The Best Probiotic Therapies for C. Difficile

Skip below to the following sections:
Proven Effectiveness of Probiotics for C. diff.
Why Some Probiotics Fail
Targeted C. difficile Benefits of Bacillus Probiotics
Additional Benefits of Bacillus
Benefits of S. Boulardii
Focused C. diff Toxin Binding
Michelle’s Recommended Probiotics
We’re Here to Support You
Beware Counterfeit Products on Amazon

Proven Effectiveness of Probiotics for C. difficile

Gut bacteria

Probiotics are scientifically proven to help recovery and prevention C. diff. infections

While many doctors tell their patients probiotics won’t help when it comes to C. difficile, the majority of scientific studies show positive results when adding probiotics along with antibiotics for treating a C. difficile infection1,2. Probiotics can also help prevent C. diff. infections3.

A 2017 analysis of 6261 adults who required antibiotics during their hospital stay found that those who used probiotics closest to starting antibiotics reduced their risk of getting C. difficile by more than 50%4. In this 2017 study, researchers found that probiotics, if given within two days of starting antibiotics, were the most protective against getting a C. diff. infection.

The above results aren’t surprising because C. diff. infections are the result of a gut microbiome imbalance. So finding and using effective probiotics are essential to help restore that balance, no matter if you’re using antibiotics or natural treatment options.

The trouble is, finding the right probiotic for C. difficile infections can be a big challenge. Probiotics are one of the latest, greatest health trends and pretty much every company is now creating a probiotic product to tap into the frenzy. And unfortunately, some of the most popular probiotics fail to provide any benefits, or their benefits are limited because of how they are made.

Why Some Probiotics Fail

Probiotic Potency

Lactobacillus and Bifidobacteria probiotics lose 99% of their potency before reaching your intestines

Most probiotic products are made with the popular species of Lactobacillus and Bifidobacteria bacteria. But these species are fragile, not tolerant of oxygen or heat and therefore many will die in the bottle before you even use them. These species are also killed by the acid in your stomach and they are destroyed by antibiotic drugs.

Manufacturers try to reduce the above problems by requiring refrigeration for their products, or making products with very high advertised potency values, measured in CFU (Colony Forming Unit). But both of these methods fail to preserve the potency, as explained below.

Likewise, high potency values are not an indication of good quality either. An advertised potency of billions of CFUs only tells you what’s in the bottle when it leaves the manufacturer’s warehouse. But the real potency goes down during shipping and storage. Survivability studies show that 99% of the potency of these products cannot survive the acid in your stomach. This means that most people are paying for products with less than 1% survivability. It’s no wonder that most people find probiotics ineffective.

In contrast, Bacillus spore probiotics are heat stable up to 400 degrees and are clinically proven to survive the gastric system.

Benefits of Bacillus Probiotics for C. difficile

For decades, Bacillus probiotics have been used widely around the world for fighting off intestinal pathogens, antibiotic associated diarrhea and improving immune system function. They produce naturally occurring antibiotic compounds right in the gut where you need them with C. difficile. See below for data on specific Bacillus strains that actually fight off C. difficile bacteria and their gut-wrenching toxins.

  • Bacillus coagulans therapy has shown to improve C. difficile colitis symptoms, reduce colon inflammation, provide better stool consistency and improve C. diff. outcomes5 as well as reduce recurring C. diff. after vancomycin treatment6.
  • Bacillus clausii makes an antimicrobial compound called “clausin” that directly inhibits C. difficile and other Gram-positive bacteria7.
  • Bacillus clausii creates an enzyme that helps break up C. difficile toxins, resulting in a strong protective effect against intestinal damage8.
  • Bacillus subtilis strain HU58 produces over 12 targeted antimicrobial substances. B. subtilis effectively targets harmful gut bacteria, making it a potent and effective tool to rebalance gut flora.
  • Bacillus subtilis enhances the immune system in elderly subjects as indicated by increased immunoglobulin A (IgA) levels9. IgA fights off invading organisms and is your body’s first line of defense.

Bacillus and Recurrent C. difficile Study Results

A 2020 study10 published in the Journal of Parenteral and Enteral Nutrition demonstrated that mice with recurring C. difficile infections had improved markers of gut integrity, inflammation and immunity when supplemented with targeted spore-forming Bacillus probiotics. Mice in the control group where no Bacillus strains were given did not receive the same improvement of gut health and immunity.

