Probiotic Therapy

 Probiotics, the Gut, LPS and Health

How to Holistically Facilate the non digestion of Probiotics

Which Probiotic resist better the Gastric Juices

  Enteric Coated

There has been a lot of research on this question, and you’d be surprised by the findings: research has shown that probiotics are better without the special coatings.

In nearly all cases, they come in capsules that are designed to withstand stomach acids in order to deliver the probiotics to the right place within your GI tract, but enteric coating is actually not the best solution. And here’s why…

It’s kind of an odd statement, since the enteric coating prevents the probiotic capsule from breaking down in the stomach (too soon to be effective). But the enteric coating process requires a lot of heat, and that heat can destroy some of the probiotics before you even get the product.

So if you start with an equal amount of probiotics in two different pills and have one of them enteric coated, the one without the coating will have a better result in the intestinal tract (when taken with food) than the one that’s enteric coated.



According to U.K. food microbiologist Glenn Gibson, quoted in a 2008 story in “The Sunday Times,” only highly resistant bacteria such as lactobacillus and bifidobacteria can survive stomach acid. Other types of bacteria, including many probiotics, are likely to be destroyed by stomach acid.

Probiotics and Dairy

One method of protecting probiotic bacteria from stomach acid is by placing this bacteria in dairy foods. According to Bethlehem University, consuming probiotics in milk, yogurt and other dairy products provides the bacteria with a better chance of survival. This is because dairy products can buffer the stomach acid, thus increasing the chances that the probiotic bacteria will survive the journey and make it into the intestine.

Coated Supplements

In the 2008 “Sunday Times” story, microbiologist Glenn Gibson points out that the only way most probiotic supplements will survive contact with stomach acid is if the supplement capsules have a special enteric coating. Enteric coatings are applied to a variety of oral medications, such as over-the-counter pain relievers, providing the medication with a protective layer that can’t be eroded by stomach acid. This allows the probiotic supplement to pass safely through the stomach so the intact bacteria can be absorbed in the intestinal tract.




Cell Metab. 2014 Dec 2;20(6):1006-17. doi: 10.1016/j.cmet.2014.11.008. Diet and feeding pattern affect the diurnal dynamics of the gut microbiome. Zarrinpar A1, Chaix A2, Yooseph S3, Panda S4.


The gut microbiome and daily feeding/fasting cycle influence host metabolism and contribute to obesity and metabolic diseases. However, fundamental characteristics of this relationship between the feeding/fasting cycle and the gut microbiome are unknown. Our studies show that the gut microbiome is highly dynamic, exhibiting daily cyclical fluctuations in composition. Diet-induced obesity dampens the daily feeding/fasting rhythm and diminishes many of these cyclical fluctuations. Time-restricted feeding (TRF), in which feeding is consolidated to the nocturnal phase, partially restores these cyclical fluctuations. Furthermore, TRF, which protects against obesity and metabolic diseases, affects bacteria shown to influence host metabolism. Cyclical changes in the gut microbiome from feeding/fasting rhythms contribute to the diversity of gut microflora and likely represent a mechanism by which the gut microbiome affects host metabolism. Thus, feeding pattern and time of harvest, in addition to diet, are important parameters when assessing the microbiome’s contribution to host metabolism.


Time-Restricted Feeding Is a Preventative and Therapeutic Intervention against Diverse Nutritional Challenges. Cell Metabolism

Interactions between the diet and the gut microbiota dictate the production of short-chain fatty acids

Nature 535, 56–64 (07 July 2016) doi:10.1038/nature18846










Which are the Best Strains

Foundational food: Endospore Probiotics

To my knowldge, Homo Sapiens’ ancestors did not have fridges. Thus, they got their probiotics from the foods they consumed. They ate off the land and much of the food and liquid they consumed was brimming with mega doses of environmental bacteria. Most of those bacteria died as it passed through the harsh gastric system (gastric barrier), but some didn’t. These specialized strains developed an outside, protective shell known as an endospore which enabled them to both survive in the outside environment, as well as to then successfully pass through the acidic gastric system and ultimately thrive in the intestines.

With thousands of years of exposure to these specialized strains of commensal organisms, humans have actually come to require the presence of these strains for proper, healthy function of many of our biological systems. With this ability to live and reproduce in two very different environments (outside the body and inside the body), these strains are said to have a “biphasic” lifecycle.

The most well-known, well studied and widely used biphasic probiotics are from the bacillusspecies. In particular bacillus subtilisbacillus clausii and bacillus coagulans. To these can a newly discovered one called Bacillus Indicus HU36. This is the first strain of probiotic shown to produce antioxidants in the digestive system where the body readily absorbs it, along with the other probiotic functions.

We have evolved to gain constant exposure to these strains from our food sources; however, in this modern age of sterilized food systems, these essential strains have been nearly eliminated and our exposure to them is very limited. This make supplementing with them a very important part of a healthy lifestyle.

Bacillus clausii is arguably the most widely used probiotic in history as it has been used in two prescription drugs, in over a dozen countries, since the early 1950s; one of those products (Enterogermina®) is still on the market today. Its safety and efficacy with regards to GI defense is undeniable and that is why it has found its way into two companies… Just Thrive and Core (See below)

As part of the strain development program at London University, the entire genome of the strains chosen for Just Thrive™ has been sequenced, published and deposited into the International strain archive as a validated Bacilli species of the sub-class subtilis. This type of verification and identification is crucial to the assurance that a product is delivering the strains it claims to on the label. In fact, numerous studies have demonstrated that a large proportion of probiotic supplements in the market contain mislabeled strains and even unknown strains (sometimes pathogens) that are not listed on the label.


