Are Your Supplements Turning into Deadly Pathogens in the Gut?

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“The human body houses somewhere in the neighborhood of one hundred trillion bacteria within the body—about 3.5 pounds worth.” But don’t think of that fact as a new method for losing weight – rather make sure you turn the porch light on and lay out the guest towels: those bacteria, including 400-500 different species in the gut alone, are responsible for your health as much as or more than the food we eat.

In fact, the bacteria in your body outnumber your own cells ten to one. It’s a good thing they’re friendly, isn’t it?

With that ratio, if the bacteria wanted to take over, they certainly would have the means.

I mentioned in this week’s Monday Mission on getting more probiotics that I recently changed the probiotic supplement I take because of a current debate over the safety of my old one. On my first visit to my new naturopath at Elder and Sage, she introduced me to the problem.

Many people, most notably Jordan Rubin of The Maker’s Diet and Garden of Life supplements, credit soil-based organisms (SBOs) for their miraculous recovery. In Rubin’s case, after seeing over 60 specialists all around the world for his severe Crohn’s Disease and related complications, it was SBOs that finally brought him back literally from the brink of death.

Why the controversy?

Soil-based organisms reproduce differently than other bacteria that are normally part of our flora in that they are spore-forming. Because of these spores, if a person does not have enough of their own healthy gut flora to compete with the SBOs, it opens the door for them to become pathogenic.

You read that right.

Supplements you take on purpose to improve your health and your gut flora could actually turn against you and become pathogens (harmful bacteria) themselves.

Isn’t that lovely?

(top photo source)

What We Don’t Know

(photo source)

This post is sponsored by Attune Foods.

The trouble with finding good information about probiotics is that research is sorely lacking. For the last century or so, our researchers and doctors have been focused on fighting the enemy rather than learning about the weapons we can utilize to protect ourselves. Most of the studies we have access to teach us what disease does to the human body and then test the effectiveness of man-made weapons, like antibiotics, in fighting them.

It’s been a very recent shift that we’re even looking into our own flora, the millions and trillions of beneficial bacteria that our bodies already possess, and how that can be a line of defense against disease. Because of that, we don’t really know how probiotics work or even how our own gut flora operates with very much detail.

There are a few studies referenced here at the Wikipedia page on microbiomes, but it’s clear that we have a lot to learn.

Currently, Washington University is host to the government-funded Human Microbiome Project, which seeks to “characterize the microbial communities found at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract, and to analyze the role of these microbes in human health and disease.” (source) 

They’re embarking on fascinating and vitally important work, and countries all over the world are also sparking an interest in the bacteria we carry around. Here’s an interesting and exciting Q&A with the Associate Director of the Genome Institute if you’d like to learn more.

One of the only studies so far involved a mere 100 people, all from the same geographic area, and although it is helpful, it’s simply too narrow to extrapolate data to the entire population quite yet. Because everybody’s resident bacteria and pathogens are different, we can pretty much say that we don’t really understand our own internal probiotics yet, and we know even less about what probiotic supplements do in the body.

No studies have been done to determine if probiotic supplementation could ever repopulate one’s gut permanently, changing the resident bacteria to a properly balanced flora. In fact, some research does show that within two weeks, most supplemented probiotics exit the gut and are excreted.

Since our resident friendly bacteria make up 70% of our immune system, responsible for fighting viral, bacterial, and fungal infections, it’s exciting that researchers are finally looking into the little guys.

Where Does Our Flora Come From?

Why all this talk about unhealthy, unbalanced flora? It’s widely believed that, at birth, babies’ guts are sterile of all bacteria. Beginning at birth and continuing through the first two years of life, the tiny human being becomes residence for various bacteria, beneficial or detrimental depending on the environment provided in the gut and what the baby comes into contact with.

Think it’s a good idea to let baby have sugar before age two? My first two babies didn’t have desserts until after age one, but poor John…there’s no way I’m letting him have sweets, if I can possibly stop it, until age two now that I’ve read that fact! Sugars and refined flours are food for pathogens, dangerous bacteria. If you feed them, they will come.

My oldest son, now seven, clearly has bacterial issues and has needed antibiotics numerous times. He had antibiotics at birth, had sugar and flour in things like Cheerios well before age one, and has certainly had his fair share of white flour in his lifetime. Le sigh. I doubt it’s a coincidence, and I think I’ll try to sneak probiotics capsules into his smoothie more often.

Do You Eat Dirt?

