life of 5 years. It is effective when taking antibiotic therapies as well. It is also unique because it is 100% spore based.

Soil Based Probiotics Side Effects

As natural and beneficial bacteria, soil probiotics have no known side effects.

Other types of probiotics are sometimes related to mild digestive issues such as gas, bloating, and changes in bowel movements.  However, these are usually short term side effects and improve after a week or so.


Soil based probiotics are all the rage these days and as the research shows, this is very exciting and positive news! If you are feeling weary about taking them as supplements supplements, consider spending more time outdoors and eating local, organic foods to acquire these naturally.

Want to learn more about Kasey?  Visit Vibrant Nutrition RD to learn more.

Want some other basic gut health tips?  Read 15 Easy Health Tips To Improve Your Health Today.

Medicinal foods by The Healthy RD





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