(Gibson, G.R. et al 2005; Elliot, E. et al 2004; J.M, et al 1999; Hamilton-Miller, et al 1999)

Bacillus coagulans has been added by the EFSA to their Qualified Presumption of Safety list[4] and has been approved for veterinary purposes as GRAS by the U.S. Food and Drug Administration‘s Center for Veterinary Medicine, as well as by the European Union, and is listed by AAFCO for use as a direct-fed microbial in livestock production. It is often used in veterinary applications, especially as a probiotic in pigs, cattle, poultry, and shrimp. Many references to use of this bacterium in humans exist, especially in improving the vaginal flora,[5][6][7] improving abdominal pain and bloating in irritable bowel syndrome patients,[8] and increasing immune response to viral challenges.[9] There is evidence from animal research that suggests that Bacillus coagulans is effective in both treating as well as preventing recurrence of clostridium difficile associated diarrhea.[10] One strain of this bacterium has also been assessed for safety as a food ingredient.[11] Spores are activated in the acidic environment of the stomach and begin germinating and proliferating in the intestine. Sporeforming B. coagulans strains are used in some countries as probiotics for patients on antibiotics.

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Sanders, M. E.; Morelli, L.; Tompkins, T. A. (2003). “Sporeformers as Human Probiotics: Bacillus, Sporolactobacillus, and Brevibacillus”. Comprehensive Reviews in Food Science and Food Safety. 2 (3): 101–110. doi:10.1111/j.1541-4337.2003.tb00017.x.

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Hong et al., 2005; SCAN

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Hun, L. (2009). “Bacillus coagulans significantly improved abdominal pain and bloating in patients with IBS”. Postgraduate Medicine. 121 (2): 119–124. doi:10.3810/pgm.2009.03.1984. PMID 19332970.

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Baron, M. (2009). “A patented strain of Bacillus coagulans increased immune response to viral challenge”. Postgraduate Medicine. 121 (2): 114–118. doi:10.3810/pgm.2009.03.1971. PMID 19332969.

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Fitzpatrick, LR. (Aug 2013). “Probiotics for the treatment of Clostridium difficile associated disease”. World J Gastrointest Pathophysiol. 4 (3): 47–52. doi:10.4291/wjgp.v4.i3.47. PMC 3740259pastedGraphic.png. PMID 23946887.

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Endres, J. R.; Clewell, A.; Jade, K. A.; Farber, T.; Hauswirth, J.; Schauss, A. G. (2009). “Safety assessment of a proprietary preparation of a novel Probiotic, Bacillus coagulans, as a food ingredient”. Food and Chemical Toxicology. 47 (6): 1231–1238. doi:10.1016/j.fct.2009.02.018. PMC 2726964pastedGraphic.png. PMID 19248815.







In humans[edit]

B. subtilis spores can survive the extreme heat during cooking. Some B. subtilis strains are responsible for causing ropiness — a sticky, stringy consistency caused by bacterial production of long-chain polysaccharides — in spoiled bread dough. For a long time, bread ropiness was associated uniquely with B. subtilis species by biochemical tests. Molecular assays (randomly amplified polymorphic DNA PCR assay, denaturing gradient gel electrophoresis analysis, and sequencing of the V3 region of 16S ribosomal DNA) revealed greater Bacillus species variety in ropy breads, which all seems to have a positive amylase activity and high heat resistance.[51] B. subtilis CU1 (2 × 109 spores per day) was evaluated in a 16-week study (10 days administration of probiotic, followed by 18 days wash-out period per each month; repeated same procedure for total 4 months) to healthy subjects. B. subtilis CU1 was found to be safe and well-tolerated in the subjects without any side effects.[52]

B. subtilis and substances derived from it has been evaluated by different authoritative bodies for their safe and beneficial use in food. In the United States, an opinion letter issued in the early 1960s by the Food and Drug Administration (FDA) recognized some substances derived from microorganisms as generally recognized as safe (GRAS), including carbohydrase and protease enzymes from B. subtilis. The opinions were predicated on the use of nonpathogenic and nontoxicogenic strains of the respective organisms and on the use of current good manufacturing practices.[53] The FDA stated the enzymes derived from the B. subtilis strain were in common use in food prior to January 1, 1958, and that nontoxigenic and nonpathogenic strains of B. subtilis are widely available and have been safely used in a variety of food applications. This includes consumption of Japanese fermented soy bean, in the form of Natto, which is commonly consumed in Japan, and contains as many as 108 viable cells per gram. The fermented beans are recognized for their contribution to a healthy gut flora and vitamin K2 intake; during this long history of widespread use, natto has not been implicated in adverse events potentially attributable to the presence of B. subtilis.[citation needed] The natto product and the B. subtilis natto as its principal component are FOSHU (Foods for Specified Health Use) approved by the Japanese Ministry of Health, Labour, and Welfare as effective for preservation of health.[54]

B. subtilis has been granted “Qualified Presumption of Safety” status by the European Food Safety Authority.[55]

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“Effect of flower-applied Serenade biofungicide (Bacillus subtilis) on pollination-related variables in rabbiteye blueberry”. Biological Control. 33 (1): 32–38. 2005-04-01. doi:10.1016/j.biocontrol.2005.01.002. ISSN 1049-9644.

