What Are Soil-Based Probiotics?

Despite your morning shower, trillions of bacteria linger on your skin. Trillions more took up permanent residence in your gut at birth. In fact, contact with your mother’s vaginal fluids provided your bacterial preparation for life on this earth. This bacterial exposure at birth may be a contributor to the decreased incidence of asthma, allergies, and celiac disease in babies experiencing a vaginal birth.1

These are just a few revelations from the new frontier of bacterial study which has been made possible with the advent of gene mapping. Scientists now have more powerful tools than ever to study the complex world of bacteria — revealing new information on a new sub-category of probiotics: traditional organisms rooted in inherent viability. These are probiotic soil-based organisms.

What Are Soil-Based Organisms and Why Are They Beneficial?

The term SBO stands for "soil-based organism" and is used to refer to a new class of probiotic supplements based on a greater understanding of the incredible diversity of the human gut, and a deeper appreciation for how humans and their commensal "helper" bacteria work together to produce a healthy system.

Soil-based bacteria, also known as spore-forming bacteria, have the ability to "seed" the digestive tract with bacteria which will flourish and support a balanced microbiome, the term used for the mini-ecology of microorganisms such as bacteria that inhabit the human body and perform vital functions such as immune support and digestion.

Some characteristics which are unique to SBO probiotics include:

  • The structure of soil-based organisms is naturally resistant to the harsh environment of the upper digestive tract and stomach.

  • Additionally, unlike other probiotics not derived from soil, probiotics containing SBOs are very stable and don’t need any special coatings or preservatives to ensure a clinically relevant amount reaches the appropriate areas of the gut.

This is due to a natural shell that preserves the probiotic spore against harm — whether in the terrestrial environment, or in the acidic environments in the stomach and upper intestines. When these probiotic microbiota are ingested, they travel all the way to the lower intestine, where they come alive. Like a seed, warm temperatures and moisture stimulate germination. Soil-based probiotics are well-adapted to the environment of the gut, and have been shown to remain in the digestive tract where they can provide long term benefit.

Soil-Based Probiotics

Though the best types of SBO probiotics are based directly on symbiotic communities of bacteria found in the natural environment or “soil”, these probiotics are not actually harvested directly from the earth before bottling, but are instead produced in safe, monitored environments which ensure specificity of the strains.

Why are soil-based probiotics so popular among clinicians, and what makes them so important?

The answer lies in an understanding of the human gut microbiome.

Introducing the Microbiome

Since 2007, scientists at the National Institute of Health (NIH)’s Human Microbiome Project have been honing in on the phenomenon of bacteria. In 2008, the European Commission and China created the Metagenomics of the Human Intestinal Tract Project (MetaHIT) to join this study.

Whereas for centuries scientists have known a limited number of "bad" bacteria that succumb to antibiotics, DNA sequencing and the Human Genome Project have made it possible to study a vast world of germs which dwarfs our previous knowledge.

While we inherit more than 22,000 genes from our parents, the bacteria that exist in — and on — our bodies sustain at least eight million bacterial genes, a whopping 360 times more bacterial genes than human genes. The bacteria which envelop the human body are known as the human microbiome.2

Your microbiome is likely similar to that of your immediate family, as we naturally inherit our family’s microbiome. And, we pick up "hitchhikers" — bacteria from food, water, and various components of our environment. Scientists estimate that we each carry 100 trillion bacteria in our intestinal tract alone!

In this teeming landscape of bacteria, the host (the human) derives benefit while the other is unaffected — known as a commensal relationship. However, some researchers favor the term mutualistic (both partners derive benefit) when describing the stable bacterial communities in the gut.

Benefits of Bacteria

In 2010, the Human Microbiome Project published an analysis of 178 genomes from bacteria that live in or on the human body. 10,000 different types of bacteria in the human body have been identified, including novel genes and proteins that serve functions in human health and disease.3 The vast numbers of bacteria discovered appear to provide benefit to the human body, not harm.

