Next Generation Probiotics: Bacillus

Found throughout the environment in soil and water, Bacillus bacteria are gram-positive, rod-shaped and form spores.  While the Bacillus family includes a few pathogenic strains, the large majority of are not harmful. Bacillus bacteria have a history of use in traditionally fermented foods, such as natto and iru. They also have been used for treating gut and urinary infections as an alternative to antibiotics, and supplemented in feed for poultry and fish farming.  The use of spore-forming organisms as probiotics is supported by research, but they are not as common as lactobacillus or bifidobacterium. Current research on Bacillus strains reveals a range of health benefits: from gut health to immunity, metabolism, weight control and nutrient intake.

Recent research is confirming how the gut barrier and the gut microbiome are foundational to health, because they affect changes in the immune system, either promoting disease or favoring immunity.  The trillions of organisms in the microbiota outnumber the cells in the human body 10 to 1.  The multi-functional role of the gut microbiota has been studied in relation to many disorders including obesity, insulin resistance, fatty liver, chronic fatigue, autoimmune disease, autism and Alzheimer’s.

Gut Health and Immunity

Bacillus organisms do their work in the gut, shifting gut health and the microbiota in a positive direction, with results that affect the entire body. The functions of Bacillus bacteria include:

courtesy of Pixabay

1) improving gut barrier function,

2) restoring balance in bacteroidetes/firmicutes ratio,

3) modulating the immune response,

4) destroying harmful organisms, and

5) increasing diversity in the gut microbiota.

A study of several Bacillus species examined their ability to reduce inflammation and bacterial endotoxin in humans.  Bacterial endotoxin causes immune cells to release inflammatory cytokines and is associated with intestinal hyperpermeability (leaky gut).  Increase in endotoxin occurs in response to processed foods, high fat meals, and diets high in glucose or fructose. Other factors such as antibiotics, stress, pain killers and pesticides disrupt the gut bacteria and gut wall permeability. The study used a combination of Bacillus strains and found that inflammatory interleukins and endotoxin were reduced an average of 60% after supplementing with 4 billion strains for 30 days. The supplement included B. indicus HU36, B. subtilis HU58, B. coagulans and B. clausii.

In a randomized controlled trial of Bacillus subtilis, people aged 60 – 74 had significantly higher secretory IgA and fewer respiratory infections when supplementing with the probiotic intermittently, for four months.  Another randomized controlled trial using Bacillus subtilis alone, or in combination with Bacillus licheniformis, found it effectively reduced antibiotic-associated diarrhea. Other research on Bacillus subtilis has shown it improves diversity in the microbiota and lowers markers of inflammation caused by endotoxin.

Several clinical trials using Bacillus coagulans in humans found it effective to treat IBS symptoms and severity.  Bacillus coagulans has been studied in rodents also, resolving diarrhea and normalizing intestinal motility, following chemotherapy.  

Research is revealing the role of Bacillus bacteria in gut health and immunity: their ability to secrete antimicrobial proteins, to remove pathogens by competitive exclusion and to boost the protective immune response.

Nutrients and Antioxidants

Bacillus organisms actually provide nutrients to the GI tract, as well as digestive enzymes.  Bacillus indicus HU36 is a marine derived bacteria which manufactures 15 different carotenoids (think of the yellow/orange pigments in vegetables). Marine carotenoids include astaxanthin, fucoxanthin, β-carotene, lutein and others that are not found in land plants. Carotenoids are associated with lower risk of chronic disease by decreasing oxidative stress.  A lab analysis of the HU36 carotenoids showed they reduce lipid peroxidation, a significant mechanism of chronic disease where the fats of the cellular membrane become damaged. Another function of carotenoids is to upregulate Nrf2, which activates several hundred genes that exert protection, detoxification and lower inflammation.

In addition to carotenoids, Bacillus bacteria produce enzymes such as amylase, protease, pectinase and cellulase which facilitate digestion and nutrient intake.

Another nutrient produced by bacteria is Vitamin K.  In the study above, the HU36 carotenoids worked synergistically with a form of vitamin K (MQ-7) produced by Bacillus subtilis. Research on menaquinone -7 (MQ-7) shows it to be effective in decreasing bone loss in postmenopausal women, as well as decreasing arterial stiffness.  Bacillus indicus HU36 and Bacillus subtilis provide essential nutrients associated with disease prevention.

Metabolism and Body Weight

Bacillus subtilis has demonstrated positive effects on developing lean body mass by regulating hormones and promoting the beneficial bacteria, Akkermansia.  In fact, recent research is revealing that people with high BMI, high fasting glucose, and insulin resistance tend to have lower amounts of Akkermansia muciniphila, while people who are lean and healthy have higher amounts of Akkermansia.  In a study of overweight adults, those with more Akkermansia had greater improvements in their blood sugar, triglycerides and body fat. Supplementation with Bacillus subtilis is one way to promote increases in Akkermansia.

In a randomized controlled study of people with obesity undergoing gastrectomy, patients received a supplement of 4.5 billion B. coagulans cells with prebiotic fiber.  After 3 months, they had improved metabolic markers: decreased triglycerides, LDL and the liver enzyme AST, as compared to the group who had surgery only.

Referring back to the study described above, the multi-strain Bacillus probiotic was also associated with lower ghrelin hormone after 30 days.  Ghrelin is a hormone that triggers hunger. Other studies have confirmed the role of the microbiota in regulating appetite and metabolism.

