Soil-based probiotics have been lauded as powerful gut restorers and tiny vitamin factories. They’ve also been vilified as dangerous and risky immune threats. Such differences of opinion aren’t very helpful to you when choosing dietary supplements.
Let’s clear up the confusion with a look at scientific research.
What Are Soil-Based Probiotics?
The age-old saying, “God made dirt, and dirt don’t hurt” may actually be true.
Soil-based probiotics are good bacteria in the soil that have evolved in contact with humans. Until very recently, humans were exposed to soil and soil-based organisms daily by eating, farming, and hunting.
Soil-based probiotics such as Bacillus subtilis are a part of our normal microbiome. They form spores that can survive harsh conditions, like stomach acid, irradiation, and high temperatures. This category of bacteria is also sometimes called spore-forming bacteria.
Which Soil-Based Probiotics Have Health Benefits?
The most studied soil-based probiotics are species in the genus Bacillus.
In some circles, soil-based probiotics have a reputation for doing harm. Some claim spore-based probiotics may become invasive in the human gut. Others claim these species may cause a severe immune response in patients with a compromised immune system. So, are soil-based probiotics unsafe, or are they safe and helpful?
Soil-based probiotics are safe, as long as the product contains known soil bacteria species from a reputable supplier.
Safe Soil-Based Bacteria
As noted in the studies above, these soil-based probiotics have been shown to be safe and effective in a number of human clinical trials:
There have also been specific studies into the safety of these two Bacillus strains for human use:
Some species of soil-based bacteria have been associated with adverse human effects, including Bacillus licheniformis and Enterococcus faecium. The EPA was asked to review the safety of Bacillus licheniformis in 1997.
In the summary of their review, the EPA concluded that Bacillus licheniformis is not pathogenic or toxic to humans . In fact, the study noted that Bacillus licheniformis is commonly found in water and soil and is known to naturally enter the human digestive tract.
There are some dangerous species of soil-based bacteria.
The most famous example is Bacillus anthracis, also known as Anthrax. Anthrax isn’t just bad bacteria — it can kill you if you aren’t treated immediately with antibiotics . Another species of Bacillus, B. cereus, is known to cause a severe form of food poisoning [41 Trusted SourcePubMedGo to source].
Are Soil-Based Probiotics Safe? A Reality Check
No one avoids eating carrots because they’re in the same plant family as poison hemlock. And yet, internet advice continues to caution people to stay away from soil-based probiotics because some Bacillus bacteria are unsafe.
Research clearly shows that specific bacillus species are beneficial and safe.
And while it’s very unlikely that your soil-based probiotic supplement would be contaminated with Anthrax, it is important to pay attention to labelling and safety when buying ANY probiotic supplements.
My experience in the clinic reflects this, as I have found that people get the best benefits of probiotics by using three categories together.
For soil-based probiotics, try one quality product, like our Soil-Based Probiotic, and see how you feel. Start with a dose of 100 billion CFU (colony forming units) per day and slowly work up to a higher dose.
If your symptoms improve, there is no need to further increase your dose. If you have any type of reaction when taking soil-based probiotics, you should stop.