Martin J. Blaser, chairman of the Department of Medicine and a professor of microbiology at the New York University School of Medicine states:

"Germs make us sick, but everyone focuses on the harm. It’s not that simple, because without most of these organisms we could never survive."4

Further, he adds: "I have been a practicing physician and medical researcher for more than thirty years, and this is the most exciting and important work of my lifetime."4

As scientists map the human microbiome, they are getting a picture of the difference between normal and abnormal. Proper bacterial balance is vital to healthy immune function, providing appropriate protection against potential infections and playing a critical role in the digestion and absorption of food and nutrients. The interaction of multiple strains of bacteria is an essential element in health and well-being.1

However, the balance of "good" and "bad" bacteria can be altered in two ways. Antibiotics kill both bad and good bacteria in the gut. Certain disease-carrying bacteria, fungi, parasites, and yeasts can also upset the balance. For example, Helicobacter pylori (H. pylori) may cause ulcers and chronic stomach inflammation. Irritable bowel syndrome, Crohn’s disease, and vaginal infections are all linked with "bad" bacteria.5

Researchers believe changes in gut bacteria may even affect the brain and personality. Germ-free mice have been shown to be dramatically more anxious and hyperactive than their counterparts with a normal microbiome. These changes have also been associated with neurochemical changes in the mouse brain.6

Evidence also supports the concept that microbiota balance can have a large impact on healthy metabolic processes. This delicate balance has a definite impact on nutrient acquisition and overall energy regulation and balance. Plentiful research has pointed to the impact of Firmicutes and Bacteroidetes balance on fat mass and obesity, and as fat mass increases so does the release of powerful signaling molecules called cytokines, many of which impact inflammatory processes. Appropriate signaling is essential to maintaining the healthy metabolic nature of the body and, when problematic, could represent an initial stage in the development of metabolic syndrome.7

These references represent only a few of the many studies examining the impact of gut microbiota balance and the connection with the health of seemingly distant systems such as:

  • The brain

  • Energy homeostasis, and

  • Complex signaling molecules such as cytokines and adipokines

Further investigation could yield powerful data to support the development of novel options to support healthy mood, metabolism, signaling molecules and much more.

Ancestral Health and Soil-Based Probiotics

An underlying concept, revealed in many studies which look at the microbiome’s interaction with the rest of the human body, is the fact that the body has evolved over the millennia to co-exist with this mass of bacteria, and when the microbiome is altered significantly, human health is affected.

How did we evolve to develop a microbiome?

During the evolution of the human microbiome, humans were exposed to a large number of bacteria through the dietary practices of the earliest homo sapiens:

  1. Prior to humans moving towards an agricultural society, the diet consisted primarily of wild plant foods; vegetables, roots, fruit and berries and a limited amount of game meat. The Paleolithic landscape was rich in fruits and vegetables gathered from bushes, trees, and from the ground.

  2. The food was eaten as it was found, without washing.

  3. If soil-based bacteria was on the fallen apple, the bacteria was ingested along with the food, and traveled to the digestive tract where it colonized the human gut and supported a symbiotic relationship humans shared with the bacteria.

  4. This continued contact resulted in a co-existence between humans and the bacterial spores naturally found in the soil.

Through an increased understanding of the microbiome and the microbiota within, researchers are framing a new understanding of how the human gut evolved to its modern form. A major component of this evolution is seen in the co-evolution of the microbiota of plant root systems and the microbiota in the human gut.8

In the midst of this landscape were bacteria, evolving in synchrony with the human body. The Paleo body adapted to bacteria encountered in their world. Soil in this pre-agricultural era was thriving with soil microbes. These soil bacteria are critical to enriching plants with important nutrients such as vitamin B-12.

Modern conventional farming practices utilizing pesticides, herbicides and other chemicals have depleted the soil of the valuable microbes and nutrients, like zinc, calcium, and selenium, which are all critical to good health. The modern day practices in farming and preparation of produce creates a situation in which much of our food is no longer teeming with the vast variety of bacterial diversity with which the human body evolved.9

The New Frontier of Probiotics

A paradigm shift is underway. Increasing numbers of farmers are focused on sustainable agriculture. They are rebuilding the soil with macronutrient fertilizers and farmyard manures with the goal of re-creating the rich Paleolithic terrestrial environment. Consumers are speaking with their dollars and seeking out natural foods that are nutritionally rich. They are shunning genetically engineered food products and want to know their food is safe.

