Probiotics Learning Lab Impartially created by the experts at OptiBac

There is currently a bit of a debate raging within natural health circles over the mooted health-benefits of a group of bacteria, referred to as soil-based organisms ('SBOs' for short - or alternatively ‘soil bacteria’, ‘soil organisms’, or ‘homeostatic soil organisms’). Advocates of soil-based organisms claim that they are probiotics, and that they have a myriad of health benefits, including: the activation of the immune system, stimulation of white blood cells and antibodies, normalisation of bowel function and an increase in resistance to harmful bacteria and fungi. SBOs have also been praised for their ‘hardiness’ and their ability to resist stomach acid and ambient temperatures, meaning that supplements containing SBOs often do not require refrigeration.

soil in hands

Opponents of SBOs however argue that due to their spore-forming nature SBOs proliferate rapidly, and can compete with our resident gut flora, rather than compliment it. In individuals with compromised immunity it is feared that these organisms can over-grow, and even become pathogenic and cause many different side-effects.

So, what are SBOs?

Soil Based Organisms are bacteria that are naturally found in soil. Before the introduction of modern farming methods and food-processing and sterilising techniques SBOs were present in abundance in our food chain. People did not used to mind if their produce had a little bit of mud on it, whereas nowadays we like to see gleaming rows of shiny vegetables and fruits in our supermarkets and grocers. Likewise, when we used to drink water from wells and springs we would have 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 of this type of bacteria left in the food that we are eating. Lack of exposure to soil-based bacteria is thought to be detrimental to the development of the immune system, and can result in allergic conditions such as asthma and eczema. You may like to read our earlier blog post reporting on a BBC Horizon programme which linked our more ‘sterile’ living environments to many childhood illnesses.

There are hundreds of different species of SBOs, with many of the most common coming from the Bacillus genus (or family), such as Bacillus subtilis and Bacillus coagulans (this species of bacteria was formerly mis-classified in 1933 as Lactobacillus sporogenes before it was correctly identified as Bacillus coagulans). One of the characteristics that separates SBOs from other live cultures, is the fact that they are spore forming, meaning that when a bacterium detects that essential nutrients are running out it is able to replicate its DNA and then pinch its plasma membranes off between the two sets of chromosomes, to create an external spore. Once this ‘endospore’ is released the bacterium that generated it dies and disintegrates. These spores are protected by a hard coating that make them very resistant to heat, acidity and even antibiotics. Whilst this resilience certainly has its advantages, particularly for the supplement manufacturers, it could also potentially have disadvantages for the delicate equilibrium of the intestinal flora.

soil based bacillus subtilis
Bacillus subtilis (above) is commonly found in the soil.

Scientific research:

Research information regarding the safety of SBOs is limited. Some in-vitro studies have been performed in a laboratory setting, such as a Polish study1 looking at the anti-fungal activity of Bacillus Coagulans (formerly Lactobacillus sporogenes). When this strain of bacteria was added to a culture containing the yeast Fusarium, some inhibition of the yeast was noted, suggesting that Bacillus coagulans exerts an anti-fungal effect.

Some mammalian studies have also been performed on Bacillus Coagulans, including a study2 on mice which looked at whether this bacterium could inhibit the growth of van****cin-resistant enterococci (VRE). The results showed that this particular strain of SBO was only successful in inhibiting one of the three VRE strains studied, which was a less conclusive result than the researchers had been hoping for.

There have been relatively few actual human trials to date, although a small 2005 study3 did show promising results using a multi-strain SBO probiotic and prebiotic formula. This SBO formulation or a placebo was given to 25 IBS patients for two weeks. Their symptoms were detailed one week before the trial started, and then at weekly intervals for three weeks. The three main symptoms of IBS: nausea, indigestion/flatulence and colitis pain all reduced by a statistically significant amount in the probiotic group during this time. This study was then followed up 60 weeks later 4, and the majority of trial participants continued to see some reduction in symptoms, even a year later. For more information about IBS & microbes, healthcare professionals can read our in depth FAQ about IBS & probiotics.

A balanced view:

I think it is important that we all take responsibility for our own health, and make informed choices. Having looked at the arguments for and against SBOs, I personally feel that I would like there to be more, larger-scale, human clinical trials on them that can guarantee their safety, before I take them myself or recommend them in my clinical practice. Anecdotally, there appears to be lots of reviews from people that have seen positive impacts on their health from taking them, however it seems that if there is any question around the integrity of the gut lining, then a patient should potentially look to heal the gut before they start on SBO supplements. Dr. Natasha Campbell McBride a specialist on intestinal permeability advocates not only healing the gut first, but also ensuring strong colonies of Lactobacillus and Bifidobacteria in the small and large intestines, before considering adding SBOs to a natural healing protocol. In this way it is supposed that there is less potential for them to over grow, due to competitive inhibition from other strains of friendly bacteria already residing in the gut.

