Bacillus Probiotics – Update


  • “B. subtilis and CEBS supplementation caused a significant increase in the numbers of Lactobacillus and Bifidobacterium in the caecum, whereas the numbers of Escherichia coli and Staphylococcus decreased significantly compared with the control.” [2016]

Bacillus probiotics are now in my “use with caution” list.


ImmunoIn a recent post I suggested MegaSporeBiotic because it is full of different bacillus species [but only if you do not have histamine issues]. A reader pointed me at John Brisson’s blog on megaspore. He raises a valid question in his post “Why I Do Not Recommend MegaSporeBiotic or My Issues With Bacillus licheniformis”.

I reviewed this in a year ago with a do not take if you have histamine issues.

A reader tried it for two weeks and reported:

I have stopped my trial of Thrive after 2 weeks for the following reasons:

  1.  Definite histamine response / immune overstimulation
  2. Burning lactic acid sensations in muscles and increase in severe fatigue.

I will not be trying them again.

The Bacillus licheniformis strain is not identified nor it’s safety is unknown. John writes:

Bacillus licheniformis is one of the worst offending soil based “probiotics” and is known to cause food poisoning, 8 septicemia, 91011 peritonitis, 12 and ophthalmitis. 13Bacillus licheniformis is not native human flora but appears to be native flora in birds. 14Bacillus licheniformis is a ubiquitous organism and likely enters the human digestive system many times a day. While data regarding its ability to survive in the human gastrointestinal tract is sparse, it is likely that the spores pass without activating. 15

John was kind enough to send me a followup draft. The manufacturer has launched a different version, Just Thrice, unfortunately it contains histamine producers still. A reader forwarded me a link to a Crohn’s Disease targeted probiot, Perfect Pass, which I have also added to the table below.

Histamines Producers Just Thrive MegaSpore
Perfect Pass Restorflora Prescript Assist
Bacillus Indicus HU36
Human sourced
Bacillus Coagulans X X X X
Bacillus Clausii X X X X
Bacillus Subtilis HU58
Human Sourced
Bacillus Licheniformis X X
Bacillus Brevis  unknown X
Bacillus Marcerans  unknown X
Bacillus Pumilus  weak [2009] X
Bacillus Polymyxa  unknown X
Saccharomyces Boulardii  ????? X

As a FYI, Bacillus Indicus HU36 was obtained from the ocean [2015] but marketing literature cites human source. While Bacillus Subtilis HU58 was from humans  [2012].  Enterogermina contains 4 strains of Bacillus Clausii only.

Immunosuppressed Patients

A reader wrote “Is it true that bacillus coagulans should not be taken by individuals immunosuppressed? I wanted to start with this probiotic for my child with ankylosing spondylitis and as you are taking immunomodulating wouldn’t know if its status would be compromised.”

I cannot give medical advise, I can provide education on what has been published else where (and the reader and their knowledgeable medical profession can draw their own conclusion).

  • Nothing found searching for immunosuppress bacillus on PubMed
  • A 1998 study on rare bacillus infections (not from taking probiotics) states: “Moreover, our finding of six B. cereus, three B. licheniformis, and two B. pumilus infections [in cancer patients] suggests that these species may be more pathogenic in immunosuppressed hosts than are other common species, such as B. subtilis or B. megaterium. ” [1987]
    • “Two cases of Bacillus cereus meningitis in immunocompromised children [in cancer patients] at our hospital within a 2-month period prompted us to review B. cereus-related invasive disease.” [2001], again — not from probiotics
  • “Despite the widespread distribution of Bacillus organisms they are rarely implicated with actual infections and are more frequently isolated as a culture contaminant.” []
  • “Live combined Bacillus subtilis and Enterococcus faecium ameliorate murine experimental colitis by immunosuppression manifested by downregulation of TLRs, macrophages, Th1, and Th2 but upregulation of Tregs.” [2014] So it appears to actually helps!
  • Recurrent septicemia in an immunocompromised patient due to probiotic strains of Bacillus subtilis [1998]. [Full Text] Patient was “73-year-old male with chronic lymphocytic leukemia”
    • “We conclude that, even if the septicemia due to the probiotic strains of B. subtilis could not be related directly to the patient’s death, high numbers of viable microorganisms (especially if polyantibiotic resistant) should not be given to any patient with severe immunodeficiency.”
    • Probiotic was “. Each dose contains a mixture of 109 spores of four distinct antibiotic-resistant derivatives of ATCC 9799 (Enterogermina; distributed by Sanofi Winthrop, Milan, Italy) (1, 4) per vial.”
    • “Moreover, probiotic products containing Bacillus species have been in the market for at least 50 years with the Italian product known as Enterogermina® registered in 1958 in Italy as an OTC medicinal supplement (Cutting, 2011). ” [2012]

So we have had one death reported associated with this in almost 60 years of OTC use.

Lactobacillus bacteremia (Lactobacillus infection) was found, very often — most of the reports below are within the last year! [80 reports for Lactobacillus bacteremia probiotic vs 5 for bacillus bacteremia probiotic ]

If you want to play it safe, then definitely no yogurt or any fermented foods of any type. IMHO, the apparent risk is very very small.

Bottom Line

John raises valid questions about safety with the assumption of no major illnesses [Future link to his updated post will be here]. In dealing with patients with CFS, we have two major choices

  • Avoid — and just accept CFS indefinitely
  • Try — knowing that there is likely a low risk of the issues that he is concerned about, and a major risk of a beneficial shift and thus improvement.
    • If there is a concern or adverse effect, then stop
    • Ideally, use a lower risk item if available and the cost is acceptable, for example Enterogermina