Soil Based Organisms

What is Soil Based Organisms?

Soil based organisms are naturally occurring, spore-forming bacteria—predominantly from the genus Bacillus—that evolved in soil environments and are naturally consumed in small amounts through contact with minimally processed foods and soil. Unlike conventional Lactobacillus or Bifidobacterium probiotics, SBO strains form protective endospores that allow them to survive heat, stomach acid, and long shelf storage without refrigeration. Commercially available SBO supplements typically contain one or more Bacillus species, sometimes combined with traditional Lactobacillus strains.

How does Soil Based Organisms work?

When ingested, Bacillus spores survive gastric acid transit and germinate in the small intestine, where they transiently colonize and interact with gut epithelial cells and the existing microbiome. SBOs produce bacteriocins, enzymes, and short-chain fatty acids that competitively inhibit pathogenic bacteria, enhance intestinal barrier integrity, and modulate mucosal immune responses—particularly by influencing regulatory T cells and secretory IgA production. Their spore-based lifecycle allows them to persist long enough to exert therapeutic effects without permanently colonizing the gut, which some researchers consider a safety advantage.

What forms does Soil Based Organisms come in?

SBO supplements are most commonly sold as capsules or vegetable capsules. Some Bacillus clausii products (e.g., Enterogermina) are available as oral suspension vials. Powders exist but are less common. Because spores are inherently stable, refrigeration is generally not required, which distinguishes SBOs from most conventional probiotic products.

Where it comes from:

Traditional hunter-gatherer diets involved regular contact with soil-borne microorganisms through unwashed root vegetables and fermented foods. The modern hypothesis—often associated with Jordan Rubin's 'Maker's Diet' and early products like Primal Defense—holds that industrialized food sanitization has depleted human exposure to these organisms, potentially contributing to dysbiosis. While the marketing claims of early SBO products exceeded the evidence, subsequent rigorous clinical research on specific Bacillus strains has validated several therapeutic applications.

What does Soil Based Organisms help with?

• Irritable Bowel Syndrome (IBS): Bacillus coagulans strain GBI-30, 6086 has been evaluated in multiple human RCTs for IBS. A randomized, double-blind, placebo-controlled trial by Dolin (2009, Postgraduate Medicine, n=44) found that B. coagulans GBI-30 significantly reduced abdominal pain and bloating compared to placebo in IBS patients over 8 weeks. A second RCT by Hun (2009, Postgraduate Medicine, n=61) in IBS-D patients showed statistically significant improvements in bloating, vomiting frequency, and global symptom scores. The proposed mechanism involves bacteriocin-mediated pathogen inhibition, increased fecal short-chain fatty acids, and normalization of colonic motility via microbiome rebalancing.
• Antibiotic-associated diarrhea: Bacillus clausii has been studied in pediatric and adult populations for prevention of antibiotic-associated diarrhea (AAD). A multi-center Italian RCT by Nista et al. (2004, Alimentary Pharmacology & Therapeutics, n=120) found that Bacillus clausii supplementation during H. pylori eradication therapy significantly reduced the rate of adverse GI events including diarrhea compared to placebo. Because B. clausii spores are naturally resistant to many antibiotics—including ampicillin, chloramphenicol, and tetracycline—they can survive co-administration and competitively restore colonization resistance during antibiotic courses.
• Traveler's diarrhea prevention: Spore-forming Bacillus strains, particularly in multi-strain formulations, have shown promise for reducing traveler's diarrhea incidence. Their stability at room temperature makes them practical for travel use without refrigeration. A published placebo-controlled study on a Bacillus-dominant multi-strain sporebiotic (Iyer et al., referenced in Khanna et al. review literature) suggested reduced stool frequency and symptom duration in travelers, though large, high-quality RCTs specifically for this indication remain limited. The mechanism involves competitive exclusion of enteropathogens and enhancement of secretory IgA in intestinal mucosa.
• Intestinal permeability (Leaky gut): A double-blind, placebo-controlled crossover study by McFarlin et al. (2017, World Journal of Gastrointestinal Pathophysiology, n=28) found that a multi-strain Bacillus sporebiotic (MegaSporeBiotic formulation) reduced post-meal dietary endotoxin (lipopolysaccharide) serum levels by approximately 42% after 30 days compared to placebo, suggesting meaningful improvement in intestinal barrier function. Bacillus strains produce lipopeptides (e.g., iturin, surfactin) that may enhance tight junction protein expression and reduce translocation of luminal antigens across the gut epithelium.
• Gut microbiome dysbiosis: SBO supplementation has been associated with increased microbiome diversity and expansion of beneficial commensal populations. The McFarlin et al. (2017) study also documented significant increases in Lactobacillus, Bifidobacterium, and Akkermansia muciniphila counts following multi-strain Bacillus supplementation. Bacillus species produce enzymes (amylases, proteases, lipases) and bacteriocins that selectively inhibit pathogenic organisms such as Clostridium difficile and Candida species while creating an environment conducive to beneficial colonizer growth.
• Immune support: Human studies on Bacillus subtilis and Bacillus coagulans have documented immunomodulatory effects including increased secretory IgA, enhanced natural killer cell activity, and modulation of pro-inflammatory cytokines (TNF-alpha, IL-6). A pilot RCT by Kalman et al. (2009, BMC Infectious Diseases) using B. coagulans GBI-30 found significant improvements in immune response to respiratory infections in community-dwelling adults. Bacillus strains interact with intestinal dendritic cells and Peyer's patches, promoting a balanced Th1/Th2 immune response rather than excessive inflammatory signaling.