This study also found that mice supplemented with the Bacillus probiotics had less loss of colon bacteria from the antibiotic treatment than the control group where no Bacillus was supplemented.

These five Bacillus probiotic strains were shown to help protect intestinal health during a C. difficile infection.

Study conclusion: Mice supplemented with targeted spore-forming probiotics exhibited improved immune responses and nutrition immunity properties, which were linked with less inflammation and enhanced intestinal barrier proteins during recurrent C. difficile colonization.

Over the years we’ve found people have great success using Bacillus spore probiotics for fighting C. difficile infections. These powerful Bacillus probiotics tested in this clinical study are in our favorite Bacillus probiotic: MegaSporeBiotic.

MegaSporeBiotic: A Bacillus Powerhouse

Bacillus probioticMeet MegaSporeBiotic. Our premier Bacillus probiotic is the first mega-dose, 100% spore, physician’s-strength probiotic with scientifically proven 100% survivability through the stomach and into the gut11. The five strains of Bacillus in the product have been shown to: stimulate the growth of beneficial GI flora, enhance the immune system, reduce the side effects of antibiotic drugs, seek out and fight gut bacterial overgrowths including C. difficile, and reduce intestinal inflammation.

As indicated in the section above, several of these Bacillus strains also provide targeted C. difficile support. And the proprietary Bacillus indicus HU36™ strain makes it the first commercially available probiotic-antioxidant combination supplement on the market, supplying antioxidants directly to the GI tract where they are best absorbed. This product is ideal for gut overgrowth infections as well as long-term, ongoing probiotic support.

RestorFlora: S. Boulardii Diarrhea Support

S. BoulardiiRestorFlora is ideal during active gut challenges when diarrhea is a concern and works best when combined with MegaSporeBiotic. The beneficial yeast probiotic species Saccharomyces boulardii (S. boulardii, or Sac. B.) is helpful for support of antibiotic-associated diarrhea, C. difficile associated diarrhea and gastrointestinal upset.

The unique properties of S. boulardii make it a beneficial addition to a probiotic regimen when extra support is needed for difficult gastrointestinal challenges. Our S. boulardii probiotic RestorFlora can survive the harsh stomach environment and arrive in the gut at full strength, unlike most probiotics.

S. boulardii is clinically proven to:

  • Support a healthy microbiome during or after antibiotic use.
  • Support C. difficile bowel disorders in adults and children.
  • Several clinical studies show that S. boulardii is helpful for support with gut disorders12, especially antibiotic-associated diarrhea and C. difficile associated diarrhea13.
  • S. boulardii secrets an enzyme that digests C. diff. toxin A and it helps prevent the formation of C. diff. toxin B14.
  • Support against Inflammatory Bowel Diseases.

Mega IgG2000: Targeted C. diff Toxin Binding

IgGMega IgG2000 is our premiere toxin binder to speed recovery and healing in the gut. Immunoglobulins (Ig) mop up and neutralize a range of disease-causing toxins in the gut, including absorption of C. difficile toxins A and B. Immunoglobulin G (IgG), the most abundant antibody in the product, is highly targeted and will not absorb drugs, other supplements, foods or nutrients. This toxin binder reduces inflammation and intestinal damage and can help to ease potential discomfort when starting high-powered probiotics, such as our Bacillus and S. boulardii probiotics above.

Unlike other milk-derived products on the market, our Ig product is made from bovine serum, making it lactose-free, casein-free, and β-lactoglobulin-free. Unlike clays, charcoal and other popular binders that indiscriminately bind to a wide range of molecules and toxins, this product specifically targets disease-causing bacterial components and toxins inside the gut.

Mega IgG2000 binds to unwanted elements inside your GI system, sticking to them like glue. The IgG then pulls the toxins safely out of your body before they have a chance to damage the fragile lining of the intestines. Immunoglobulins reduce the toxic impact on the gut and immune system.

