Soil-Based Microorganisms

Mary W: For those of you, who are curious about soil-based microorganisms, here’s my experience to date. I’ve been on it for 3 weeks. I started it after a bad relapse in overgrowth when no natural antifungals seemed to be keeping pace. Within 2 days of being on it, my digestive system had calmed way down. After a week, I could tolerate fats again and my bloated stomach was and is about 50% less bloated than it was. Didn’t have any noticeable die-off ‘til yesterday (diarrhea and stomachache when I ate). Today ok. Been able to increase the dose pretty consistently so I’m up to 7 capsules a day. Don’t know if I ‘m going to make it to 20 per day. I am also taking Thera-zyme SmI which has cellulase designed to digest the yeast die-off. phone (800) 662-2630. I take it off and on because I’m not sure if it’s doing anything and I find it very constipating.

I know a lot of people have trouble with soil-based microorganisms, especially in the beginning. (I was able to start right away with 1 capsule; some people take less.) It must depend on the nature of each bacterial overgrowth. I am now intensely allergic (gastro-intestinally) to many things, including the fillers in all capsules and tablets, even vitamins in their pure form (have started doing vitamin/mineral IVs on a weekly basis) and yet I tolerate soil-based microorganisms — at least for now. So, you never know…

Polly: The bacteria in soil-based probiotics are normally found in the soil, and are not the usual residents of the human intestine. For this reason, there is some concern about their possible long-term effects on the user. However, soil-based organisms can be very effective. Natasha Campbell-McBride, MD, claims soil probiotics (Primal Defense brand) were of dramatic benefit in her child’s autism symptoms. [9] A study of patients with enteric infections demonstrated rapid improvement in patients put on 2 billion soil-based microorganisms per day. (The experiment used a combination of Bacillus subtilis and Bacillus licheniformis). [10] Of interest, Bacillus subtilis creates a biosurfactant that is particularly damaging to lipid envelope viruses like measles, herpes and retroviruses. [11] Bacillus licheniformis is also valuable. It kills many different types of fungus. [12]

If you decide to try soil-based organisms, start with only a half capsule per day, and gradually work up to the recommended amount. According to an article by the keep-hope-alive group, Nature’s Biotics (contains Bacillus subtilis and Bacillus licheniformis) may give the user flu-like symptoms or a cold during the first month of use. It may break up old fecal matter in the intestines. The experience of patients suggests that the product may be shifting the immune system away from the Th2 and towards the Th1 arm. [13]

Jenny: I’ve found that the soil-based microorganisms are really helping me with my digestion. I started to gain weight right away, a sure sign that everything I ate was in fact being absorbed.

Polly: That might be what is happening. The proper flora is needed to absorb our food. Rats without any flora need 30% more calories in their diet. [14]

Mona: Threelac and Hydroxygen (oxygen elements) truly gave me my life back. I have been candida overgrowth free for 10 months. GONE. It hasnt come back. It took me 4 1/2 yrs of trying other things and I never could get rid of it. It always came back whenever a stressful event would come into my life. It wasnt until the Threelac and oxygen that I actually was able to start getting well.

Polly: I’ve not tried the Threelac, but Health Trax’s Oxygen Elements Plus is the strongest oxygen product that I’ve tried so far. I liked it. However, I noticed that it had to be used consistently, or else it made things worse instead of better.


Table of Some Soil-Based Microorganism Products

(Approximate Price as of March 2013)


Primal Defense from

$47 for 90 capsules

Composistion: The primal Defense formulation keeps changing. As of March, 2012, it no longer contains Bacillus lichenformis, but it still contains Bacillus subtilis. They no longer tell you how many bacteria are in a pill. They don’t tell you any details about the base material anymore. (They used to advertise the grasses, phytosterols and sterolins of the base material.)


Body Biotics, (formerly Nature’s Biotics)

$54 for 90 capsules

Composition: Bacillus subtilis and Bacillus lichenformis along with some normal resident bacteria in a host medium of Humic Acids, Fulvic Acids, minerals, and micro-nutrients.


Flora Balance from

$25 for 60 capsules

Composition: Bacillus laterosporus (BOD strain)


Threelac from Global Health Trax

$50 for 60 packets

Composition: The composition has changed over the years. However, it is still a soil based probiotic formulation that, as of March 2013, contains Bacillus Coagulans, Fructo-Oligosaccharides (FOS), Refined Dry Yeast Powder, Dietary Fiber as Galactomannan, Bacillus Subtilis, Enterococcus Faecalis, along with some casein from milk, beta cyclodextrin, Erythritol, lemon juice powder, canola oil.


Attogram SBX from

$40 for 90 capsules

Composition: A proprietary blend of organisms that include Bacillus subtilis in a base of 60 fruits, vegetables, herbs, grass juices and algae.

Mr. Articles,

Thanks for the assembly of soil-based probiotic links! I am currently investigating their efficacy compared to other probiotics. I’ve also recently begun the GAPS diet and think it’s odd that if Dr. Campbell- McBride had such great success with soil-based microorganisms in treating her son’s autism that her own brand (Bio-kult) isn’t soil-based–as far as I can tell.

isn’t soil-based–as far as I can tell.


