Supplements: Probiotic & Prebiotic

By Cat, Dec 2006; updated Mar 2008, Feb, Aug 2017

Real foods should always be your first choice in both sickness and health; supplements are only for adding-to foods. Always use supplements made/derived from real foods, as opposed to synthetic ones, as they are more likely to be recognized as ‘family’ by your body. The best source of beneficial microbes (probiotics) is from raw foods, especially garden vegetables pulled from well-composted soil. Another exceptional source are foods fermented by their own microbiome (rather than fermented by added culture).

Supplemental probiotics typically are strains developed in a lab from native microbes for a specific health purpose, or to supplement what you can get from your food.

  • See also: 1. Whole Foods (About) Menu;
  • Includes: 1. Probiotic supplements: Lactobaccilus-based,  SBO/HSO spore-based, and yeast-based; 2. Prebiotic supplements;

Probiotic foods

This includes cultured and fermented foods, which are foods you can produce in your own kitchen; see my Culturing, Curing, Fermentation, & Tonics Menu for recipes.

  • Culturing refers production of lactic acid from sugars, starches or fibers. It most commonly involves conversion of lactose to lactic acid in dairy, to produce yogurt, kefir, buttermilk, sour cream, and cheeses.
  • Fermenting produces converts sugars to acids, gases, or alcohol. Examples of fermented foods include sauerkraut, kimchi, pickled vegetables and fruits, and sourdough.

Beer, wine and distilled alcoholic beverages also involve fermentation, but are not generally considered ‘probiotic,’ especially since most are heat-treated after fermentation is complete. However, non-pasteurized beers may have probiotic value.

Probiotic supplements

The most common probiotic supplements are milk-derived and produce lactic acid from sugars, starches and fibers; the most well-known brand is Jarrow EPS. The viability of these is questionable due to limited shelf life and storage conditions; also, most of them are not likely to survive the harsh acidic environment of the stomach without enteric coating.

However, obtaining them from cultured dairy and fermented foods has a better chance of survival and viability, because of the protective synergy provided by other nutrients in those whole foods.

NOTE: If you’ve never taken probiotics, start with a low dose, then slowly increase it when you’re confident it is not causing issues (or if you remain strong to it during NAET testing). New-to-you probiotics may have increased symptoms if your gut flora changes too rapidly. If you’ve found that you can tolerate that dose, but have not reached your gut health goals, you can work your way up to higher doses.

Lactobaccillus-Based Probiotics

This is the kind you will find in your local health food store, and I’ve been using them since the late 1980s. These contain the types of bacteria that produce lactic acid (similar to probiotic foods), and are similar to the species that normally colonize the human gut (but the subspecies used in the supplements may not be the same as those in a healthy gut). The brands I regularly use are:

  • Jarrow EPS; 5 billion CFU*  (iHerb product code JRW-03024)
  • Primadophilus Bifidus; 5 billion CFU*  (iHerb product code NWY-06860)
  • iFlora; 32 billion active cells per serving (2 capsules)  (iHerb product code SED-21001)

*NOTE: CFU means “colony forming unit” and is determined at time of manufacture.

Izabella Wentz criticizes common brands because their recommended doses do not provide enough bacteria to do any good – she recommends at least 50 billion CFU. I suspect she is right, but I have found if I stop them for several weeks, I notice my gut is having issues: increased gas and candida infection being the most noticeable problems; this indicates they are helping me when I take them. Still, there might be even better ones to take.

I have not tried increasing the dose of my probiotics, but am interested in trying brands that provide at least 50 billion per capsule. Izabella recommends (16) the following (I’ve not yet tried them):

  • Probiotic 50B by Pure Encapsulations is a great one to start with;
  • VSL #3 contains 450 billion CFU’s per dose. According to Izabella, it has been “clinically studied for ulcerative colitis and irritable bowel syndrome. The probiotic has been so successful in inducing remission, it has been labeled as a ‘medical food.'” She also notes it is very expensive but may be covered by insurance if you have the right diagnostic code.
  • Klaire Ther-Biotic is another high-dose, multi-strain product, but less expensive than VSL #3.

Mercola recommends probiotics that include a particular strain of L. acidophilus: the DDS-1 strain, which he includes in his probiotic formula. He notes this strain can enhance human health because it (17a):

  • Adapts well to the human body
  • Is acid- and bile-resistant for intestinal survival
  • Helps promote your digestive health
  • Aids in supporting your immune system
  • Contributes to the good balance of your intestinal flora
  • Produces significant quantities of lactase to potentially aid in lactose intolerance challenges.