Before conclusive evidence showing the health benefits of taking SBOs in supplement form is available, I would suggest that using the correct strain of ‘regular’ probiotic would be the best approach to optimising gut health. The fact that SBOs are resistant to both stomach acid and heat is of no additional advantage when comparing them to our own range of probiotics, as we test each strain of bacteria that we use to ensure that they survive both of these factors (and more) to reach the intestines alive anyway.

If you suffer from any type of digestive discomfort, my recommendation would be to find the best strain of probiotic for your specific condition, be that constipation, diarrhoea, bloating, cramping etc. The strain(s) you select should have relevant clinical trials for the indication that you are using it for, and preferably be taken at the same dosage as the clinical trial was performed at.

For further reading, you might be interested in:

Probiotics for animals and farming: A new trend on the rise?

Probiotics could be used to clean NHS hospitals


1. Acta Microbiol Pol. 2002;51(3):275-83. Antifungal activity of Bacillus coagulans against Fusarium sp. Czaczyk K1, Trojanowska K, Mueller A. 2. Lett Appl Microbiol. 2001 Jul;33(1):84-8. Effect of oral Bacillus coagulans administration on the density of van****cin-resistant enterococci in the stool of colonized mice. Donskey CJ1, Hoyen CK, Das SM, Farmer S, Dery M, Bonomo RA. 3. Bittner et al, 2005. “Prescript-Assist probiotic-prebiotic treatment for irritable bowel syndrome: a methodologically oriented, 2-week, randomized, placebo-controlled, double-blind clinical study.”, Bittner et al, 2007. “Prescript-assist probiotic-prebiotic treatment for irritable bowel syndrome: an open-label, partially controlled, 1-year extension of a previously published controlled clinical trial”,
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  • I have been taking a soil based probotics for four months now on and off. It has helped me tremendously but should I be worried? I am afraid of antibiotic resistance :/

  • Probiotics Learning Lab

    Dear Melanie,

    Thank you for your feedback about the use of soil-based probiotics.
    Regarding your question: as Kathy reports, the simple truth is that there is not enough evidence available for me to be able to advise you one way or another, and this is why we don't currently carry this type of bacteria within our range.

    As the article outlines, the issue of antibiotic-resistance in soil-based organisms, and whether they should be considered to be a probiotic or pathogen, is still being debated, though there are many people like yourself who swear by these probiotics and report positive benefits from using them.

    I would not worry about taking the probiotics, especially if you have noted a positive difference. At the end of the day, we will encounter countless different bacteria every single day, and in general this diversity is considered to be a good thing.

    The property of a probiotic being resistant to antibiotics is not in itself a cause for concern, and can sometimes be a blessing (read my latest blog about the use of Lacidofil probiotic in clinical trials alongside antibiotics:
    The real concern is whether regularly introducing large numbers of SBPs on an ongoing basis will negatively affect the delicate populations of beneficial bacteria that are so necessary for good health.

    As Kathy says in the blog, I'd recommend that it's best to use well-researched strains if you're choosing to supplement with probiotics.

    I hope this helps - we will definitely be keeping an eye on the research into the use of SBPs as it develops.

    Hope this helps,

    Customer Care and Nutritional Advisor
    OptiBac Probiotics

  • Hi
    I took a digestive enzyme which unfortunately contain bacillus subtilis which I am afraid may have destroyed my gut flora. What do I do now?


  • Probiotics Learning Lab

    Dear Reina,

    Thank you for your comment, and the first thing that I would say to you is to try not to worry!

    As we don't carry this strain of bacteria within our range, primarily because there is not a huge amount of research to support its use as a probiotic supplement, I'm not able to offer you any in-depth advice about its use; however, I do know that we are likely to encounter this type of bacteria widely in nature, through exposure to soil, water and air.
    So I really would not worry about taking the supplement, though if you have any concerns perhaps you should contact the supplier of this product for more information on the research they have to support its use.

    For total peace of mind, in future, I'd stick to a probiotic that contains very well-researched strains.

    I hope this helps,

    Nutritional advisor
    OptiBac Probiotics

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