soil based organism melbourne

All About Soil-Based Organisms

Soil-based probiotics have been lauded as powerful gut restorers and tiny vitamin factories. But, unfortunately, they've also been vilified as dangerous immune threats. Unfortunately, such differences of opinion aren't very helpful to you when choosing dietary supplements.

Soil-based probiotics are bacteria naturally found in the earth. One of the most common types of soil-based probiotics (bacillus) has been used to ferment foods for hundreds of years.

If you've tried other types of probiotics and they haven't worked for you, soil-based probiotics might be worth a go. Read on to find out how soil-based probiotics could boost your health.

For most of human history, we have been living close to the earth. We got our food from the ground, not the supermarket, and we didn't use disinfectants to wash it. So today, unless you grow your own food or eat organic produce straight from the field, you won't ever come across soil-based probiotics.

Probiotics are living microorganisms that can be found in the human digestive system and help with digestion. The enzymes within these organisms allow for breakdown of food. Different types of bacteria can also help regulate immune responses, moods and even weight loss. There is a question about whether or not soil-based probiotics are safe to take, so let’s explore this topic together!

Soil-based probiotic supplements contain live bacteria grown on agricultural byproducts such as plant matter or animal manure, which can pose some health risks if taken improperly under certain conditions. Many questions also arise, are soil-based probiotics safe? 

The idea of taking soil-based probiotics may seem strange to some people, but there are many benefits that come with using this type of supplement. For one, the bacteria found in earthy soil is different than what you find in yogurt or other supplements because it has been exposed to a wider range of organisms and elements over time. This means the bacterial strains could be more helpful for your gut health. Soil-based probiotics can also be taken either orally or topically on wounds, so they have several uses! 

organic soil

What Are Soil-Based Probiotics?     

Soil-based organisms are bacteria that are naturally found in our soil. Before introducing modern farming methods, food-processing and sterilising techniques, SBOs were abundant in our food chain. In the past, people expected to see a little soil on their fresh produce, whereas nowadays we like to see gleaming rows of clean, shiny vegetables and fruits in our supermarket. Likewise, when we used to drink water from wells and springs, we exposed our digestive tracts to a wide range of bacterial species. Currently, unless we are consuming home-grown, or at least organic, raw produce, there is very little bacteria left on the food we are eating. Lack of exposure to these soil-based bacteria is thought to be detrimental to the development of the immune system, and 'being too clean' is associated with allergic conditions such as asthma and eczema1. You may like to look at our Probiotics for allergies page, which explores why allergies develop and if probiotics can help.

The age-old saying, "God made dirt, and dirt don't hurt", may be true.

Soil-based probiotics are good bacteria in the soil that have evolved in contact with humans. Until recently, humans were exposed to soil and soil-based organisms daily by eating, farming, and hunting.

Soil-based probiotics such as Bacillus subtilis are a part of our normal microbiome. They form spores that can survive harsh conditions, like stomach acid, irradiation, and high temperatures. Thus, this category of bacteria is also sometimes called spore-forming bacteria.

What Makes Soil-Based Probiotics Different?

Most probiotic supplements on the market today contain strains of lactic-acid producing bacteria of the Lactobacillus and Bifidobacterium genera.

Unlike these lactic-acid producers, SBOs are spore-forming bacteria.

This spore-forming characteristic enables these bacteria to essentially "hibernate" in extreme environmental conditions when nutrients are scarce then germinate once again when food becomes available.

Which Soil-Based Probiotics Have Health Benefits?

The most studied soil-based probiotics are species in the genus Bacillus.

Like other types of probiotic bacteria, soil-based probiotics help maintain digestive health and regulate the immune system. However, unlike other types of probiotics, they appear to colonise the digestive tract.

Clinical studies into bacillus probiotic strains show benefits that are similar to better-studied probiotic species like Lactobacillus and Bifidobacterium.

Enterococcus Faecium

Enterococcus faecium, also known as E. faecium, can be commensal in the guts of humans and animals, but it may also cause diseases like neonatal meningitis or endocarditis.

Bacillus Coagulans BGI-30, 6086

Bacillus coagulans is the most studied soil-based probiotic. In nine clinical trials, B. coagulans positively affected diarrhea, bloating and abdominal pain, SIBO, and constipation.

This strain was deemed safe for chronic human consumption in 2009, both in Europe and the USA3. Since then, it has been used widely in food and drink products, including infant milk formula, healthy food bars and naturally found in fermented products like sauerkraut and kombucha.