Ilinskaya ON, Ulyanova VV, Yarullina DR, Gataullin IG. Secretome of Intestinal Bacilli: A Natural Guard against Pathologies. Front Microbiol. 2017 Sep 1;8:1666. doi: 10.3389/fmicb.2017.01666. PMID: 28919884; PMCID: PMC5586196. Trusted SourcePubMedGo to source
Derrien M, van Hylckama Vlieg JE. Fate, activity, and impact of ingested bacteria within the human gut microbiota. Trends Microbiol. 2015 Jun;23(6):354-66. doi: 10.1016/j.tim.2015.03.002. Epub 2015 Apr 1. PMID: 25840765. Trusted SourcePubMedGo to source
Majeed M, Nagabhushanam K, Natarajan S, Sivakumar A, Ali F, Pande A, Majeed S, Karri SK. Bacillus coagulans MTCC 5856 supplementation in the management of diarrhea predominant Irritable Bowel Syndrome: a double blind randomized placebo controlled pilot clinical study. Nutr J. 2016 Feb 27;15:21. doi: 10.1186/s12937-016-0140-6. PMID: 26922379; PMCID: PMC4769834. Trusted SourcePubMedGo to source
Dolin BJ. Effects of a proprietary Bacillus coagulans preparation on symptoms of diarrhea-predominant irritable bowel syndrome. Methods Find Exp Clin Pharmacol. 2009 Dec;31(10):655-9. doi: 10.1358/mf.2009.31.10.1441078. PMID: 20140275. Trusted SourcePubMedGo to source
Khalighi AR, Khalighi MR, Behdani R, Jamali J, Khosravi A, Kouhestani Sh, Radmanesh H, Esmaeelzadeh S, Khalighi N. Evaluating the efficacy of probiotic on treatment in patients with small intestinal bacterial overgrowth (SIBO)–a pilot study. Indian J Med Res. 2014 Nov;140(5):604-8. PMID: 25579140; PMCID: PMC4311312. Trusted SourcePubMedGo to source
Rogha M, Esfahani MZ, Zargarzadeh AH. The efficacy of a synbiotic containing Bacillus Coagulans in treatment of irritable bowel syndrome: a randomized placebo-controlled trial. Gastroenterol Hepatol Bed Bench. 2014 Summer;7(3):156-63. PMID: 25120896; PMCID: PMC4129566. Trusted SourcePubMedGo to source
Hun L. Bacillus coagulans significantly improved abdominal pain and bloating in patients with IBS. Postgrad Med. 2009 Mar;121(2):119-24. doi: 10.3810/pgm.2009.03.1984. PMID: 19332970. Trusted SourcePubMedGo to source
Urgesi R, Casale C, Pistelli R, Rapaccini GL, de Vitis I. A randomized double-blind placebo-controlled clinical trial on efficacy and safety of association of simethicone and Bacillus coagulans (Colinox®) in patients with irritable bowel syndrome. Eur Rev Med Pharmacol Sci. 2014;18(9):1344-53. PMID: 24867512. Trusted SourcePubMedGo to source
Saneian H, Pourmoghaddas Z, Roohafza H, Gholamrezaei A. Synbiotic containing Bacillus coagulans and fructo-oligosaccharides for functional abdominal pain in children. Gastroenterol Hepatol Bed Bench. 2015 Winter;8(1):56-65. PMID: 25584177; PMCID: PMC4285933. Trusted SourcePubMedGo to source
Minamida K, Nishimura M, Miwa K, Nishihira J. Effects of dietary fiber with Bacillus coagulans lilac-01 on bowel movement and fecal properties of healthy volunteers with a tendency for constipation. Biosci Biotechnol Biochem. 2015;79(2):300-6. doi: 10.1080/09168451.2014.972331. Epub 2014 Oct 23. PMID: 25338680. Trusted SourcePubMedGo to source
Kang S, Park MY, Brooks I, Lee J, Kim SH, Kim JY, Oh B, Kim JW, Kwon O. Spore-forming Bacillus coagulans SNZ 1969 improved intestinal motility and constipation perception mediated by microbial alterations in healthy adults with mild intermittent constipation: A randomized controlled trial. Food Res Int. 2021 Aug;146:110428. doi: 10.1016/j.foodres.2021.110428. Epub 2021 May 19. PMID: 34119240. Trusted SourcePubMedGo to source
Liu YP, Liu X, Dong L. [Lactulose plus live binary Bacillus subtilis in the treatment of elders with functional constipation]. Zhonghua Yi Xue Za Zhi. 2012 Nov 13;92(42):2961-4. Chinese. doi: 10.3760/cma.j.issn.0376-2491.2012.42.003. PMID: 23328284. Trusted SourcePubMedGo to source