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Pepe O, Blaiotta G, Moschetti G, Greco T, Villani F (April 2003). “Rope-producing strains of Bacillus spp. from wheat bread and strategy for their control by lactic acid bacteria”. Applied and Environmental Microbiology. 69 (4): 2321–9. doi:10.1128/AEM.69.4.2321-2329.2003. PMC 154770pastedGraphic.png. PMID 12676716.

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Lefevre, Marie; Racedo, Silvia M.; Denayrolles, Muriel; Ripert, Gabrielle; Desfougères, Thomas; Lobach, Alexandra R.; Simon, Ryan; Pélerin, Fanny; Jüsten, Peter; Urdaci, Maria C. (1 February 2017). “Safety assessment of Bacillus subtilis CU1 for use as a probiotic in humans”. Regulatory Toxicology and Pharmacology. 83: 54–65. doi:10.1016/j.yrtph.2016.11.010.

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“FDA partial list of microorganisms”. Food and Drug Administration. 2002.

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Gibson G.R., 2005. Functional Foods: Perspectives on foods for specific health uses (FOSHU), Colette Shortt, Yakult UK. Volume 1, page 7-1.

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EFSA Panel on Biological Hazards (BIOHAZ) (2010). “Scientific opinion on the maintenance of the list of QPS microorganisms intentionally added to food or feed (2010 update)”. EFSA Journal. 8 (12): 1944.





B. subtilis has about 4,100 genes. Of these, only 192 were shown to be indispensable; another 79 were predicted to be essential, as well. A vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related to cell energetics.[12]

The complete genome sequence of B. subtilis sub-strain QB928 has 4,146,839 DNA base pairs and 4,292 genes. The QB928 strain is widely used in genetic studies due to the presence of various markers [aroI(aroK)906 purE1 dal(alrA)1 trpC2].[13]

Several noncoding RNAs have been characterized in the B. subtilis genome in 2009, including Bsr RNAs.[14] Microarray-based comparative genomic analyses have revealed that B. subtilis members show considerable genomic diversity.[15]




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What is Bacillus subtilis natto?

Bacillus Subtilis Natto

Bacillus subtilis natto (Figure 1 & 2) was found by Dr. Sawamura in 1906 and named Bacillus natto Sawamura. Since then it obtained the approvals for the manufacture of drug medicine in 1968, for animal drug in 1990, and for dietary additive in 1996, and it is now attracting attention as it has lately started being used for health food. Bacillus subtilis natto is a type of fungus that produces salt-free fermented soy food such as Japanese traditional sticky natto, Kinema from Nepal and Thuanao from Thailand. It is one sort of Bacillus subtilis, not an indigenous intestinal fungus in a strict sense, and it has endospore and is the most stable kind of fungus in nature Bacillus subtilis natto gets activated and strengthen beneficial intestinal flora (e.g.: bifidobacteria, lactic acid bacterium) which all animals intrinsically carry through making an appearance of various sorts of physiological effects.



Functions of Bacillus subtilis natto

1. Increase of beneficial bacteria

2. Inhibition of harmful intestinal bacteria

3. Producing a proper balance of intestinal flora by the functions above

4. Producing strong protein degradation enzymes and starch degradation enzymes

5. Elaborating B-complex vitamins abundantly

Intake of Bacillus subtilis natto

Recommended intake of Bacillus subtilis natto is 7.5×108/ day. This amount is set considering its safety (*), the economic efficiency and actual results of usage. (*) The safety was confirmed by promoting multiplication of lactic acid bacterium by mixed culture; the effect of inhibition of harmful intestinal bacteria and pathogen growth; and repeated oral administration for toxicity assay in rats.

Experimental Report of Bacillus subtilis natto

• Growth stunting action of Bacillus subtilis natto against animal-derived pathogen


• Antibacterial activity of Bacillus subtilis natto



• Experiment of mixed culture of Bacillus subtilis natto and Candida albicans by repeated flux cultivation






Evolutionary Diet, we understand that a nutrient supports our genotype if that nutrient was available to and consumed by our ancestors over the thousands and even millions of years of evolution. For a probiotic to claim to fit the evolutionary paradigm, one has to prove that the strains in the product were abundant in the environment our ancestors evolved in.



A simple literature search seeking published studies on the prevalence of the bacillus species will reveal the fact that bacillus seems to be a universal probiotic. Bacillus species are quite abundant in the environment and subsequently found as commensal, transient organisms in the gastrointestinal systems of mammals, insects, invertebrates, birds, marine life and even reptiles.

Although they have always been classified as “soil organisms”, studies are starting to reveal that they are actually digestive tract organisms that use the soil as a vector for transfer from host to host and they have been doing this for thousands and based on some strong evidence, for even millions of years.

Further research into the prevalence of bacillus species in the prehistoric periods reveals that bacillus species even pre-date early humans before the Paleolithic era. Certainly early humans such as Homo habilis and Homo erectus were abundantly exposed to bacillus, but the data suggests that perhaps even dinosaurs enjoyed the probiotic benefits of this amazing species.