DSC03883 (475x356)

The probiotic strains in yogurt and kefir are usually lactobacilli or bifidobacteria (I wonder if I’m making those plural correctly…), both of which are part of our resident bacteria, generally. The probiotics in the Garden of Life supplements are “soil-based organisms,” which are bacteria that literally live in the soil. They are still friendly to humans, but they’re not automatically part of our resident flora. “Transient micro organisms [like SBOs] are different from resident micro organisms in that they do not take up permanent residence in the gastrointestinal tract. Instead, they establish small colonies for brief periods of time before dying off or being flushed from the intestinal system via normal digestive processes, or by peristaltic bowel action.” source

Until about 100 years ago, SBOs were a regular part of people’s diets. When food processing got between farmers and eaters, the food chain, in a sense, was literally interrupted, and consumption of SBOs drastically diminished. Also I must imagine that the clean-to-the-point-of-sterile society we live in has reduced our interaction with these friendly little guys, further removing SBOs from our guts.

I’ve always wondered aloud while watching my babies put everything in their mouths how that could possibly be a good evolutionary trait. Maybe the good Lord made a little “oops” on that one, since dirty things and items small enough to choke a baby don’t seem helpful when placed into the mouth at mind-warping speed by chubby little fingers.

Now, I understand.

Human babies were created to crawl around in the dirt, getting intimate with the soil-based organisms they might find. Putting everything in the world in their mouths is a unique form of inoculation, brilliant in its simplicity. Those babies under two are working to populate their guts with healthy bacteria, and who knew? Eating dirt is a darn good idea.

In fact, research shows that children do better than adults with SBO supplements. The theory is that their little bodies are primed for the SBOs, and that perhaps, adults who simply haven’t been exposed to them much in the past can’t quite handle the influx of SBOs when they start a supplementation regimen. Here’s where the story gets ugly…

When Good Bacteria Goes Rogue

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Because so many adults have damaged flora, they don’t have enough of their own healthy bacteria to even stake a claim in their gut. Soil-based organisms, being spore-forming, proliferate very rapidly, and one theory is that without enough resident bacteria to hold up the front lines, the SBOs literally take over a person’s gut, becoming pathogenic in their aggression.

“Research from California has concluded that a deficiency of medicinal ‘superbugs’ – known as Soil Based Organisms (SBO) – from our soil and food chain may be responsible”(1) for intestinal illnesses and diseases such as irritable bowel syndrome (IBS), Crohn’s disease, colitis, candidiasis, and colon cancer. source

Because we’re deficient, some people can’t handle them when they come. Dr. Doran-Fisher has anecdotal evidence of clients who took a turn for the worse when they started SBO supplements and improved once they used a refrigerated strain with lactobacilli and bifidobacteria.

If you’re taking a probiotic and it’s not doing anything good for you, and especially if you noticed negative changes after an initial possible issue with constipation or flatulence as the body adjusts the the new bacterial balance, stop and look for a new one.

This pathogenic SBO issue really is a problem, and I’m hopeful that some of the newer research coming out will determine if adults who haven’t been exposed to SBOs can somehow rebalance their gut first and then use SBOs. Check this out:

Studies conducted in regard to SBOs provide evidence that “without SBO’s to police digestion our bowels often end up as toxic waste dumps for rotting faecal matter which builds layer upon layer until the intestinal wall cannot absorb anything useful and we start to drown on our own toxins….With an intestinal wall starved of nutrients however it can quickly become porous like Swiss Cheese leading to the much maligned ‘Leaky Gut Syndrome’ where undigested waste food can leak into the blood leading to fierce immune reactions ”(5) By supplementing SBOs into daily dietary habits, the occurrences illnesses and diseases such as these may be reduced or altogether prevented. source

In other words, because we’re deficient in soil-based organisms in our clean society, we’re getting sick. Because we’re sick and out of balance, some of us might not be able to handle getting the SBOs that could help us, and they’ll make us sicker instead.

UPDATE 7/10/12: I found a few more sources about soil-based organisms being harmful. This one is particularly packed with academic sources at the end, AND it discusses how Garden of Life has changed their formula to remove all but one SBO. This one touches on nomenclature in the probiotic world.

If You Poop Once a Day, You’re Not “Regular”

My 4-year-old will tell you that “brown, orange, red, brown, orange, red” is a pattern…but that doesn’t mean it will look good on your shirt.

Just because your bowels follow a regular pattern doesn’t mean you have healthy digestion.

Healthy digestion is determined by the consistency of your stool (see here for a lovely pictorial chart), frequency of elimination (2 or more times per day, every time you eat usually optimal), and how satisfied you feel when  you’re finished. Click here for some questions to help you consider your own digestion.