Furthermore, B. coagulant GBI-30, 6086, has decreased upper respiratory and gastrointestinal symptoms in a study of 80 healthy school children. The strain significantly decreased the incidence of respiratory symptoms, including:

  • Nasal congestion
  • Bloody nasal mucus
  • Itchy nose
  • Hoarseness

 The duration of these respiratory associated symptoms, including hoarseness, headache, red eyes, and fatigue, was also decreased4.

Bacillus Subtilis HU58

Bacillus subtilis has shown some benefit in clinical trials for constipation on its own. It has also been studied in combination with the soil-based probiotic Enterococcus faecium. It is helpful for irritable bowel syndrome (IBS), constipation, and H. pylori treatment. Research data also suggests that laxatives or motility agents combined with Bacillus subtilis are more effective than the motility agents alone or a placebo.

This strain produces a beneficial enzyme called nattokinase, which has been shown to support healthy blood pressure and cholesterol levels5. In addition, one study showed that Bacillus spores, including B. subtilis HU58, were able to stimulate an increase of cells within the gut and promote a positive immune response6.

Interestingly, soil-based organisms, including the Bacillus subtilis species, have shown promise in supporting complex digestive issues like Small Intestinal Bacterial Overgrowth7. Health professionals can read more about this here on the Professionals site: Small Intestinal Bacterial Overgrowth. In the debate of soil-based organisms vs probiotics for dealing with SIBO, it looks like soil-based strains do not exacerbate symptoms of SIBO in the way regular probiotics can do.

Bacillus Clausii 

organism on soil melbourne

Bacillus clausii has been shown in clinical trials to reduce side effects from H. pylori treatment, including nausea, diarrhea, and pain. It has also been shown to decrease acute diarrhea and to help in the treatment of SIBO.

Bacillus licheniformis reduced the risk of gastrointestinal side effects from radiotherapy treatment, such as nausea, diarrhea, and vomiting. It also improved diarrhea symptoms in another clinical trial.

Soil-based probiotics have also been shown in studies to:

  • Increase secretory IgA, which plays an important role in immune function
  • Decrease leaky gut
  • Decrease respiratory tract infection rates 
  • Encourage a healthier gut microbiome 
  • Decrease inflammation 
  • Decrease post-exercise muscle soreness 
  • Help manufacture nutrients, such as B vitamins 
  • Decrease side effects from antibiotics 

Are soil-based organisms safe?

Some health professionals have previously argued that soil-based organisms may not be safe. This is because they produce such resilient spores that may not activate in the small intestine, thus producing little benefit. However, these fears are unfounded for probiotic SBOs, as they will have been thoroughly trialled and deemed safe by regulatory authorities. In addition, most studies show the spores activate in the small intestine when surrounded by various nutrients8.

When an individual consumes the inactive spore, the spore can make it to the small intestine, largely unaffected by the stomach acid. With plenty of nutrients available, the spores germinate ('activate') and begin to elicit positive effects, depending on the strain. They can also replicate as normal when conditions are favourable. As they pass down to the colon, when nutrients once again become limited, many of the vegetative ('active') cells sporulate, meaning they return to spore format and are excreted in our poo!

Large scale human studies have now been conducted on SBOs, identifying the most effective strains, with no adverse side effects recorded. In addition, SBOs have been shown to create a more hospitable environment for our own good bacteria to flourish9, further crowding out bad bacteria or yeasts like Candida. 

Soil-based strains are used extensively in producing food and drink products and therefore have been widely studied. This also means that they must have GRAS status (Generally Recognised as Safe and approved by the FDA) or have met the European equivalent, QPS (Qualified Presumption of Safety) accreditation criteria. In addition, their bacterial genome has been sequenced and deemed as 'non-pathogenic, which means that this type of bacteria is not regarded as having any ability to be harmful to health in any way.

One 2017 study on the safety of Bacillus probiotics concluded that, although they have had "an overall excellent health-promoting record", especially for diarrhoea, H. pylori, and maintaining the delicate balance of microbes in your gut, if you have any issues with your immune system, you should probably steer clear.

No one avoids eating carrots because they're in the same plant family as poison hemlock. And yet, internet advice continues to caution people to stay away from soil-based probiotics because some Bacillus bacteria are unsafe.

Research clearly shows that specific bacillus species are beneficial and safe.