With this shift in dietary practices comes an accompanying shift towards ancestral health practices, one of which includes increased exposure to the beneficial microbiota humans have been co-existing with for millennia prior to recent times. As a health practice many are turning to soil-based bacteria as a naturally resilient source of healthy probiotic bacteria, and medical research on SBO probiotics is backing up this shift.

In mouse studies, researchers note the presence of significant levels of germination and spore-creation denoting rapid reproduction of the strains and the ability to remain in the intestines instead of just being a transient visitor, thus becoming a component of the microbiome and further supporting its health and resilience. Further evidence exists to support the notion that spore-forming bacteria are well adapted to not only surviving in the harsh environment of the digestive tract, but thriving. Mice given a dose of spores excreted more spores than they were given pointing to the fact they germinated and repopulated the gut. The presence of probiotic bacteria spores has been documented in the mouse gut up to 27 days following a single dose as well.10

In animal applications the use of soil-based probiotics may serve as an alternative to antibiotics, which is important due to the increased scrutiny on current antibiotic practices amongst farm animals. The lead author of the study also notes that spore-form bacteria have been shown to prevent gastrointestinal disorders, "and the diversity of species used and their applications are astonishing."

Unlike lactic acid bacteria (e.g., Lactobacillus), the many Bacillus species have their own cycle of spore-proliferation and spore-release in the gut, says Hong. This activity continues long after the spore-forming bacteria are ingested — creating a truly unique symbiotic relationship with the human host.11

Enviromedica's Matrix of Symbiotic SBO Probiotics

Enviromedica's soil-based probiotic stands out from the rest as its full strains are selected based on communities of synergistic bacteria found in nature. Enviromedica’s matrix of soil-based microbial strains is derived from tilth, the top productive layer of healthy organic soil, and blended with a natural pre-biotic which nurtures the microflora as they enter the gut. Due to the source of strains, it is naturally very hardy and effectively colonizes the human digestive tract.

Our products contain Bacillus subtilis, a proven probiotic species found in traditional foods. But it is the combination of the symbiotic strains that most successfully mimics the natural flora found in traditional and Paleolithic diets. Due to the complexity and vast variety of bacteria residing in the gut, the human microbiome thrives when fed this multi-strain mix.

Because these microflora found in our probiotics are naturally hardy, they are proven shelf-stable. It requires no refrigeration when stored at 98˚F/37°C and is supported by peer-reviewed, published clinical studies.12, 13

Lacto Probiotics

What About Yogurt?

Lactobacillus, acidophilus and bifidobacteria, the bacterial species typically found in yogurt and traditional probiotic supplements, do not have the naturally protective shell inherent to all spore-forming bacteria, so they cannot withstand gastric acids. While these types of bacteria can have benefits, unfortunately very few of these organisms ever reach the lower intestine.

Scientific study has demonstrated that yogurt and other products with these probiotic strains don’t measure up to the hardiness of spore-forming probiotic bacteria. A recent study found that such yogurt products have only subtle effects on gut bacteria. The study involved seven pairs of identical twins. One in each pair ate twice-daily servings of yogurt containing five strains of lactic-acid bacteria. The research team performed DNA sequencing on the bacteria in the twins’ stool samples. They found that the yogurt bacteria did not take up residence in the young women’s guts and there was no evidence the bacteria became part of the microbial community in the intestines. The researchers concluded that the yogurt, heavily fortified with billions of lactic acid probiotic bacteria, had no effect on the women’s health.14

Soil-Based Probiotics: A Natural Advantage

SBO probiotics have a simple, natural advantage. "Bacterial spores offer the advantage of a higher survival rate during the acidic stomach passage and better stability during the processing and storage of the food product," writes researcher Johannes Bader, from the Technische Universitat Berlin.15

Unlike most probiotic supplements, made from fragile, lactic-acid based organisms, SBOs are naturally hardy and will survive its journey to the gut. You can be confident your probiotic supplement contains active, living flora, supporting your body where it needs it the most.



