As the name suggests – these strains come from the earth! We were naturally exposed to these types of bacteria, but due to modern day farming techniques these soil strains are less abundant in our diet. Further, due to many reasons our gut microbiome is disrupted, such as:

• Antibiotic use
• Processed food diet
• Excessive sanitation (more on this below)
• Chronic stress
• Food poisoning
• Vagal nerve dysfunction
• Unresolved systemic infections
• High refined sugar consumption

And the list goes on.

So where does spore based probiotics come in? First, let’s look at the regular strains. Some of the most common strains of regular probiotics are:

• Lactiobacillus rhamnosus
• Lactobacillus salivarius
• Lactobacillus acidophilus
• Lactobacillus casei
• Bifidobacterium lactis
• Bifidobacterium bifidum
• Bifidobacterium longum

Regular probiotics are strains which naturally occur in our body and can be found in foods such as yogurt, sauerkraut, kimchi, kombucha and kefir. Whilst probiotic food and supplements can be beneficial in certain circumstances, if you find yourself reacting to them, it may be due to a common condition called small intestinal bacterial overgrowth aka SIBO. In this instance probiotics can worsen symptoms such as bloating and distention due to the overgrowth of Lactobacillus and Bifidobacterium in the small intestine producing methane or hydrogen.

Soil-based probiotics, which are also called spore based, are as the name suggests – found in the soil! Historically, we were exposed to soil based strains from naturally eating produce with soil residual and walking bare foot on the dirt more frequently like our ancestors did. Some strains of spore based probiotics include:

• Bacillus coagulans
• Bacillus subtilus
• Bacillus clausii
• Bacillus indicus
• Bacillus licheniformis
• Clostridium butyricum
• Enterococcus faecium

Unlike regular probiotics, spore-based contain an “endospore”, meaning it contains a protective layer that allows it to safely travel through the entire digestive tract. Further, the endospore allows the bacteria to remain dormant until there is a hospitable environment where it is needed.
Spore-based probiotics are beneficial in the presence of intestinal hyperpermeability aka “leaky gut”, this is because leaky gut has been correlated with excessive amounts of gram negative bacteria in the gut which produce endotoxins. In contrast, Bacillus strains are gram positive bacteria and have been shown in research to reduce endotoxin load by 42% in just 30 days of supplementation [1].

Other benefits of spore-based probiotics include:
• Treatment of SIBO [2]
• Anti-inflammatory [3]
• Improves leaky gut [3]
• Reduces allergies [4]

In conclusion, individuality always determines which type of probiotic you may need as there are specific mechanisms both spore based and regular strains possess. Book in with your functional medicine practitioner to see which option is best suited for your specific health goals.


[1] McFarlin BK, Henning AL, Bowman EM, Gary MA, Carbajal KM. Oral spore-based probiotic supplementation was associated with reduced incidence of post-prandial dietary endotoxin, triglycerides, and disease risk biomarkers. World J Gastrointest Pathophysiol. 2017;8(3):117-126. doi:10.4291/wjgp.v8.i3.117
[2] Chen WC, Quigley EM. Probiotics, prebiotics & synbiotics in small intestinal bacterial overgrowth: opening up a new therapeutic horizon!. Indian J Med Res. 2014;140(5):582-584.
[3] Gong Y, Li H, Li Y. Effects of Bacillus subtilis on Epithelial Tight Junctions of Mice with Inflammatory Bowel Disease. J Interferon Cytokine Res. 2016 Feb;36(2):75-85. doi: 10.1089/jir.2015.0030. Epub 2015 Dec 31. PMID: 26720180.
[4] Ciprandi G, Tosca MA, Milanese M, Caligo G, Ricca V. Cytokines evaluation in nasal lavage of allergic children after Bacillus clausii administration: a pilot study. Pediatr Allergy Immunol. 2004 Apr;15(2):148-51. doi: 10.1046/j.1399-3038.2003.00102.x. PMID: 15059191.

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