And while it's very unlikely that your soil-based probiotic supplement would be contaminated with Anthrax, it is important to pay attention to labelling and safety when buying ANY probiotic supplements.

The authors also stressed how important it is for future researchers to include populations of immune-compromised people in their studies. This is because they are most likely to suffer from soil-based probiotics side effects or react badly to them.

If you're fit and well, there's no reason why you shouldn't try one of the well-researched strains. There are no best soil-based probiotics; just consider the specific strain of bacteria when deciding which one to buy. If the strain isn't listed on the label, contact the manufacturer to ask them which one they use in that product. If they can't tell you, stay away!

Soil Based Probiotic Dangers

While SBOs have been around for a while, the issue isn't black and white. Some experts are gung-ho on soil-based probiotics because they say they can help re-seed gut microbes. But, on the other hand, other experts warn of soil-based probiotic dangers.

The idea is if a person does not have enough of their healthy gut flora to compete with the SBO spores, it opens the door for them to become pathogenic.

Now that our gut microbiomes are less familiar with SBOs (from a decrease in exposure), and because most of our gut microbiomes are compromised, SBOs can compete with our resident gut flora rather than compliment them. In some instances, SBOs can even become pathogenic, and this scenario is more likely in an out of balance microbiome.

One of the primary reasons to supplement with probiotics is to help counteract the devastation that environmental toxins, the overuse of antibiotics, and modern dietary choices have wrought on our gut flora balance. However, while it may seem logical to supplement with SBOs since we no longer ingest them regularly, this line of logic is a major cause of disagreement among experts.

Some studies have suggested that SBOs are similar to the dreaded super germs that resist traditional antibiotic treatments. For example, many of the most common strains of SBOs come from the Bacillus genus, including the subtilis and lichenous species. Bacillus strains are extremely hardy and form spores that can resist stomach acids and antibiotics. This characteristic makes SBOs more desirable to marketers because they will survive stomach acids, extreme heat, and even food processing.

The shelf life for SBOs is simply amazing, which also happens to be the biggest challenge manufacturers must overcome for microbes that reside in the human gut. And, since they technically fall under the label of "probiotics," it's an incredibly convenient and easy way to add probiotics to everything from supplements to hot teas and nutritional bars without having to figure out a way to keep the organisms alive. Problem refrigeration required!

It's also this spore-forming trait that makes a Bacillus overgrowth incredibly difficult to treat. The spores are so tough that they can hibernate in the intestines throughout a course of intense antibiotic therapy, only to resurface after the threat has passed.

According to the U.S Environmental Protection Agency (EPA), many bacillus species can cause serious health issues, while others are opportunistic bacteria that make great insecticides. For example, Bacillus subtilis, considered a comparatively benign member of this genus, is one of the species used in SBO supplements. Still, subtilis is also an active ingredient in many industrial detergents and cleaners the EPA cautions against allergic reactions and sensitivities to products containing these microbes.

These soil-based organisms make their way into our systems as well. Some hitch a ride on our hands or on raw fruits and vegetables that we eat. You also get some soil-based organisms in natto and traditionally pickled vegetables.

Soil-based probiotics are bacteria found in the soil that have been shown to balance gut bacteria, produce antioxidants, improve leaky gut, and lower inflammation in the body. In addition, unlike traditional probiotics, these spore-producing bacteria survive harsh digestion conditions, making them much more effective. 

Frequently Asked Questions About Soil-Based Probiotics

Lack of exposure to these soil-based bacteria is thought to be detrimental to the development of the immune system, and 'being too clean' is associated with allergic conditions such as asthma and eczema.

Soil-based probiotics are bacteria found in the soil that have been shown to balance gut bacteria, produce antioxidants, improve leaky gut, and lower inflammation in the body. In addition, unlike traditional probiotics, these spore-producing bacteria survive harsh digestion conditions, making them much more effective.


There are two main differences between probiotics with soil-based organisms and other probiotics. First, both are down to their hardiness: Soil-based probiotics have a longer and more stable shelf-life, so they don't need to be refrigerated. That means they might be easier to take with you when you're travelling.

SBOs are vegan non-dairy strains that don't require refrigeration, and unlike many dairy-based probiotics, they're much heartier. They can survive stomach acid to implant in your gut, creating the balance you need! This formula includes prebiotics to feed the probiotic strains and help them take root and proliferate.

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