The earliest identification of bacillus sp. on earth was published by Vreeland R.H., et al (2000) in the journal of Nature. The researchers were able to isolate and then grow viable bacillus cells from a brine inclusion within a 250 million-year-old salt crystal from the Permian Salado Formation. The second earliest identification of bacillus sp. published in the literature was by Cano R.J., et al (1995) where the researchers isolated and identified a viable bacillus species from the abdominal contents of extinct bees preserved for 25 to 40 million years in buried Dominican amber. This finding is significant in two respects; first that bacillus was found to be present 25-40 million years ago and second, that bacillus was found in the gastrointestinal system of the extinct bee – evidence of ancient probiotic function!

Moving forward on the time scale, Gilichinsky et al. (2008) published research showing the identification and characterization of bacillus species in Siberian and Antarctic permafrost samples dating back 3-5 million years old. 


Besides the age, it is significant to note that bacillushas managed to span the globe from pole to pole – this further shows evidence of its abundance in the early earth environment including the period of human evolution. Further, Christner B.C., et al (2003) isolated and characterized bacillus species from ancient glacial ice-cores of the Qinghan-Tibetan plateau in Western China dating back 750,000 years old. This period in time is a crucial time for human development from Homo erectus to Homo sapiensand sure enough, bacillus was present.

Moving further ahead, Christner B.C., et al (2000) published a more in depth analysis of microbial existence in various locations and age range of ice-cores ranging from 5 to 20,000 years old from China, Bolivia, Peru, Greenland and Antarctica. The researchers found bacillus to be abundant in all samples spanning all the regions and periods tested. Further significance of their findings were that they identified bacillus subtilis specifically in all samples and time periods and were able to compare the genomic make-up of the ancient samples to validated bacillus subtilis genome of today – the researchers found 90% and greater homology between the current and ancient strains. Considering that bacteria mutate and replicate very quickly, it is amazing to think that this species (bacillus subtilis) has remained the same for tens of thousands of years. This indicates that the organism is supremely adapted to its environment and function as a transient gastrointestinal microbe and there are no selection pressures favoring a new genotype.

Among the most interesting findings on the prevalence of the bacillus species, is the work of Horneck, G. et al (1994) on the survival of bacillus subtilis in space. The researchers demonstrated that bacillus subtilis was able to survive in space for six years despite the harsh radiation, vacuum, temperatures and other conditions that typically do not support life. In fact, Horneck, et al. and other scientist postulate that bacillus endospores are the most likely candidates to support the Panspermia hypothesis that life exists throughout the Universe, distributed by meteoroids, asteroids, comets and planetoids by interstellar and interplanetary collisions. Studies show that bacillus subtilis is able to survive an interplanetary lithopanspermic journey. This outlines the possibility that not only is bacillus a probiotic (meaning “for life”), but perhaps the source of life itself on our planet.

Bacillus and Bacillus subtilis have functioned as probiotics since life spawned on this earth and certainly throughout the time that humans evolved. We have a highly ordered co-evolution with the species as is demonstrated by their function in the human GI and the molecular specificity with which they interact with human cells.

  • We share genetic material with them for human cellular protein synthesis and we are dependent on them for the proper development of our immune system. A number of studies have shown that bacillus subtilis plays a key role in the tutoring/training of the immune system and in mitigating a systemic pro-inflammatory and autoimmune state.
  • We rely on them for proper digestion and assimilation of our food and we need them to detoxify our highly exposed gastrointestinal system.
  • They produce over 24 different antibiotics in vivo that help defend our GI from invading species and even over-growth of our own bacteria.
  • Lastly, we count on them for the production of key nutrients (i.e. vitamins, enzymes, carotenoids, lipids, etc.) right at the sites of absorption where we experience the highest bioavailability.

They are not a luxury in a healthy lifestyle, they are a necessity. They are truly “Foundational Food” that our ancestors co-evolved with to bring us to our evolutionarily most fit genotype and phenotype.



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Bacillus Clausii: The European Probiotic You’ve Likely Never Heard Of

By Ty Bollinger

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“Wash up, kiddos − it’s time for supper!” I don’t know about you, but I can still hear the tenderhearted voice of my mother giving this routine beck and call. My childhood days were spent fighting imaginary wars with my brother and sister in our back yard, playing baseball with my dad, picking strawberries with mom, and having fun outside in the hot Texas sun.

My mother’s hope was that all the grit and grime we picked up during our backyard escapades and baseball games would keep from settling on and around her dinner table. This was a reasonable expectation, considering the copious amounts of dirt we most certainly tracked all over her carpets and floors.

Now, to be honest, mom’s concern wasn’t so much about the “dirtiness” of dirt, as it was about its unsightliness. Mom simply wanted to keep her house and children looking clean, especially during mealtimes. She wasn’t all that concerned about the supposed “danger” of germs. This was because it was generally understood back then that being outside is good for kids and helps them build a strong immunity.

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Here’s an old photo with me, my brother Ron, my sister Cherith, and two of our friends playing “cops and robbers” (circa 1976). Yes, that’s me on the left in my pink tank top. LOL!

This is in stark contrast to the sterility mindset of many of today’s parents today who try to keep their children away from dirt in order to protect them from infection and disease.

Why am I bringing all this up, you might be asking? The answer is simple: our natural world is filled with germs. But many of these germs are beneficial for our health, conferring all sorts of protections both in plants and people.

