Probiotics and Spores: What’s the Difference?

Many health conditions stem from having a dysfunctional digestive system at their core. In fact, the gut can be seen as “ground zero” of several of these health issues. Primary digestive conditions can be a result of digestive disruption, where digestion is weak. When you take a probiotic, you hope to see obvious improvements in digestive health and immunity – this is especially true in frustrating and chronic health conditions.

Unfortunately, most probiotics can’t get past the acidic environment of the stomach. If a probiotic can’t survive outside of a refrigerated environment, is it going to survive in the acidic environment of the gastrointestinal tract (GIT)? The answer is “no”.

How do I know which probiotics to take? Aren’t all probiotics the same?

There has been a lot of research done on different strains of bacteria. However, there is considerable confusion on why you should take specific strains. What strains should be in a probiotic? Most of the probiotic products on the market are lactobacillus and bifidobacterium based products. Some need to be refrigerated and some don’t. These organisms are the ones that are most concentrated in the digestive tract. We get these bugs from our mother during development, the birth process, and breastfeeding. These organisms are anaerobic – which means that they cannot survive in an oxygen rich environment 1; they are also not found in our food supply. Research shows us now that these bugs do not survive the stomach acid 2.

What are true probiotics?

True probiotics should survive the stomach acid and must exist in your digestive tract as well as in your environment, where we can get access to them through our food supply. A healthy microbiome is a diverse microbiome.

The World Health Organization (WHO) defines probiotics as:

“live microorganisms which when administered in adequate amounts confer a health benefit on the host”; in order to be labelled a probiotic, scientific evidence for the health benefit would have to be documented3

A research study performed at Reading University in England took 35 of the most widely used probiotics used in the marketplace and found that none of these strains completely survived the harsh environment of the stomach 4.

Very few organisms fit the definition of what a true probiotic is. But there is one category of organisms that are very interesting – and these are called bacillus spores. There are a number of different Bacillus bacteria that are probiotic organisms, and they exist in spore form. When they are in their spore form, they have the capacity to survive the stomach acid 100% intact.

Spores? Tell me more!

Interestingly, Bacillus spores have been used in other industries for over 50 years and have been used extensively in agriculture and aquaculture. Bacillus are the most widely studied and most widely used probiotics outside of the supplement market! Bacillus spores were the first prescription probiotics, dating back to 19585. The most widely used and well-studied strains in humans are Bacillus Subtilis, Bacillus Licheniformis, Bacillus Coagulans, Bacillus Clausii and Bacillus Indicus HU36™.

Bacillus spores are known as universal probiotics. They are found in the digestive tract of insects, animals, marine life and humans. Research shows that the development of the human immune system is dependent on exposure of bacillus spores – and it is not just immune stimulation but immune development that is dependent on exposure 6.

All humans have binding sites for Bacillus spores because they belong in the gut. Therefore, you can take a probiotic with a daily amount of ‘only’ 3 Billion colony forming units (CFU) and have an effect on the immune system that a true probiotic is supposed to have.


[1] Hentges DJ. Anaerobes: General Characteristics. In: Baron S, editor. Medical Microbiology. 4th edition. Galveston (TX): University of Texas Medical Branch at Galveston; 1996. Chapter 17. Available from:

[2] Gorbach SL. Microbiology of the Gastrointestinal Tract. In: Baron S, editor. Medical Microbiology. 4th edition. Galveston (TX): University of Texas Medical Branch at Galveston; 1996. Chapter 95. Available from:

[3] Mack DR. Probiotics-mixed messages. Can Fam Physician. 2005;51:1455–7. 1462–4.

[4] Gibson GR, Rouzaud G, Brostoff J, Rayment N. An evaluation of probiotic effects in the human gut: Microbial aspects. Final technical report for Food Standards Agency (FSA) project ref 2005;G01022

[5] Celandroni F, Vecchione A, Cara A, Mazzantini D, Lupetti A, Ghelardi E. Identification of Bacillus species: Implication on the quality of probiotic formulations. PLoS One. 2019 May 20;14(5):e0217021. doi: 10.1371/journal.pone.0217021. PMID: 31107885; PMCID: PMC6527297.

[6] Oh Y, Kim JA, Kim CH, Choi SK, Pan JG. Bacillus subtilis spore vaccines displaying protective antigen induce functional antibodies and protective potency. BMC Vet Res. 2020 Jul 28;16(1):259. doi: 10.1186/s12917-020-02468-3. PMID: 32723323; PMCID: PMC7385935.

By Jessica Sanders, Gutsi® Naturopath.