Soil Organisms vs Traditional Probiotics

Bacillus bacteria have been known as ‘soil bacteria’ but, increasingly, research points to their role as commensal bacteria in human health.  Several characteristics of these bacteria offer advantages over the traditional probiotic strains found in supplements.

The typical probiotic contains Lactobacillus and Bifidobacteria species.  As these bacteria are more sensitive to environmental conditions, there is great variability among supplements regarding the number of live viable bacteria. In testing of supplements, some probiotics were found to contain no living organisms.  After the supplement is consumed, stomach acid acts an anti-bacterial and further reduces the number of live organisms reaching the gut. Compared to traditional probiotic strains, the major benefit of Bacillus bacteria is their resistance to stomach acid and bile acids, and their stability under heat treatment and variations in pH.

Where to Find Bacillus Bacteria

courtesy Pixabay

Excellent sources of Bacillus organisms are organically grown raw vegetables and supplements containing strains verified by DNA sequencing.  In choosing a probiotic supplement, look for…

  1. Strains that are supported by research for efficacy and safety.
  2. Specific strains are verified by DNA sequencing.
  3. Product is free of allergens (corn, dairy, soy, gluten and yeast).

Products that we recommend are CoreBiotic™ by Researched Nutritionals (available only through practitioners) and Just Thrive® which is available directly to consumers.  Note that Bacillus supplements are not recommended for immunocompromised individuals or elderly persons.

Clinical trials of Bacillus probiotics are ongoing, to study their potential to treat gingivitis, periodontal disease, acne, rheumatoid arthritis and diabetes.  Register to follow our blog and you’ll get email notification as we share updates on Bacillus bacteria research.


Pickard JM et al. Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease. Immunol Rev. 2017 Sep;279(1):70-89.

Saad MJ  Linking Gut Microbiota and Inflammation to Obesity and Insulin Resistance.
Physiology (Bethesda). 2016 Jul;31(4):283-93.

Wang R et al.  Genetically Obese Human Gut Microbiota Induces Liver Steatosis in Germ-Free Mice Fed on Normal Diet. Front Microbiol. 2018; 9: 1602.

Jiang C et al. The Gut Microbiota and Alzheimer’s Disease.  J Alzheimers Dis. 2017;58(1):1-15

Lopetuso LR et al. Bacillus clausii and gut homeostasis: state of the art and future perspectives. Expert Rev Gastroenterol Hepatol. 2016 Aug;10(8):943-8. doi: 10.1080/17474124.2016.1200465.

McFarlin et al.  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.

Lefevre M et al. 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

Horosheva T et al. Efficacy of Bacillus probiotics in prevention of antibiotic‐associated diarrhoea: a randomized, double‐blind, placebo‐controlled clinical trial. JMM Case Reports , 2014 1, doi: 10.1099/jmmcr.0.004036

Urgesi R et al. A randomized double-blind placebo-controlled clinical trial on efficacy and safety of association of simethicone and Bacillus coagulans in patients with irritable bowel syndrome.Eur Rev Med Pharmacol Sci. 2014;18(9):1344-53.

Immunotropic aspect of the Bacillus coagulans probiotic action. J Pharm Pharmacol. 2017 Aug;69(8):1033-1040. doi: 10.1111/jphp.12726.

Sy C et al. Interactions between Carotenoids from Marine Bacteria and Other Micronutrients: Impact on Stability and Antioxidant Activity. Mar Drugs. 2015 Nov 19;13(11):7020-39. doi: 10.3390/md13117020.

Gammone M et al  Marine Carotenoids against Oxidative Stress: Effects on Human Health. Mar Drugs. 2015 Sep 30;13(10):6226-46. doi: 10.3390/md13106226.

Knapen NH et al. Three-year low-dose menaquinone-7 supplementation helps decrease bone loss in healthy postmenopausal women. Osteoporos Int. 2013 Sep;24(9):2499-507. doi: 10.1007/s00198-013-2325-6

Du R et al. Probiotic Bacillus amyloliquefaciens C-1 Improves Growth Performance, Stimulates GH/IGF-1, and Regulates the Gut Microbiota of Growth-Retarded Beef Calves. Front Microbiol. 2018 Aug 28;9:2006. doi: 10.3389/

Dao MC et al. Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut. 2016 Mar;65(3):426-36. doi: 10.1136/gutjnl-2014-308778

Kazzi F et al. Effect of Bacillus Coagulans and Galactomannans on Obese Patients Undergoing Sleeve Gastrectomy, A Randomized-Controlled Clinical Trial. Altern Ther Health Med. 2018 Jun 6. pii: AT5989

van de Wouw M et al. Microbiota-Gut-Brain Axis: Modulator of Host Metabolism and Appetite. J Nutr. 2017 May;147(5):727-745. doi: 10.3945/jn.116.240481

Elshaghabee F et al. Bacillus as potential probiotics: status, concerns, future perspectives. Front. Microbiol., 10 August 2017 |

1 comment on “Next Generation Probiotics: Bacillus

  1. Thanks for a super post.
    Healing the Gut is key to fixing many issues.
    It is said that nearly every disease originates in your digestive system. I mean both physical and mental disease. Once you heal and fix your gut lining, and make your digestive system work properly again, disease symptoms may be eradicated.
    Fermented foods, good probiotic supplements and even organic apple cider vinegar, like this one :


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