Tompkins TA, Xu X, Ahmarani J. A comprehensive review of post-market clinical studies performed in adults with an Asian probiotic formulation. Benef Microbes. 2010 Mar;1(1):93-106. doi: 10.3920/BM2008.1005. PMID: 21840798. Trusted SourcePubMedGo to source
Lee H, Kim YH, Kim JH, Chang DK, Kim JY, Son HJ, Rhee PL, Kim JJ, Rhee JC. A feasibility study of probiotics pretreatment as a bowel preparation for colonoscopy in constipated patients. Dig Dis Sci. 2010 Aug;55(8):2344-51. doi: 10.1007/s10620-009-1011-1. Epub 2009 Oct 15. PMID: 19830558. Trusted SourcePubMedGo to source
Li SR, Wang HH, Wu ZY, Liu RH, Tong MH, Wang CH, Wang RL, Zhao HC, Wei W. [Efficacies of lactulose plus live combined Bacillus subtilis and Enterococcus faecium capsules in the treatment of functional constipation: a multicenter, randomized, double blind, controlled trial]. Zhonghua Yi Xue Za Zhi. 2012 Nov 13;92(42):2955-60. Chinese. doi: 10.3760/cma.j.issn.0376-2491.2012.42.002. PMID: 23328283. Trusted SourcePubMedGo to source
Choi CH, Kwon JG, Kim SK, Myung SJ, Park KS, Sohn CI, Rhee PL, Lee KJ, Lee OY, Jung HK, Jee SR, Jeen YT, Choi MG, Choi SC, Huh KC, Park H. Efficacy of combination therapy with probiotics and mosapride in patients with IBS without diarrhea: a randomized, double-blind, placebo-controlled, multicenter, phase II trial. Neurogastroenterol Motil. 2015 May;27(5):705-16. doi: 10.1111/nmo.12544. Epub 2015 Mar 25. Erratum in: Neurogastroenterol Motil. 2015 Nov;27(11):1684-5. Dosage error in article text. PMID: 25809913. Trusted SourcePubMedGo to source
Park SK, Park DI, Choi JS, Kang MS, Park JH, Kim HJ, Cho YK, Sohn CI, Jeon WK, Kim BI. The effect of probiotics on Helicobacter pylori eradication. Hepatogastroenterology. 2007 Oct-Nov;54(79):2032-6. PMID: 18251154. Trusted SourcePubMedGo to source
Nista EC, Candelli M, Cremonini F, Cazzato IA, Zocco MA, Franceschi F, Cammarota G, Gasbarrini G, Gasbarrini A. Bacillus clausii therapy to reduce side-effects of anti-Helicobacter pylori treatment: randomized, double-blind, placebo controlled trial. Aliment Pharmacol Ther. 2004 Nov 15;20(10):1181-8. doi: 10.1111/j.1365-2036.2004.02274.x. PMID: 15569121. Trusted SourcePubMedGo to source
Sudha MR, Bhonagiri S, Kumar MA. Efficacy of Bacillus clausii strain UBBC-07 in the treatment of patients suffering from acute diarrhoea. Benef Microbes. 2013 Jun 1;4(2):211-6. doi: 10.3920/BM2012.0034. PMID: 23443952. Trusted SourcePubMedGo to source
Gabrielli M, Lauritano EC, Scarpellini E, Lupascu A, Ojetti V, Gasbarrini G, Silveri NG, Gasbarrini A. Bacillus clausii as a treatment of small intestinal bacterial overgrowth. Am J Gastroenterol. 2009 May;104(5):1327-8. doi: 10.1038/ajg.2009.91. Epub 2009 Apr 7. PMID: 19352343. Trusted SourcePubMedGo to source
Du SX, Jia YR, Ren SQ, Gong XJ, Tang H, Wan-Shui W, Li-Ming S. The protective effects of Bacillus licheniformis preparation on gastrointestinal disorders and inflammation induced by radiotherapy in pediatric patients with central nervous system tumor. Adv Med Sci. 2018 Mar;63(1):134-139. doi: 10.1016/j.advms.2017.09.005. Epub 2017 Nov 6. PMID: 29120854. Trusted SourcePubMedGo to source
Heo J, Kim SK, Park KS, Jung HK, Kwon JG, Jang BI. A Double-Blind, Randomized, Active Drug Comparative, Parallel-Group, Multi-Center Clinical Study to Evaluate the Safety and Efficacy of Probiotics (Bacillus licheniformis, Zhengchangsheng® capsule) in Patients with Diarrhea. Intest Res. 2014 Jul;12(3):236-44. doi: 10.5217/ir.2014.12.3.236. Epub 2014 Jul 25. PMID: 25349598; PMCID: PMC4204727. Trusted SourcePubMedGo to source
Lefevre M, Racedo SM, Ripert G, Housez B, Cazaubiel M, Maudet C, Jüsten P, Marteau P, Urdaci MC. Probiotic strain Bacillus subtilis CU1 stimulates immune system of elderly during common infectious disease period: a randomized, double-blind placebo-controlled study. Immun Ageing. 2015 Dec 3;12:24. doi: 10.1186/s12979-015-0051-y. PMID: 26640504; PMCID: PMC4669646. Trusted SourcePubMedGo to source