My mother and many others like her never would have been able to verbalize this with any sort of scientific precision. But, they seem to have understood (more so than many people do today), that our relationship with nature is synergistic. That it’s something to be revered and respected, rather than feared.

People from other countries seem to understand this concept better than many Americans do. However, we’re slowly catching on to the myriad ways in which bacteria can aid our health and protect our bodies against disease. I’d like to further help this awakening by introducing you to one of the most amazing probiotic bacterial strains which you’ve likely never heard of.

Bacillus Clausii: Nature’s Resilient Remedy for Respiratory and Gastrointestinal Ailments

It’s known as Bacillus clausii, and it’s widely co-administered alongside antibiotic treatments at health clinics throughout Europe, but not yet in the U.S.

This gram-positive, rod-shaped bacteria is a soil-based microbe that’s been in use throughout Europe since at least the 1960s. However, it is said to have been identified by name in 1995 by German bacteriologist Dieter Claus. What sets B. clausii apart from most other probiotic bacterial strains is its unique ability to withstand high pH environments. B. clausii also bears an exceptional tolerance for antibiotics, making it an effective adjunct for replenishing one’s microbial flora during antibiotic treatment.

This can be a good thing or a bad thing, depending on the nature of the bacteria in question. B. clausii, after all, is just one species in the larger genus of Bacillus bacteria. This grouping boasts roughly 77 different unique bacterial strains.

The ability of Bacillus bacteria to outsmart antibiotics rather than succumb to an inevitable death like most other bacteria do has the potential to make it a malignant “superbug.” Thankfully, B. clausii operates much differently.

A 2007 pilot study published in the Journal of Therapeutics and Clinical Risk Management demonstrates the specific immunoprotective properties of B. clausii in children with chronic respiratory infections. Researchers out of Italy found that a three-month treatment regimen with B. clausii was enough to help reduce not only the intensity, but also the frequency of respiratory infections. Its benefits persisted beyond the trial period, suggesting that B. clausii‘s benefits are potentially permanent.

A study published several years later in the Journal of Yoga & Physical Therapy came to similar conclusions about the benefits of B. clausii in children with chronic diarrhea. I mentioned earlier that this unique bacterial strain survives high pH environments. But this particular study found that B. clausii also survives low pH environments, having a unique affinity for the bowel wall where it affixes and colonizes the bowel mucosa.

The beneficial effects of this, the research reveals, include the ability of B. clausii to survive its way past the digestive juices of the stomach and into the small intestine. There it works its magic in targeting the viruses and bacteria that cause diarrhea both in children and adults. After just 10 days of treatment, patients with watery stools suddenly had soft ones, all without any negative side effects.

B. clausii was also shown to help mitigate the damage caused by antibiotic treatments for Helicobacter pylori, a major cause of intestinal ulcers and other gastrointestinal problems. Diarrhea from other causes was also found to respond positively to B. clausii treatment. This led researchers to conclude that the probiotic strain possesses both antimicrobial and immunomodulatory (able to modify immune response) activities.

All in all, the sum of existing scientific research definitively shows that B. clausii is a unique and powerful bacterial strain. It releases antimicrobial substances that target some of the worst “superbug” strains that humanity faces today, including Staphylococcus aureus (Staph infection), Enterococcus faecium, and Clostridium difficile (C. diff.).

At the same time, B. clausii helps boost the immune system while repopulating the gut with “good” bacteria − a win-win for public health.








[-] Sources and References

Efficacy of Bacillus clausii spores in the prevention of recurrent respiratory infections in children: a pilot study

Bacillus clausii – The Probiotic of Choice in the Treatment of Diarrhoea

Probiotic Therapy

Bacillus clausii Probiotic Strains: Antimicrobial and Immunomodulatory Activities














Bacillus clausii is a rod-shaped, Gram-positive, motile and spore-forming bacterium that lives in the soil. It is classified as probiotic; microorganisms that maintain a symbiotic relationship with the host organism.[1] It is currently being studied in respiratory infections[2] and some gastrointestinal disorders.[3] Bacillus clausii, has been found to produce antimicrobial substances that are active against gram positive bacteria including Staphylococcus aureus, Enterococcus faecium, and Clostridium difficile.[1]

Genome structure[edit]

Bacillus clausii has relatively small genome that contains 4.30 Mbp with 4,108 protein coding genes.[1]


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a b c Urdaci, MC; Bressollier, P; Pinchuk, I (Jul 2004). “Bacillus clausii probiotic strains: antimicrobial and immunomodulatory activities”. Journal of Clinical Gastroenterology. 38 (6 Suppl): S86–90. doi:10.1097/01.mcg.0000128925.06662.69. PMID 15220667.

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Marseglia GL, Tosca M, Cirillo I, et al. (March 2007). “Efficacy of Bacillus clausii spores in the prevention of recurrent respiratory infections in children: a pilot study”. Journal of Therapeutics and Clinical Risk Management. 3 (1): 13–7. doi:10.2147/tcrm.2007.3.1.13. PMC 1936284pastedGraphic.png. PMID 18360611.

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Gabrielli M, Lauritano EC, Scarpellini E, et al. (May 2009). “Bacillus clausii as a treatment of small intestinal bacterial overgrowth”. The American Journal of Gastroenterology. 104 (5): 1327–8. doi:10.1038/ajg.2009.91. PMID 19352343.