I always thought once a day was great, and as long as I wasn’t in pain, I wasn’t constipated.


When I give up all grains and sugar (for Lent), something changes. I end up moving my bowels just about every time I sit down to urinate. Thank you for not grimacing or laughing as you read that. Winking smile

When the grains and sugar come back, things immediately change. This is something I had never realized in 30 years of living, people! You really can learn new things about your body, even when you think you’re in perfect health.

Some odd issues have come up in my personal health lately – I’ll share more once I feel like I’ve beaten them – but one result of my battle against pathogens in my body was to switch up my probiotic regimen. I stopped taking Garden of Life probiotics and started eating my homemade lacto-fermented sauerkraut and kimchi (which I learned to make via the fermented foods eCourse) at every meal, and I ate a probiotic chocolate bar every day for two weeks.

I always thought people were a little (or a lot) off their rockers when we’d talk sauerkraut, which I’ve always despised despite the half-Polish blood coursing through my veins, and they would tell me that I would begin to crave the stuff after eating it for a while.

No way.

The only thing sauerkraut will make me do is cringe, I always thought.

During the time of really working on my flora imbalance, intellectually I knew I needed it at every meal, so I forced myself.

And I couldn’t believe it, but after just a few days of regular fermented foods consumption, I did start to want a bite when I opened the refrigerator door for a snack. I’m working on enjoying it (and remembering it) even more.

Probiotic Chocolate?

Attune Foods Dark Chocolate Probiotic Bar ( 4x7/.7 OZ)

Too good to be true, right?

Attune Foods, the sponsor of this post, has a clear goal: They want information about probiotics to be more widespread. To do so, they wanted to create a product that could bring probiotics into the mainstream beyond just yogurt, which is often oversweetened and doesn’t deliver the number of probiotics possible in other forms, simply because it’s too moist. explains that capsules are the best way to get probiotics, because liquids are only viable for a few weeks and powders are opened to the air and moisture each time the container is opened. For those who can’t or don’t want to swallow pills, the powder is the next best thing but still requires careful handling, and, I would point out, a change in one’s routine to fit it in. That makes chocolate perhaps the really best thing, especially for people who just don’t like yogurt or lacto-fermented flavors, or children who can’t swallow pills.

Attune, whose tagline is “what matters most is what’s inside,” has their corporate heart in the right place. I’ve been very impressed talking with them about how the company began and its mission. In 2006, Attune Foods was created with the intention of bringing probiotics into the Standard American Diet. They brainstormed about what sort of food could be infused with probiotics that Americans would all enjoy, and when they happened upon chocolate, with its low moisture content, they knew they’d found the perfect vehicle.

I tend to agree.

I’m a bit of a chocoholic myself, so the “prescription” to eat one (small) chocolate bar every day wasn’t the most terrible product review I’ve ever had, that’s for sure. Winking smile I knew I could tell you if the chocolate is good (it is; could be even darker in my opinion, but I’m not a “standard American”), but I really wasn’t sure if I’d be able to determine if the probiotics “worked” since I was already a regular homemade yogurt eater and taking the Garden of Life probiotics for over a year.

I can’t say I figured out anything when I began, but when I ran out of the Attune Foods probiotic chocolate bars, I had one bout of clear diarrhea and then was almost immediately constipated, not feeling accomplished for a few days. I’m looking into getting a subscription through Amazon so I don’t run out anymore! Even though I now enjoy the fermented foods considerably more than a few months ago, there’s no denying that chocolate is my new favorite way to get probiotics.

(They’re pricey, yes. But I’m thinking that the probiotics I was taking already were about sixty cents a day, and if you add in the cost of high quality dark chocolate that I won’t need anymore, it’s not really that bad.)

Do You Take Probiotics?

UPDATE 2015: For a few years, we’ve actually been taking the Miessence probiotics, both powder and liquid, and we’re very happy with them. It seems that they help me beat back some nasty candida, for starters. And the liquid is super super easy to give to kids, a welcome relief!

I also want you to read this post with a perspective from another naturopath on the refrigerated issue (myth?).

I never thought I had poor digestion, and I always thought of myself as the picture of health. But maybe I didn’t eat enough dirt as a child. I’m guessing, not as a medical professional of any kind, but as a thinking person in the 20th century, that all Americans should probably take a probiotic supplement.