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 Aug 15;8(3):117-126. doi: 10.4291/wjgp.v8.i3.117. PMID: 28868181; PMCID: PMC5561432. Trusted SourcePubMedGo to source
Zhang HL, Li WS, Xu DN, Zheng WW, Liu Y, Chen J, Qiu ZB, Dorfman RG, Zhang J, Liu J. Mucosa-reparing and microbiota-balancing therapeutic effect of Bacillus subtilis alleviates dextrate sulfate sodium-induced ulcerative colitis in mice. Exp Ther Med. 2016 Oct;12(4):2554-2562. doi: 10.3892/etm.2016.3686. Epub 2016 Sep 8. PMID: 27698758; PMCID: PMC5038491. Trusted SourcePubMedGo to source
Anaya-Loyola MA, Enciso-Moreno JA, López-Ramos JE, García-Marín G, Orozco Álvarez MY, Vega-García AM, Mosqueda J, García-Gutiérrez DG, Keller D, Pérez-Ramírez IF. Bacillus coagulans GBI-30, 6068 decreases upper respiratory and gastrointestinal tract symptoms in healthy Mexican scholar-aged children by modulating immune-related proteins. Food Res Int. 2019 Nov;125:108567. doi: 10.1016/j.foodres.2019.108567. Epub 2019 Jul 21. PMID: 31554075. Trusted SourcePubMedGo to source
Nyangale EP, Farmer S, Cash HA, Keller D, Chernoff D, Gibson GR. Bacillus coagulans GBI-30, 6086 Modulates Faecalibacterium prausnitzii in Older Men and Women. J Nutr. 2015 Jul;145(7):1446-52. doi: 10.3945/jn.114.199802. Epub 2015 May 6. PMID: 25948780. Trusted SourcePubMedGo to source
Plaza-Diaz J, Gomez-Llorente C, Fontana L, Gil A. Modulation of immunity and inflammatory gene expression in the gut, in inflammatory diseases of the gut and in the liver by probiotics. World J Gastroenterol. 2014 Nov 14;20(42):15632-49. doi: 10.3748/wjg.v20.i42.15632. PMID: 25400447; PMCID: PMC4229528. Trusted SourcePubMedGo to source
Jäger R, Shields KA, Lowery RP, De Souza EO, Partl JM, Hollmer C, Purpura M, Wilson JM. Probiotic Bacillus coagulans GBI-30, 6086 reduces exercise-induced muscle damage and increases recovery. PeerJ. 2016 Jul 21;4:e2276. doi: 10.7717/peerj.2276. PMID: 27547577; PMCID: PMC4963221. Trusted SourcePubMedGo to source
Hempel S, Newberry SJ, Maher AR, Wang Z, Miles JN, Shanman R, Johnsen B, Shekelle PG. Probiotics for the prevention and treatment of antibiotic-associated diarrhea: a systematic review and meta-analysis. JAMA. 2012 May 9;307(18):1959-69. doi: 10.1001/jama.2012.3507. PMID: 22570464. Trusted SourcePubMedGo to source
Dutta P, Mitra U, Dutta S, Rajendran K, Saha TK, Chatterjee MK. Randomised controlled clinical trial of Lactobacillus sporogenes (Bacillus coagulans), used as probiotic in clinical practice, on acute watery diarrhoea in children. Trop Med Int Health. 2011 May;16(5):555-61. doi: 10.1111/j.1365-3156.2011.02745.x. Epub 2011 Feb 20. PMID: 21332891. Trusted SourcePubMedGo to source
Canani RB, Cirillo P, Terrin G, Cesarano L, Spagnuolo MI, De Vincenzo A, Albano F, Passariello A, De Marco G, Manguso F, Guarino A. Probiotics for treatment of acute diarrhoea in children: randomised clinical trial of five different preparations. BMJ. 2007 Aug 18;335(7615):340. doi: 10.1136/bmj.39272.581736.55. Epub 2007 Aug 9. PMID: 17690340; PMCID: PMC1949444. Trusted SourcePubMedGo to source
Hanifi A, Culpepper T, Mai V, Anand A, Ford AL, Ukhanova M, Christman M, Tompkins TA, Dahl WJ. Evaluation of Bacillus subtilis R0179 on gastrointestinal viability and general wellness: a randomised, double-blind, placebo-controlled trial in healthy adults. Benef Microbes. 2015 Mar;6(1):19-27. doi: 10.3920/BM2014.0031. PMID: 25062611. Trusted SourcePubMedGo to source