Efficacy of Bacillus clausii spores in the prevention of recurrent respiratory infections in children: a pilot study

Gian Luigi Marseglia,1 Mariangela Tosca,2 Ignazio Cirillo,3 Amelia Licari,1 Maddalena Leone,1 Alessia Marseglia,1 Anna Maria Castellazzi,1 and Giorgio Ciprandi4

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Probiotic milk has been previously demonstrated to reduce the number of respiratory infections (RI) among children attending day care centres. Thus, this pilot study was aimed to assess the efficacy and the safety of 3 month treatment with Bacillus clausii in the prevention of recurrent respiratory infections (RRI) in children. Eighty children with RRI were studied: 40 of them were randomly treated with B. clausii for 3 months, and followed up for further 3 months; 40 were included in the control group during the same period. Children treated with B. clausii had shorter duration of RI in comparison with the control group both during the treatment phase (mean 11.7 days vs 14.37; p=0.037) and the follow-up period (mean 6.6 days vs 10.92; p=0.049). This effect was evident also in allergic children during the follow-up. In conclusion, this pilot study provides the first preliminary evidence that B. clausii may exert a significant and persistent impact on RI in children and is safe and well tolerated.

Keywords: probiotic, children, respiratory infections, allergy











Species most common to spore probiotic formulations include: Bacillus subtilis, Bacillus clausii, Bacillus cereus, Bacillus coagulans (Lactobacillus sporogenes) and Bacillus licheniformis (10).

Bacillus Spores – Gut and Immune Health:

The gut is an important center of immune activity for the whole body. It strongly maintains the interface between the “outside” & “inside” world – supporting the “good guys” & keeping “bad guys” out.

It’s been known for at least 50 years that Bacillus subtilis strains can produce a variety of antibiotic compounds that help crowd out potential pathogens (11).

Bacillus spores may have direct immune supportive properties that help support the development of gut-associated lymphoid tissue (GALT). GALT promotes healthy and balanced immune function, while also keeping the intestinal lining robust & healthy. A happy gut leads to a happy and balanced immune system.

Spore probiotics may also stimulate the production of key immune cells such as macrophages, interferon and natural killer cells that protect us against pathogens.

As such, Bacillus probiotics may safely help to reduce the incidence and improve our response to allergy and infection, small intestinal bacterial overgrowth, as well as abdominal pain, bloating, and diarrhea commonly associated with gut dysbiosis and irritable bowel syndrome (121314; 15; 161718; 19; 20; 21).

The spore itself, independent from antibacterial compounds produced, may help crowd out pathogenic microbes in the gut, simply by stimulation of gut & immune tissue (7). The immune stimulation may be useful against viral exposure as well (22).

As a group, Bacillus species are able to product at least 24 different known antibiotic compounds.

Bacillus coagulans can produce bacteriocin, an antibacterial compound that may help with urinary tract infections (23; 24; 25).

Bacillus subtilis is also able to produce antimicrobial compounds such as “amicoumacin A” that may help control overgrowth of Helicobacter pylori (26). Additionally, Bacillus supplementation may help reduce side effects of those H. pylori patients taking conventional antibiotics (27).

Anti-Aging and Heart Health

Bacillus species are also able to produce antioxidant compounds known as carotenoids such as lycopene that may help protect from oxidative stress which is involved in cardiovascular disease, inflammation, cancer, and aging (28; 29; 30).

Bacillus subtilis is also involved in the production of natto – a traditional food in Japan made from fermented soybeans. In the presence of Bacillus subtilis, various active compounds such as nattokinase are found that can help with blood clotting and cardiovascular health risks. Natto is also one of the best sources of menaquinone K2-7 – a special form of vitamin K made by Bacillus subtilis.

And, if I didn’t get your attention yet, the Bacillus-produced products found in natto may even help with hangover symptoms by helping to clear alcohol & aldehyde build-up (31).

Safety of Bacillus Supplements






These “breakthrough” probiotic strains are called gut commensal spore bacillus and learning about how they function in the gut has entirely changed the way I look at what a microbiome needs to remain healthy.

It is true that the majority of the bacterial population in the human gut is made up of lacto and bifido strains.  However, the strains of lacto and bifido that thrive in our gut are NOT exactly the same as ones that grow in lacto-fermented foods or in probiotic pills.  Why not?

Because the strains in our gut are ANAEROBIC, that is, they thrive in an environment that has no oxygen.

The strains in fermented foods, or those grown in a lab, have been produced an oxygen-exposed environment. This exposure genetically alters them into the AEROBIC version and, therefore, unable to bind to the correct receptor sites in the intestines.

Without that binding ability, conventional strains (aerobic lacto, bifido, etc.) are unable to colonize the gut.

Instead, microbiologists say our newest technology clearly shows that, even if some miniscule amount manages to remain alive through stomach acid, conventional bacteria simply pass through the intestines in a matter of hours to be excreted in the bowel movement.

If all they do is pass through, does that mean the lacto and bifido strains from fermented food or probiotic pills are worthless?

Absolutely not!  Because we also know that we get well-documented immune benefit from consuming these kinds of non-colonizing bacteria, even if microbiologists, at this point, don’t fully understand the mechanism for how.

Sandor Katz, author with Sally Fallon of the fermentation classic, Wild Fermentation,  in a panel discussion on May 11, 2016 at UCLA called Microbes: From Your Food to Your Brain offered a possible explanation.