Probiotics for Immune System SupportIntestinal Permeability, Leaky Gut, and Probiotics

What’s Next?

  • Visit our Online Store.

  • Learn about Enviromedica, distributor of Ancient Minerals, Magnetic Clay Baths, and Nascent Iodine.


1. Ley, R. E., Peterson, D. a., & Gordon, J. I. (2006). Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell, 124(4), 837–848. doi:10.1016/j.cell.2006.02.017. Link

2. "NIH Human Microbiome Project Defines Normal Bacterial Makeup of the Body." U.S National Library of Medicine. U.S. National Library of Medicine, n.d. Web. 22 June 2015.

3. NIH/National Human Genome Research Institute. (2010, May 21). Human microbiome project: Diversity of human microbes greater than previously predicted. ScienceDaily. Retrieved June 22, 2015 from www.sciencedaily.com/releases/2010/05/100520141214.htm. Link

4. "Germs Are Us - The New Yorker." The New Yorker. N.p., n.d. Web. 22 June 2015.

5. Getting To Know "Friendly Bacteria". NCCAM, National Institutes of Health. Volume XIII, Number 2: Summer 2006

6. Neufeld, K. M., Kang, N., Bienenstock, J., & Foster, J. A. Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterology & Motility, Volume 23, Issue 3, pages 255–e119, March 2011. DOI: 10.1111/j.1365-2982.2010.01620.x. Link

7. DiBaise, J. K., Zhang, H., Crowell, M. D., Krajmalnik-Brown, R., Decker, G. A., & Rittmann, B. E. (2008). Gut Microbiota and Its Possible Relationship With Obesity. Mayo Clinic Proceedings, 83(4), 460–469. doi:10.4065/83.4.460. Link

8. Ramírez-Puebla, S. T., Servín-Garcidueñas, L. E., Jiménez-Marín, B., Bolaños, L. M., Rosenblueth, M., Martínez, J., … Martinez-Romero, E. (2013). Gut and root microbiota commonalities. Applied and Environmental Microbiology, 79(1), 2–9. doi:10.1128/AEM.02553-12. Link

9. Welch, Ross M. "Micronutrients, Agric. & Nutrition." Micronutrients, Agric. & Nutrition. USDA-ARS, U.S. Plant, Soil and Nutrition Laboratory, n.d. Web. 24 June 2015.

10. Tam, N. K. M., Uyen, N. Q., Hong, H. a, Duc, L. H., Hoa, T. T., Serra, C. R., … Cutting, S. M. (2006). The intestinal life cycle of Bacillus subtilis and close relatives. Journal of Bacteriology, 188(7), 2692–700. doi:10.1128/JB.188.7.2692-2700.2006. Link

11. Hong, H. A., Duc, L. H., & Cutting, S. M. (2005). The use of bacterial spore formers as probiotics. FEMS Microbiology Reviews, 29(4), 813–35. doi:10.1016/j.femsre.2004.12.001. Link

12. Bittner, A. C., Croffut, R. M., & Stranahan, M. C. (2005). Prescript-Assist probiotic-prebiotic treatment for irritable bowel syndrome: a methodologically oriented, 2-week, randomized, placebo-controlled, double-blind clinical study. Clinical Therapeutics, 27(6), 755–61. doi:10.1016/j.clinthera.2005.06.005. Link

13. Bittner, A. C., Croffut, R. M., Stranahan, M. C., & Yokelson, T. N. (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. Clinical Therapeutics, 29(6), 1153–60. doi:10.1016/j.clinthera.2007.06.010. Link

14. McNulty, N. P., Yatsunenko, T., Hsiao, A., Faith, J. J., Muegge, B. D., Goodman, A. L., … Gordon, J. I. (2011). The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins. Science Translational Medicine, 3(106), 106ra106–106ra106. doi:10.1126/scitranslmed.3002701. Link

15. Bader, J., Albin, A., & Stahl, U. (2012). Spore-forming bacteria and their utilisation as probiotics. Beneficial Microbes, 3(1), 67–75. doi:10.3920/BM2011.0039. Link