And if you don’t see a change in two weeks, you should probably try something different. Look for probiotics in the refrigerated section of your health food store (that’s where Attune chocolate is too). If it’s not refrigerated, it’s either SBO probiotics or something is amiss. Here are some examples:

Thanks to Whole New Mom for some good ideas of which probiotics are best.

I didn’t list any SBOs, you may notice.

Do some people do very well with soil-based organisms in probiotics? Well, yes.

Does it scare me a little that some predict SBOs may kill more people than they help? Um. Yeah…

Natural health is a lot of guessing and checking, and that can get annoying at times…but it’s better than pathogens taking over your gut, yes?

What kind of probiotic do you take? Do you notice a difference if you stop taking it?

The source for this article is mostly an interview with Kathryn Doran-Fisher, N.D., who researched using the book sold at, as well as whatever sources are listed within the text.

Find more fascinating information:

Disclosure: Although Attune Foods sponsored this post, my opinions on their product are exclusively my own, and my research is also my own, to the best of my meager ability. I earn commissions from Amazon purchases, Tropical Traditions, Miessence, and GNOWFGLINS. See my full disclosure statement here.


Click here for my disclaimer and advertising disclosure - affiliate links in this post will earn commission based on sales, but it doesn't change your price.

109 Bites of Conversation So Far

  1. Chris via Facebook says

    Wait, you’re saying you should NOT poop once a day–my husband’s family SWEARS by it. So how often should you poop? More often? Less often?

  2. says

    Babies and young children poop 2 – 3 times a day…food goes all the way through their system in 6 – 18 hours. Adults are way slower…and that’s not always a good thing.

  3. says

    Thanks for this article. I like how much information you put into your “sponsored” posts. I have come to know that I can trust your opinion. I think I will try the chocolate bars, soon.

  4. says

    I have been making my own kefir for many years now and it has helped our gut so much. I just put a half of a cup in a smoothie every morning.

    • Carol says

      Lori, just got dairy kefir grains from my niece for the first time, wondering if you can tell me how to use them…

  5. Tricia says

    I’ve seen a couple studies suggesting that taking probiotics at the end of pregnancy and while nursing can help prevent eczema in infants. With #4 expected in just 2 months and #2 & #3 having dealt with severe eczema, probiotics have been on the top of my list. Thanks so much for all this wonderful information. I’ll definintely be checking out that chocolate! :)

    • Crystal Smith says

      I agree! My twins had horrible excema, and constant diaper rash. I have changed my eating with this baby by taking organic vitamins with probiotics and eat yogurt everyday and sometimes kefir. I also stopped drinking milk (until I get raw milk) and as low sugar as I can go. And this little man has only had excema and diaper rash once…when we went away for the weekend and I had cake and milk and cookies and did not have my yogurt!!! That told me a lot! So I try to be real careful.

  6. says

    Valuable information! I am still trying to understand the sbo’s better… Has anyone reading this learned about the new Beyond Organic venture? Jordan Rubin creates nutrient dense, probiotic rich foods fr his own ranch, raw cultured dairy, green-fed(grass, legumes, sun, but no grains, pesticides, hormones and strain of cow that produces digestible protein unlike conventional varieties today) and even probiotic chocolate fr Italy. As I read this great post, I figured this might be of interest to some.

  7. Marcie says

    I am dealing with yeast during nursing. I have been taking Biokult that is not refrigerated. How can I find out if it is an SBO? Do you like this new one you are taking?

    Also, my daughter is taking the refrigerated Nature’s Way powder. Do you know if that is an SBO?

    Thanks for this great info!

    • Katie Kimball @ Kitchen Stewardship says

      I’m sure the bottle would say something about soil-based organisms…I hear that Biokult is a really good one and am surprised it’s not refrig’d. The bottle should list the live and active cultures, though. I’m terrible at deciding whether things “work” for me…so I don’t know if I like the new one or not! I figure I’ll switch it up, as my naturopath says that first, many strains of probiotics cover the same ground, so you can take different things for the same purposes, and second, it’s good to give your body different things so it doesn’t get too “used to” the same old stuff. ??

      Good luck beating the yeast!! There’s a convo in comments at another post recently about beating thrush…Oh, good, I found it for you:

      :) Katie

    • Healing_Ways says

      Bio-Kult contains the well researched and generally trusted human strains of friendly bacteria but it also contains a strain of bacillus subtilis which is a soil based organism.

      It is also one of those in question due to its spore forming nature and potential pathogenic properties.

      I have decided against taking any supplements that contain it because it is too unknown and in some cases they found it wasn’t even the strain listed on the packaging.