One scientific guess, Katz said, about the origin of the benefit of fermented foods is that there may be an advantageous genetic exchange between the alive microbes residing in the gut with the dead transient microbial passersby as they move through the intestines.  Or another possibility, as my doctor friend suggested, is that the dead cell bodies of the consumed microbes provide nutrition for the live bacteria.

Bottom line?  We just don’t know enough yet to state definitively how the bacteria in live, fermented  foods can produce benefit to the immune system; we just know that to a degree they do.

So how do the spore bacillus function differently? 

Spore bacillus is a family of bacteria that has naturally evolved over time to be particularly hardy by developing a shell. This outside spore not only protects it against extremes like moisture and dehydration, heat and cold, and the harsh acids of the bile and stomach, but also enables it to naturally survive in environments that are both oxygen-rich, like air, as well as anaerobic, like the human intestines.

This allows the gut commensal spore bacillus to safely exist in our external environment for eons in their inactive spore form, literally just waiting for the chance to be inhaled, drunk or consumed by, oh, say… a human.

And once they reach the small intestines, because they are of the gut commensal family (meaning the gut is their natural home), the shell falls away so the bacteria can bind to the correct sites.

Designed by nature to be our gut cleaners, these gut commensal strains then immediately begin killing pathological strains and supporting beneficial ones. At the end of about 3-4 weeks, they have moved down the entire length of the gut, correcting and rebalancing the microbial population wherever they travel.

I learned this by getting exposed to a new probiotic that has only recently launched here in the U.S.  Ten years in the making, this is the first 100% gut commensal spore probiotic to be sold at the retail level in this country. It  has been shown in third party gastric survivability testing to arrive 100% alive in the intestines, actively colonize the gut, and produce antioxidants.





In fact, testing has shown that these four proprietary strains stimulate a 30% change for the better in the microbiome in just about two weeks with one cap daily. 

Update:  It’s now been proven to work — it has been shown to reverse Leaky Gut at one cap daily in 30 days with no other changes in diet or lifestyle. Those results were peer reviewed and published August 2017:  Oral spore-based probiotic supplementation.  It involved 100 people. Half got the probiotic, half didn’t. Everyone who got the probiotic improved, while very little to no change for those with the placebo. 

(*For those suffering from depression, keep in mind that 90% of serotonin is produced by specific probiotic strains in the gut.  Do you have enough of the right bacteria?)

















New Study Links Alzheimer’s to Bacterial Endotoxins from the Gut

Alzheimer’s disease (AD) is a progressive form of dementia that destroys memories and other cognitive functions. This chronic neurodegenerative disease is the 6th leading cause of death in the US, affecting over 5 million Americans.

Scientists believe that damage to the brain likely begins a decade or more before memory loss and other cognitive symptoms arise. During this preclinical stage of AD, abnormal deposits of proteins can form amyloid plaques and tangled fibers throughout the brain. Meanwhile, neurons begin to lose function and die.

The initial damage appears to take place in the hippocampus, where memories are formed. However, as more neurons die, the damage continues to spread to other parts of the brain, and the brain tissue begins to shrink.

While the underlying cause of AD is not fully understood, more and more research continues to highlight the important bi-directional connection between the gut microbiome and the brain.

One such study, published this month in the Frontiers in Immunology journal, found that pro-inflammatory lipopolysaccharide (LPS) from the human gastrointestinal tract was abundant in the neocortex and hippocampus of AD-affected brains.

Lipopolysaccharide, or LPS, is a structural component of gram-negative bacterial cell membranes that reside in the human GI tract. When these gram-negative bacteria die, they shed the LPS from their cell membrane, and it begins to float freely in the lumen of the intestine as a bacterial endotoxin.

Inside the intestinal lumen, LPS is harmless to humans. However, if there is damage to the intestinal lining, then LPS can enter into the bloodstream, where it can trigger low-grade inflammation. This condition is better known as metabolic endotoxemia.

The findings of this ground-breaking study suggest that metabolic endotoxemia is an important contributor in inflammatory neurodegenerative diseases like AD. LPS in the brain has also been linked to mood disorders like anxiety and depression.

Fortunately, MegaSporeBiotic was formulated to target inflammation caused by bacterial endotoxins. In fact, a double-blind, placebo-controlled human clinical trial, published in the World Journal of Gastrointestinal Pathophysiology, found that just 30 days of supplementation with MegaSporeBiotic was enough to reduce serum LPS levels by a whopping 43% in healthy college students without any additional interventions.

These findings suggest that the unique strains found in MegaSporeBiotic were able to strengthen the integrity of the intestinal lining to keep endotoxins like LPS out of the bloodstream and the brain.

For more information on these topics, visit the Practitioner’s Corner by logging into your online account. If you’d like to create an account with us, you can register at


Zhao Y, Cong L, Jaber V, Lukiw W. Microbiome-Derived Lipopolysaccharide Enriched in the Perinuclear Region of the Alzheimer’s Disease Brain. Front Immunol. 2017;8:1064.

Boutagy NE, McMillan RP, Frisard MI, Hulver MW. Metabolic endotoxemia with obesity: Is it real and is it relevant? Biochimie. 2016;121:11-20.

Stevens BR, Goel R, Seungbum K, et al. Increased human intestinal barrier permeability plasma biomarkers zonulin and FABP2 correlated with plasma LPS and altered gut microbiome in anxiety or depression. Gut. 2017;pii:314759.