Since there can be poor reactions to either soil based probiotics or high dose normal resident probiotics, I think the two should not be mixed in a supplement. People need to try them separately and carefully monitor their reactions. There are some reports of people getting worse when they try soil based probiotics.

Hi everyone,
This is my 1st post here, and I would like to say thank you to the Moderator and admin for putting up this web-site.

I am currently debating if I want to start a Soil based Probiotic or not. I have been tested positive for SIBO (High on Methane) about 2 months ago. While I have benefited from changing my diet and cutting out all the grains (similar to GAPS ) I have not had much success with None Soil based Probiotics in the past. In fact, the more I am learning about SIBO the more it seems like I need to be careful about Probiotics considering SIBO is a condition of Bacteria Overgrowth to begin with.

But the idea of this new concept of the Probiotic being different because it is soil based and it will help SIBO has been very intriguing to me, so I got some samples of a product called Prescript-Assist and I have been trying it out.
I have been trying 2 capsules a day (1 at night and 1 in the morning) … I have noticed when I wake up in the morning, my usual bloating does lessen. And since SIBO sufferers often suffer from bloating/inflammation, I see less bloating as a good sign to continue… However, I am still not sure and wanted to ask your opinion about SIBO and Soil based bacteria….. It seems like there are 2 schools of thought when it comes to SIBO and Probiotics in general… One says to stay away from any Probiotics because the whole problem with SIBO is not that we don’t have enough good bacteria, it’s that the bacteria is traveling from the Colon to the SI and taking more Probiotics will only make it grow even worst, and the other school of thought says that Soil based bacteria are different and will help SIBO sufferers because the type of bacteria in a soil based Probiotic is different from the ones that are growing and will help bring balance…

So my question to you is this: Do you think for a SIBO patient, Soil based bacteria is beneficial? Or should they leave Probiotics alone for now and concentrate on other things until the bacteria is gone before introducing any Probiotics??

I must says that I did go thru 1 round of antibiotics (Xifaxan and Aliana) which did nothing really… It only worked for less than a week and bacteria came back. At that time I did not know about Soil based Probiotics, and right after the course of Antibiotics, I started a Probiotic called “Align” (My GI’s suggestion!) when shortly I found out it made thigns worst and helped the bacteria come back faster and contributed to slow motility I stopped it…. I wish I had never taken Align right after the course of Antibiotics..but oh well…

Anyways, Any impute regarding SIBO and Soil based Probiotics would be greatly appreciated. And thank you again for putting up this wonderful site. I hope more people come and exchange ideas here. We really need it.


You are the first person that I’ve come across who has tried the soil based probiotics and has also a confirmed diagnosis of SIBO. It is good that the soil based seems to have helped you. The bacteria count on a soil based probiotic is much less than with a normal resident bacteria probiotic. So, with the soil based products, you aren’t adding nearly as many bacteria into the small intestine. I therefore think it would be less likely to cause a SIBO problem for that reason. However, I’m still wary of soil based probiotics, and I think only a short course is appropriate for people, and I don’t think it is a good idea for someone whose health is extremely compromised like in AIDS or cancer. Another relatively low dose probiotic is Dr. Ohhira Probiotics, and it isn’t soil based.

Your SIBO test showed high methane. The current suggestion is to use a combination of Rifaxamin and Neomycin. The combination works a lot better than taking either antibiotic separately. I do not know which herbs are best for reducing methane production, but human bile, fish oil, coconut oil and lauric acid will help get rid of the methane production.

Certain organisms (methanogenic archaea) can use the hydrogen produced by bacteria to help create their methane. So, as part of the protocol to get rid of the methane production, I think it is important to eliminate the excess production of hydrogen. To that end, certain herbs should be useful. Herbs known to reduce the population of hydrogen producing bacteria include: Allium sativum [garlic], Hydrastis canadensis [goldenseal] and other berberine-containing herbs, Origanum vulgare [Wild Oregano], Cinnamomum species [cinnamon], and Azadirachta indica [Neem]. Allison Siebecker, ND has found the following doses effective in eliminating SIBO from hydrogen producing bacteria: allicin extract of garlic (450 mg twice daily or 3 times a day), goldenseal and berberine (5 g once daily in split dosage), emulsified [wild] oregano (100 mg twice daily), and neem (300 mg 3 times a day). This herbal treatment needs to be continued for 30 days, which is longer than the typical 14 days of antibiotic treatment. Note, Dr. Siebecker was using only one of these herbs at a time to get rid of the overgrowth. (Personally, I would try Kyolic garlic instead of the allicin extract of garlic. It works better for some people.)

Some of the soil based products have FOS or inulin added. That isn’t a good idea if you are trying to get rid of SIBO. The FOS and inulin will increase the growth of the bacteria.

There is currently a very active yahoo group that talks about SIBO. If interested, it is called SIBOnation.

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