IgG is clinically proven to:

  • Immunoglobulins are clinically proven to support immune health and digestive function.
  • Gut infections and overgrowths: IgG protects against infections and binds to bacteria, fungi, mold, viruses and their associated toxins15. It binds inflammatory LPS (lipopolysaccharides) toxins, H. pylori (gram negative bacteria found in the stomach), mycotoxins, Staphylococcus, Salmonella, E. coli and other pathogenic bacteria.
  • C. diff. toxins: IgG binds both C. difficile toxins A and B16,17,18
  • Irritable Bowel Syndrome (IBS) support: IgG improves pain and diarrhea and manages chronic loose and frequent stools19. Multiple studies show benefit for IBS management.
  • Irritable Bowel Disease (IBD) support: Significantly improves symptoms of IBD20,21, multiple studies show benefit for IBD management.
  • SIBO support: IgG therapy can resolve diarrhea symptoms and allow for normal bowel function22
  • IgG supports a healthy gut mucosal layer and strengthens gut barrier function so fewer toxins enter the bloodstream.
  • Mega IgG2000 is an easier and safer choice for long-term usage than traditional binding products. This is because Mega IgG2000 is highly targeted and will not absorb drugs, foods, other supplements or nutrients as traditional binders do.

Michelle’s Recommended Probiotics

Save 10% on your first order and get free shipping over $99 in the United States on Michelle’s favorite spore-based probiotics and highly targeted C. diff. toxin binder. Made by Microbiome Labs, an industry leader in the research and manufacture of professional strength probiotics and gut restoration products. Use coupon code SAVE10. We provide C. diff. specific usage guides and ongoing support for our product customers.

Get Michelle’s favorite Bacillus spore-based probiotics and targeted toxin binder from her online supplement store today.


If you only choose one product, then this is a good choice. Ideal for gut reconditioning and long-term daily use.

$60 $54



Mega Plus Pack. Added toxin binding and inflammation support. To cleanse and recondition the gut during healing and recovery.

$120 $108



Gut Restoration Pack. Added diarrhea and toxin biding support. To cleanse, recondition and defend the microbiome.

$164 $148


*Beware of fraudulent MicroBiome Labs products on Amazon*

We’re Here to Support You

SupportOur products are personally vetted, backed by solid science and used clinically by healthcare professionals. And our experienced staff is here to answer your questions, walk you through Michelle’s methods and provide ongoing support on your path to health. We’ll provide email support to answer any questions you may have along the way. You can also get Michelle’s free email newsletter and free probiotic video e-course.

Please note: Our usage guides, information and support are for educational purposes and are not intended to replace a relationship with a doctor. We encourage you to make your own health care decisions based upon your research in partnership with a qualified healthcare professional.

Guarantee, Privacy and Security

We strive to provide exceptional customer service, to protect your security and privacy and to provide you with the best value and the most benefit from our products. If you are not satisfied with our products, you may return new, unopened products for a refund. See our support page for details.


Beware Counterfeit Products on Amazon

Beware Counterfeit Products on AmazonMicrobiome Labs, the maker of these professional products, does not sell their products on Amazon, nor do they authorize any sellers on

Many unsuspecting Amazon customers believe they are ordering directly from Microbiome Labs, but they are purchasing from fraudulent sellers. According to reviews, many have received ineffective or fake products.

Microbiome Labs products may only be sold through authorized professionals on their own websites. Our online supplement store web store has been an authorized seller for Microbiome Labs since 2017. Rest assured, you will receive genuine products through our store.

We have the lowest prices on the Microbiome Labs probiotics on the internet, and frequently have discounted sales. Order through our online supplement store at and you get personalized support and care on using our professional grade products. You also support our family-owned business that’s been helping people overcome chronic infections since 2007.

If you have questions please let us know.

Michelle Moore, microbiologist
To your very best health,


Microbiologist and Health Advocate

* Disclaimer: Always consult with your doctor before using any new supplement or dietary change. Healthcare professionals who are experienced in using herbal medicines usually provide the highest level of support for using this protocol or other alternative methods.
These statements have not been evaluated by the US Food and Drug Administration (FDA) and they are not intended to diagnose, treat, cure, or prevent any disease.