His Complete Probiotics supplement (iHerb code MCL-01318) states that it provides 70 billion CFU (at time of manufacture), and includes the DDS-1 strain.

He has two new probiotics that are discussed in the next section.

NOTE:  lactobacillus probiotics may be problematic for people with SIBO, which can be caused by an overgrowth of various bacteria, including Lactobacillus and Streptococcus bacteria, which are often found in probiotics

SBOs (Soil Based Organisms) and HSOs (Homeostatic Soil Organisms)

These are basically the same thing – mostly bacterial microbes that are spore-forming and native to rich soils. They are recommended by many practitioners to help heal the gut.

In earlier times, we consumed soil bacteria with our root crops like carrots, beets and radishes that are grown in good, rich soil.  Humans and other animals need probiotic bacteria in our guts, which they initially get from ‘mothers milk’ – a main reason why the most common probiotics are milk or lax-based. Plants also need probiotic bacteria which they get from their soil microbiome. Indeed, some of  the same species that are found to be native in the human gut are also found in good rich soil (and in your compost pile).

Once we started sterilizing our soil with pesticides and herbicides, we reduced the available soil organisms to a negligible level. And the foods grown in that inferior soil are not very rich in HSOs. (reference in original article were 17, 18, but those links have been lost). Regenerative Agriculture (13) is working to restore the soil’s microbiome, but that’s another story.

SBOs/HSOs are not without controversy, however. Especially Bacillus subtilis, which has been implicated in causing septicemia (13). Some (but not all of the species used in SBO/HSO probiotic supplements may colonize in the gut. Most are not opportunists that can cause harm, but some can become opportunists given the right conditions. It has been suggested that B. Subtilis is not an appropriate species for the human gut.

However, 2006 study on mice and humans in the Journal of Bacteriology concludes:

If the animal gut is not an appropriate environment for B. subtilis, we would predict that either all of the ingested spores would be excreted in the feces or spores would germinate and then be destroyed. That we observe quite significant levels of germination and sporulation indicates that B. subtilis has adapted to the GIT [gastro-intestinal tract] for use as a natural habitat. This is supported by not only the increasing number of studies showing that Bacillus species can be recovered from the GIT  of animals (20) but also by our study here which showed that 30 volunteers all carried Bacillus spores in their feces. While the numbers may be small compared to Bifidobacteria and Lactobacillus species (that can reach as many as 1011 CFU/g of feces), the importance of Bacillus should not be overlooked, since B. subtilis has been shown to be of primary importance in development of the GALT [Gut-Associated Lymphoid Tissue].

The referenced 2005 article in the above quote, The use of bacterial spore formers as probiotics. by Hong. et. al., states in its conclusion:

Among the large number of probiotic products in use today are bacterial spore formers, mostly of the genus Bacillus. Used primarily in their spore form, these products have been shown to prevent gastrointestinal disorders and the diversity of species used and their applications are astonishing. Understanding the nature of this probiotic effect is complicated, not only because of the complexities of understanding the microbial interactions that occur within the gastrointestinal tract (GIT), but also because Bacillus species are considered allochthonous microorganisms [an organism that originates from a place other than that in which it is found, in this case, originated in soil but can be found in the human gut]. This review summarizes the commercial applications of Bacillus probiotics. A case will be made that many Bacillus species should not be considered allochthonous microorganisms but, instead, ones that have a bimodal life cycle of growth and sporulation in the environment as well as within the GIT.

How SBOs/HSOs work to Improve Intestinal Health

HSOs are impervious to stomach and bile acids and the digestive process, making them ideal for oral treatment. They move through the intestine where they (in theory) form colonies along the intestinal walls.  There, they compete with harmful bacteria and yeast for receptor sites on the intestinal mucosa. From there, they produce the proper environment for absorption of nutrients and to re-establish proper pH. They also dislodge (detox) accumulated decay on the wall, so those wastes can be flushed in the stool (9).

They produce specific antigenic proteins, to stimulate the immune system, and to stimulate production of natural alpha-interferon (a potent immune system enhancer, and inhibitor of viruses).  In this way, HSOs are very aggressive against pathological molds, yeasts, fungi, bacteria, parasites and viruses (9).

Precautions During Treatment with HSOs and other Probiotics

The following is from Jim (6); however as of Feb 2017 update of this posting, that website no longer has this information.