What can Soil Based Organisms help prevent?

• Antibiotic-associated diarrhea (supported by Bacillus clausii RCT data)
• Traveler's diarrhea (emerging but not yet high-certainty evidence)
• Exercise-induced immune suppression (limited pilot data with B. coagulans GBI-30)

Which foods are rich in Soil Based Organisms?

1. Unwashed organic root vegetables (carrots, beets, radishes): Root vegetables grown in healthy, biodiverse soil and consumed with minimal washing naturally carry trace Bacillus spores and other soil-associated microorganisms on their surface.
2. Fermented vegetables (traditionally fermented sauerkraut, kimchi, beet kvass) — Traditional open-vessel fermentation, especially from garden-grown produce, can introduce environmental Bacillus strains alongside Lactobacillus species, supporting a more diverse fermented microbiome profile.
3. Organic raw herbs (fresh parsley, cilantro, chives from garden) — Fresh herbs grown in living soil and minimally washed carry surface microorganisms including Bacillus species, especially when eaten raw and unwashed as done in traditional cultures.
4. Natto (fermented soybeans): Natto is fermented with Bacillus subtilis var. natto, making it the most reliable food-based source of a Bacillus species with documented health effects; it provides meaningful quantities of live B. subtilis and its metabolites including nattokinase.
5. Raw apple cider vinegar (with 'mother'): Unfiltered apple cider vinegar contains diverse microbial communities including sporulating bacteria; while not a primary SBO source, it supports the broader microbiome environment and gut pH conducive to beneficial Bacillus colonization.

Practical Tips:

Natto is the only common food with a well-characterized Bacillus species (B. subtilis) at therapeutic concentration. Other items on this list provide low-level environmental SBO exposure, not a clinically equivalent dose to supplementation. A diet rich in diverse vegetables, especially from minimally processed or garden-grown sources, supports a gut environment hospitable to SBO colonization. Prebiotic fibers (inulin, FOS from chicory, garlic, onion, leeks) should be emphasized as they support SBO germination and persistence in the gut.

What are the side effects of Soil Based Organisms?

• Transient bloating or gas (most common, usually resolves within 1-2 weeks)
• Loose stools or mild diarrhea during initial use
• Constipation (less common, reported with some formulations)
• Mild abdominal cramping at initiation
• Herxheimer-like die-off reaction in individuals with significant dysbiosis (fatigue, brain fog, temporary symptom flare)
• Extremely rare: bacteremia in severely immunocompromised patients (case report level evidence only)

Good to know:

SBO supplements have a generally favorable safety profile in healthy adults and children. The most commonly reported adverse effects are mild and transient GI symptoms during the initial adjustment period, typically resolving within 1-2 weeks. Serious adverse events are extremely rare and largely limited to case reports in severely immunocompromised individuals. Regulatory bodies including the FDA have classified several Bacillus strains (including B. subtilis and B. coagulans) as GRAS (Generally Recognized As Safe).

How much Soil Based Organisms should you take?

• Recommended daily: 1-4 billion CFU per day for Bacillus-based SBO products; specific products vary—MegaSporeBiotic recommends starting at 1 capsule every other day (approximately 3.4 billion CFU) and titrating to 2 capsules daily. Bacillus clausii (Enterogermina) is typically dosed at 2 billion spores 2-3 times daily for acute GI indications.
• Best time of day: No strong clinical evidence mandates a specific time; many practitioners recommend taking with the first meal of the day to leverage increased gastric pH during eating, which may support spore germination. Evening dosing is also acceptable.
• With or without food: Best taken with or just before a meal. Food buffers stomach acid and the presence of dietary nutrients supports spore germination in the small intestine. Avoid taking with very hot beverages.
• Time to effect: Digestive symptom improvement: 2-4 weeks; measurable microbiome changes: 4-8 weeks; immune and systemic effects: 8-12 weeks of consistent use.
• How long to take it: For acute GI conditions (antibiotic-associated diarrhea, traveler's diarrhea): 1-4 weeks. For chronic conditions (IBS, dysbiosis, leaky gut): minimum 8-12 weeks of consistent use. Some practitioners use SBOs on a rotating basis (8 weeks on, 4 weeks off) to encourage endogenous microbiome independence, though there is no strong RCT data to define an optimal cycling protocol. Long-term daily use appears safe based on available evidence.