McFarlin BK, Henning AL, Bowman EM, 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;8(3):117-126.



The four strains in Just Thrive produce a range of nutrients, detoxifiers and antioxidants, including:

•Quinols (as in CoQ10-Quinol, etc)

•Vitamin B Complex

•Vitamin K2 (read my article here about how I was able to rid my teeth of virtually all tartar by getting correctly diagnosed by a microbiome expert as being K2 deficient)








  • Sorted by:
Oral spore-based probiotic supplementation was associated with reduced incidence of post-prandial dietary endotoxin, triglycerides, and disease risk biomarkers  
Brian K McFarlin, Andrea L Henning, Erin M Bowman, Melody A Gary, Kimberly M Carbajal
World J Gastrointest Pathophysiol 8(3):117-126. Published online Aug 15, 2017. doi: 10.4291/wjgp.v8.i3.117


Just Thrive’s patent-pending Bacillus indicus HU36 is completely unique because it makes seven antioxidants in amounts as high as the Recommended Daily Amount (RDA) – so not just a dusting, but substantial, measurable levels.

Furthermore, these vitamins and antioxidants are produced exactly at the microvilli site of nutrient uptake, virtually guaranteeing high absorption rates.

Avoiding the body’s destructive digestive acids is important to any kind of absorption because, no surprise, stomach and bile acids can negatively impact the nutrients in any supplement or food, not just probiotics.

Bacillus Indicus HU36 produces:


2Alpha carotene

3Beta carotene





So, overall what’s the best thing I can do?

My personal approach these days now is, on a daily basis, to take both this gut commensal spore bacillus probiotic as well as at least one serving of live, fermented foods.  (Such as real, raw sauerkraut, dairy kefir, etc.)


Gut Reactions to Beneficial Bacteria



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Victoria Roberts

Q. When you eat yogurt or take a probiotic supplement, why aren’t the probiotic bacteria killed by stomach acids?

A. The point of consuming a probiotic supplement in a food like yogurt, a powder or a capsule is to introduce beneficial bacteria in the gut, said Dr. Christine Frissora, a gastroenterologist at the Center for Advanced Digestive Care at NewYork-Presbyterian/Weill Cornell hospital.

There are questions about whether these bacteria survive the gastric acid, make it down to the small intestine or colon and live to have any biological effects. “Certain bacteria have the capability to survive gastric acid and others do not,” Dr. Frissora said.

Some bacteria have a polysaccharide (or complex carbohydrate) capsule that protects the inner organism like armor, she said. Others have a complex electrolyte pump that pumps acid out of the cell, providing protection from destruction.

One public health concern is that patients taking acid-suppressing drugs called proton pump inhibitors have a gastric pH level that is often quite high, allowing many more bacteria to survive, Dr. Frissora said. This increases the risk of aspiration pneumonia and perhaps even a Clostridium difficile infection, which causes fever, diarrhea and a high white blood cell count, and can be life-threatening.

A more basic question: Is a probiotic supplement actually needed?

Not by most people, Dr. Frissora said. “Oftentimes prebiotic foods, like a banana or honey, will do just as well,” she said.



Which Are the Better-Known Bacillus Species?

Some of the famous and infamous species include:

  • B. anthracis, the deadly agent of anthrax disease. All strains are pathogens.
  • B. cereus, a species with harmful (usually associated with food poisoning and opportunistic infections) and useful strains (used for fungus and bacterial control on crops)
  • B. coagulans, with many strains used as probiotics or for industrial applications, but some with harmful toxin production
  • B. indicus, an interesting species with pigmented spores and vegetative cells
  • B. licheniformis, another species with harmful (usually associated with food poisoning and opportunistic infections) and useful strains (industrial, food industry, probiotic, veterinary and medical applications)
  • B. subtilis, a species with probiotic strains, food industry usage (including natto), GMO usage, and industrial applications as well as harmful toxin-producing strains and opportunistic-infection strains
  • B. thuringiensis, source of the Bt toxin that is used as a pesticide and in some GMO crops such as corn, cotton, canola and soy.

Since this site is about probiotics, more information can be found on these species:


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Vegan Coconut Yogurt Recipe



3/4 to 1 cup coconut water

16 ounces (453 grams) raw coconut meat

Probiotic powder (approximately 2 capsules worth)


Blend the coconut water and coconut meat until smooth.

Add the probiotic powder (or simply open the capsules and dump the contents into the blender) and blend briefly.

Pour into a bowl (or jar) big enough to allow a bit of room to expand. Gently place a lid on top and set your coconut yogurt to culture on your counter for 8-16 hours. The longer it cultures, the more yogurt-y it becomes in taste.

When you’re ready to eat it, feel free to sweeten it and/or add extracts like vanilla, fresh fruit, etc.

NOTE: Yogurt will culture faster in warmer weather so the culturing time may vary. If you live in a cooler climate, you may want to use a temperature controlled yogurt maker. Once cultured, this yogurt will keep for up to seven days in a sealed container in the fridge.

Just Thrive™ is built around the Bacillus Subtilis HU58 strain that has been isolated, studied and verified by Royal Holloway London University. The product is then rounded out by the three other very powerful bacillus strains – bacillus clausii, bacillus coagulans and Bacillus Indicus HU36.


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