  • Avoid chlorinated water. Invest in a filter (such as Brita, or one installed to a faucet at your sink), and replace the filter regularly.  While chlorine is added to water to kill coliform bacteria, it can also kill the good bacteria in our guts.
  • Don’t take antibiotics during treatment, as these can also kill your fledgeling HSOs. If you need antibiotic treatment, take S. boulardi instead – it is a protective yeast that is not killed by antibiotics (see S. Boulardi, above, for more). If you are taking berberine, a natural antibiotic, I do not believe it kills the good bugs in probiotic supplements.
  • Avoid herbal parasitic killers, such as black walnut, wormwood, pau d’arco, etc.  These may interfere with the HSOs/probiotics and their ability to colonize.
  • Eliminate all simple sugars and simple carbs.  These foods feed the bad bugs and parasites in the intestines, and this can increase candida growth, leading to dysbiosis (intestinal imbalance).
  • Eat lots of fresh veggies, to facilitate proper balance of gut flora.
  • Drink lots of filtered water, which helps in flushing out toxins, and helps the good bugs adhere to the intestinal lining. 

Beneficial Yeast Probiotics

I first learned of the benefits of beneficial yeast, from Izabella Wentz, author of Hashimoto’s Protocol. She recommends S. boulardi; from her website (16):

Saccharomyces boulardii (S. boulardii) is a beneficial yeast that helps to clear out pathogenic bacteria, candida, some parasites (including Blastocystis hominis), and H. pylori, an infection that has been implicated in ulcers and has been linked to Hashimoto’s.

S. boulardii does not colonize the gut wall, but instead, it causes an increase of secretory IgA, which supports our own body’s natural defense against infections and opportunistic gut bacteria.

My experience with HSOs/SBOs and Beneficial Yeast Probiotics

In 2008 I looked into HSOs which are found in rich native soil. They are working colonies that are impervious to stomach acids (primarily due to endospores) and pass through to the intestines intact, where they help restore pH balance and gut flora colonies. Microflora Restore brand of HSO supplements has a lengthy discussion of this topic. (5)

I initialy tried a couple HSO supplements:

  • Garden of Life Primal Defense (3), available in capsules or powder to mix with water or juice; iHerb product ID GOL-11156 (caps) and GOL-11125 (powder)
  • NOW Foods Probiotic Defense Powder  (4), a less expensive HSO product; iHerb product ID NOW 02917.

but they didn’t seem to help any better than the lacto-bacteria I’d been using, so I gave them up and went back to using Jarrow-dophilus EPS and iFlora. However, this was before I eliminated my ascaris parasite that dominated my small intestine.

In the fall of 2016 I tried a new-to-me spore-based probiotic called Syntol AMD (7). I took a capsule before bed at 11 PM, then woke up at 2 AM with gut pain. 30 minutes later, I puked (I never puke, so this was a horrible surprise). I didn’t know whether it was the food at a new-to-me restaurant I’d had at lunch, or the new probiotic that caused the problem, so a week later I tried the Syntol again at bedtime, and had a similar response as before. So I gave up on it. However, in retrospect, I do think it helped me. I believe it became quickly active in my intestines, ‘kicking butt’ with the bad denizens (which made me puke them out), because after these two episodes, my gut had far fewer problems and my candida overgrowth went into retreat.

On Dec 8, 2016, I started using Prescript Assist (or the “Pro” version), as recommended by my Naturopath. They don’t provide CFU information, but they are spore based, which means they have an excellent chance of surviving warehousing and then passing through your stomach acids. They also contain plus Leonardite prebiotic (fulvic and humic acids) to help me heal my leaky gut and keep candida under control. See below for more about this probiotic.

Feb 2017 update: I’m still taking Prescript Assist, and it seems to help. It contains the following SBOs (listed in families):

  • Arthrobacter family: A. agilis, A.citreus, A.globiformis, A. luteus, A. simplex,
  • Acinetobacter calcoaceticus,
  • Azotobacter: A. chroococcum, A. paspali,
  • Azospirillum: A. brasiliense, A. lipoferum,
  • Bacillus: B. brevis, B. marcerans, B. pumilus, B. polymyxa, B. subtilis,
  • Bacteroides: B. lipolyticum, B. succinogenes,
  • Brevibacterium: B. lipolyticum, B. stationis,
  • Kurthia zopfii,
  • Myrothecium verrucaria,
  • Pseudomonas: P. calcis, P. dentrificans, P. fluorescens, P. glathei,
  • Phanerochaete chrysosporium,
  • Streptomyces: S. fradiae, S. cellulosae, S. griseoflavus.