Lefevre M, Racedo SM, Denayrolles M, Ripert G, Desfougères T, Lobach AR, Simon R, Pélerin F, Jüsten P, Urdaci MC. Safety assessment of Bacillus subtilis CU1 for use as a probiotic in humans. Regul Toxicol Pharmacol. 2017 Feb;83:54-65. doi: 10.1016/j.yrtph.2016.11.010. Epub 2016 Nov 5. PMID: 27825987. Trusted SourcePubMedGo to source
Lee NK, Kim WS, Paik HD. Bacillus strains as human probiotics: characterization, safety, microbiome, and probiotic carrier. Food Sci Biotechnol. 2019 Oct 8;28(5):1297-1305. doi: 10.1007/s10068-019-00691-9. PMID: 31695928; PMCID: PMC6811671. Trusted SourcePubMedGo to source
Tompkins TA, Hagen KE, Wallace TD, Fillion-Forté V. Safety evaluation of two bacterial strains used in Asian probiotic products. Can J Microbiol. 2008 May;54(5):391-400. doi: 10.1139/w08-022. PMID: 18449224. Trusted SourcePubMedGo to source
Lakshmi SG, Jayanthi N, Saravanan M, Ratna MS. Safety assesment of Bacillus clausii UBBC07, a spore forming probiotic. Toxicol Rep. 2017 Jan 5;4:62-71. doi: 10.1016/j.toxrep.2016.12.004. PMID: 28959626; PMCID: PMC5615088. Trusted SourcePubMedGo to source
Holzapfel W, Arini A, Aeschbacher M, Coppolecchia R, Pot B. Enterococcus faecium SF68 as a model for efficacy and safety evaluation of pharmaceutical probiotics. Benef Microbes. 2018 Apr 25;9(3):375-388. doi: 10.3920/BM2017.0148. Epub 2018 Apr 10. PMID: 29633645. Trusted SourcePubMedGo to source
Carroll LM, Wiedmann M, Mukherjee M, Nicholas DC, Mingle LA, Dumas NB, Cole JA, Kovac J. Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges. Front Microbiol. 2019 Feb 12;10:144. doi: 10.3389/fmicb.2019.00144. PMID: 30809204; PMCID: PMC6379260. Trusted SourcePubMedGo to source
Bansal P, Arora M, Gupta V, Maithani M. Bioinformatics-Based Tools and Software in Clinical Research: A New Emerging Area. Methods Mol Biol. 2019;1939:215-230. doi: 10.1007/978-1-4939-9089-4_12. PMID: 30848464. Trusted SourcePubMedGo to source
Di Pierro F, Polzonetti V, Patrone V, Morelli L. Microbiological Assessment of the Quality of Some Commercial Products Marketed as Lactobacillus crispatus-Containing Probiotic Dietary Supplements. Microorganisms. 2019 Nov 3;7(11):524. doi: 10.3390/microorganisms7110524. PMID: 31684185; PMCID: PMC6921017. Trusted SourcePubMedGo to source
Ansari JM, Colasacco C, Emmanouil E, Kohlhepp S, Harriott O. Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling. PLoS One. 2019 Mar 22;14(3):e0213841. doi: 10.1371/journal.pone.0213841. PMID: 30901338; PMCID: PMC6430388. Trusted SourcePubMedGo to source
Jeżewska-Frąckowiak J, Seroczyńska K, Banaszczyk J, Jedrzejczak G, Żylicz-Stachula A, Skowron PM. The promises and risks of probiotic Bacillus species. Acta Biochim Pol. 2018 Dec 6;65(4):509-519. doi: 10.18388/abp.2018_2652. PMID: 30521647. Trusted SourcePubMedGo to source
Patrone V, Molinari P, Morelli L. Microbiological and molecular characterization of commercially available probiotics containing Bacillus clausii from India and Pakistan. Int J Food Microbiol. 2016 Nov 21;237:92-97. doi: 10.1016/j.ijfoodmicro.2016.08.012. Epub 2016 Aug 13. PMID: 27543819. Trusted SourcePubMedGo to source
American College of Gastroenterology Task Force on Irritable Bowel Syndrome, Brandt LJ, Chey WD, Foxx-Orenstein AE, Schiller LR, Schoenfeld PS, Spiegel BM, Talley NJ, Quigley EM. An evidence-based position statement on the management of irritable bowel syndrome. Am J Gastroenterol. 2009 Jan;104 Suppl 1:S1-35. doi: 10.1038/ajg.2008.122. PMID: 19521341. Trusted SourcePubMedGo to source
Zhang C, Jiang J, Tian F, Zhao J, Zhang H, Zhai Q, Chen W. Meta-analysis of randomized controlled trials of the effects of probiotics on functional constipation in adults. Clin Nutr. 2020 Oct;39(10):2960-2969. doi: 10.1016/j.clnu.2020.01.005. Epub 2020 Jan 14. PMID: 32005532. Trusted SourcePubMedGo to source
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