  1. Recommendations for probiotic use – Floch et al, J Clin Gastroenterol. 2008 Jul.
  2. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children, Joshue Z Goldenberg et al, 31 MAY 2013 The Cochrane.
  3. Probiotics are effective at preventing Clostridium difficile-associated diarrhea: a systematic review and meta-analysis. Christine SM Lau, Ronald S Chamberlain. Int J Gen Med. 2016; 9: 27–37.
  4. Timely Use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: A Systematic Review With Meta-Regression Analysis. Shen NT et al. Gastroenterology. 2017 Jun;152(8):1889-190.
  5. Bacillus Coagulans GBI-30 (BC30) improves indices of Clostridium difficile-Induced colitis in mice. Fitzpatrick L, Small J, Greene W, Karpa K, Keller D. Gut Pathog. 2011; 3: 16.
  6. Bacillus coagulans GBI-30, 6086 limits the recurrence of Clostridium difficile-Induced colitis following vancomycin withdrawal in mice. Fitzpatrick L, Small J, Greene W, Karpa K, Farmer S, Keller D. Gut Pathog. 2012; 4: 13.
  7. Probiotics for Prevention of Clostridium difficile Infection. Mills J, Rao K, Young V. Curr Opin Gastroenterol. 2018 Jan; 34(1): 3–10.
  8. Secreted Compounds of the Probiotic Bacillus clausii Strain O/C Inhibit the Cytotoxic Effects Induced by Clostridium difficile and Bacillus cereus Toxins. Ripert G. et al. Antimicrob Agents Chemother. 2016 Jun; 60(6): 3445–3454.
  9. Probiotic strain Bacillus subtilis CU1 stimulates immune system of elderly during common infectious disease period: a randomized, double-blind placebo-controlled study. Lefevre M, Racedo SM, Ripert G, et al. Immun Aging. 2015;12:24
  10. A Spore-Forming Probiotic Supplement Improves the Intestinal Immune Response and Protects the Intestinal Health During Recurrent Clostridioides difficile Colonization in Mice. Fatemeh Ramezani Kapourchali, Bryan Glueck, Yingchun Han. JPEN J Parenter Enteral Nutr. 2020 Nov;44(8):1428-1438.
  11. Commissioned gastric model study by Silliker Food Science Center – Crete, IL
  12. Bacteria and yeasts in the treatment of acute and chronic infectious diarrhea. Part II: Yeasts. Vandenplas Y, July 1999, Clin. Microbiol. Infect. 5 (7): 389–395
  13. Role of probiotics in antibiotic-associated diarrhea, Clostridium difficile-associated diarrhea, and recurrent Clostridium difficile-associated diarrhea. Surawicz CM, July 2018, J Clin Gastroenterol. 42 (Suppl 2): S64–70
  14. Saccharomyces boulardii protease inhibits Clostridium difficile toxin A effects in the rat ileum. Castagliuolo et al. Infect Immun. 1996 Dec;64(12):5225-32
  15. Detzel CJ, Horgan A, Henderson AL, et al. Bovine immunoglobulin/protein isolate binds pro-inflammatory bacterial compounds and prevents immune activation in an intestinal co-culture model. PLoS one. 2015;10(4):e0120278.
  16. Crawford C., Panas R. Post-Infectious Irritable Bowel Syndrome with Functional Diarrhea Following C. difficile Infections: Case Studies of Responses Using Serum-Derived Bovine Immunoglobulin. Journal of Gastroenterology and Hepatology Research, Vol 4, No. 4 (2015).
  17. Silver S., Burnett, B. C. difficile Infection (CDI) Unresponsive to Antibiotics Resolved by Co-Administration of Serum Derived Bovine Immunoglobulin/ protein Isolate, a Nutritional Support Product: A Case Study. Advanced Research in Gastroenterology and Hepatology. Volume 6 Issue 2 – June 2017 DOI: 10.19080/ARGH.2017.06.555685
  18. Ferm, S. Varadi, N. Fisher, C. et al. Serum-Derived Bovine Immunoglobulin as Novel Adjunct in Complicated Clostridium difficile Colitis Treatment May 2017 DOI:10.14309/crj.2017.64
  19. Good L. Rosario R., Panas R. New therapeutic option for irritable bowel syndrome: Serum-derived bovine immunoglobulin. World J Gastroenterol 2015 March 21; 21(11): 3361-3366.
  20. Good L, Panas R. Case Series Investigating the Clinical Practice Experience of Serum-Derived Bovine Immunoglobulin/Protein Isolate (SBI) in the Clinical Management of Patients with Inflammatory Bowel Disease. Journal of Gastrointestinal &Digestive System. 2015; 5(2)
  21. Shafran et al. Management of inflammatory bowel disease with oral serum-derived bovine Immunoglobulin. Therapeutic Advances in Gastroenterology. 2015; 8(6):331-9
  22. Taxman, T, Panas R. Efficacy of Serum-derived Bovine Immunoglobulin/Protein Isolate (SBI) in Pediatric Patient with Acute Diarrhea Due to Small Intestinal Bacteria Overgrowth. EnteraHealth, Presented at Disease Week DDW® 2015 May 16 – 19, 2015 • Washington, DC


Image credits: Gut probiotics and potency bottle: ©Lester Moore.