New and Old labels, Prescript Assist Probiotic

2018 update: The original distributor, Enviromedica, has discontinued distribution of this product because the formula has been changed (pea protein has been added, with potential allergic issues, and some of the microbes have been changed). The original formula was extensively studied, but this new version has not. See Chris Kresser’s article (19a) for more info. I’m disappointed, so am now looking for a replacement.

How to tell the difference on the label: the old version had a puzzle-piece and the new version has a ghost-like person in front of a cross-shape; see image, right, from Power of Probiotics (19b).

So I decided to switch to spore-based probiotics. I looked into four options:

  • MegaSporeBiotic (Microbiome Labs), the one recommended by Izabella Wentz; and
  • Complete Spore Restore and Complete Probiotics (from Mercola).
  • YouTheory Spore Probiotic (iHerb code YOU-00722) in combination with Primadophilus Bifidus (iHerb code NWY-06860), which is a less expensive option.
  • Jarrow’s S. Boulardi+MOS (iHerb product code JRW-03004), which contains 5 billion CFU per capsule. I tested quite strong to this (NAET testing).

I decided on Mercola’s combination. He calls these “The 2 R’s” of probioticsReconditioning and Re-seeding.; see references (17b) and (17a), respectively. [See more about his Complete Probiotics in the previous section (Lactobaccillus-Based Probiotics)]. I am currently taking them (May 2018), and they do seem to help, but I miss the fulvic/humic acids that were in Prescript Assist, so I added a Fulvic/Humic acid plus minerals supplement to my regimen.

2019 update: To avoid a food sensitivity to any of the probiotics, I started alternating Mercola’s combo with a YouTheory/Primadophilus Bifidus/S. Boulardi combo every 2 weeks. For the S. Boulardi, I started with  1 cap daily, then increased to 2 caps daily.

Prebiotic supplements

These are primarily fiber, such as:

  • FOS (Fructo-oligosaccharides) which are short chains of fructose (as opposed to ‘starches’ which are chains of glucose.
  • Inulin (longer chains of fructose), usually derived from Jerusalem artichokes.
  • Resistant Starches (RS), which can act like fiber in that they can be broken down by gut bacteria to form short-chain fatty acids (such as butyrate) produced by bacterial fermentation of RS in the colon. The short-chain fatty acids are essential for the liver’s detox function. In contrast, ordinary starches are broken down to glucose to be used as fuel or converted into body fat. (12)

Another option is lactulose, a synthetic sugar that can also be used as a prebiotic to feed the good guys in the gut (it is also prescribed to treat constipation caused by opioids), but I’m not big on synthetic foods, as they may trigger an immune-attack.

  • Synthetic lactulose is a disaccharide of fructose and galactose;
  • Natural lactose is a disaccharide of glucose and galactose

Lactulose is not digestible by our own enzymes, so is not absorbed, but stays in the digestive bolus as it transits the gut, absorbing water (similar to fiber); in the colon it is converted by bifido-bacteria to short-chain fatty acids like lactic and acetic acid which are essential for liver function and maintaining an acidic colon that supports the growth of probiotic microbes. Or it may be fermented by other gut microbes. (10,11).


NOTE: Reference numbers in parenthesis (for example, the first one below) are the original reference numbers for which I’d lost the reference text by the time I did my Feb 2017 update, and had to redo.

  1. (12)
  2. (13)
  3. (6) Garden of Life Primal Defense (
  4. (7) NOW Foods Probiotic Defense Powder (
  5. (1) Microflora Restore (
  6.  (11) Probiotics, an emerging alternative (
  7. Syntol AMD:
  8. Prescript-Assist Pro:
  9. (19) Good Gut Solution, What are HSOs (Homeostatic Soil Based Organisms) Probiotics: and Homeostatic Soil Organisms for one’s ‘Primal Defense’:
  10. Wikipedia on lactulose:
  11. Medline Plus on Lactulose (
  12. My article on Carbs and Resistant Starch:
  13. Regeration International on Regenerative Agriculture (
  14. The Intestinal Life Cycle of Bacillus subtilis and Close Relatives, Journal of Bacteriology. 2006 Apr; 188(7): 2692–2700. Nguyen K. M. Tam, (
  15. (reference 20 in the above J. Bacteriology study). Hong, H. A., L. H. Duc, and S. M. Cutting. 2005. The use of bacterial spore formers as probiotics. FEMS Microbiol. Rev. 29:813-835.  []
  16. Izabella Wentz:
  17. Mercola: (17a); (17b)
  18. About MegaSporeBiotics:
  19. Prescript Assist: (19a) Chris Kresser article about old vs new versions:; (19b) image of new/old labels: 

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