      • Tammy says

        Bio-kult was formulated with Dr. Natasha Campbell-McBride’s help. I trust her on that one. It was also designed with children and sick adults in mind, where the capsules can be opened and also unrefridgerated, and taken in small doses. Working up to maybe 10 capsules a day.

  8. says

    What an awesome, packed post! Has anyone told Jordan Rubin his probiotics are dangerous? No, seriously!

    We count on cultured raw milk and lacto-fermented veggies for our probiotics.

  9. Pam says

    We make kefir (both milk and water) and try to consume that whenever we can. We also make kombucha and drink that regularly. My husband claims it was the kombucha that has been the most beneficial to his digestion. The kids and I take Biokult, and my son also gets Culturelle for Kids. I make non-dairy smoothies daily (my kids are off dairy for now) and I add either water kefir or kombucha to them. Both my husband and I used to be able to tell when our 5 y.o. son would miss his probiotic because his breath would be awful. It’s fine now, and thankfully still fine if he accidentally misses his normal dose. We’re assuming the good bacteria are outnumbering the bad! We also do our own sauerkraut, kimchi, and pickles.

  10. says

    Wow! Thank you so much for this information-packed post! I am currently going through my own bout with Crohn’s disease (meaning I am going through way too many tests and finding no results). I am definitely going to try upping my intake of probiotics to see if it makes a difference.

  11. says

    This is so fascinating! And so very helpful! Thanks for writing about this! :) I’ll definitely be checking into the subject of SBO’s more.

  12. Renee says

    Fascinating! This leads me to think of people on the Spectrum, and the phenomenon of them eating soil… perhaps part is a natural need to help their systems that they are instinctively acting on.

  13. says

    Our family looks a lot like Pam’s. My husband used to have to eat yogurt/milk kefir and kombucha at every meal, but now only has to do that with a select few, to avoid digestive issues. My kids’ favorite sources of probiotics are definitely the water kefir (which they drink like…water:) and milk kefir smoothies. DH and I are fond of the sour cream and fermented salsa I make, and even the baby thinks that pickle relish is great (picture chubby baby hands shoveling pickle relish toward mouth).

    However, I’ve found that when I take an actual probiotic supplement, it makes me constipated. Don’t know what’s up with that.

    • Katie Kimball @ Kitchen Stewardship says

      Have you given it a few weeks for your system to adjust to rebalancing flora? From what I understand, that is normal in the adjustment phase…

      :) Katie

  14. Leanne says

    Wow, this is a lot of great information to digest 😉 I had no idea about some probiotics being harmful, although I’m not surprised because, as you stated, so little research has been done in this area! Thanks for an eye-opening post that’s given me a lot to look into.

  15. Andrea says

    Great article–as always thank you for your thoroughness! It makes me wonder though, how many probiotics do we need? Can we get enough through consuming fermented foods, or should we also supplement? I always like to get what I can through my food, so we eat yogurt, kombucha, and saurkraut. Is that enough?

    • Katie Kimball @ Kitchen Stewardship says

      My hunch is no…but maybe if you really have a lot of fermented foods and don’t have any issues that need probiotics, then it’s okay. I wish I knew more! Maybe someone else can weigh in on the issue…

      :) Katie

  16. Janice says

    Doug Kauffmans show “know the cause” and his books are incredibly informative & lifechanging…learned about affect of fungí on my body-I wouldn’t believe it myself if i hadn’t experienced it myself! Things I attributed to aging were result of my body hosting TOO much fungi…i tried the phase I diet and antifungals and they made a world of difference…probiotics will help for sure but if you don’t rid your body of fungus you won’t get the full benefit of probiotics. Sorry this is so long but I KNOW how beneficial this info was to me!

  17. Elizabeth via Facebook says

    Very interesting. Too long for me to read all the way though right now, but I want to get back to it later!

  18. Nathan via Facebook says

    From what I read we should be pooping 2 or more times a day. I normally do once in the morning and once at night, and my wife’s always commented on how it seemed excessive compared to her once every couple days. But now we eat more whole foods, and she’s at more of one a day. But I’ve always been one to ‘eat dirt’, and as a bachelor, maybe some things that weren’t quite as…..still good as they should’ve been compared to my wife who loves a good clean nearly sterile environment(which has its place, I don’t knock her for it). I’ve always said that has contributed to a stronger immune system, as I rarely catch the bugs that sweep through the household, and if I do catch them, usually 24-48 hrs of hibernation to allow my body to do its thing and I’m back up and at em. Now I’m not saying I’m the picture of health, but I have to say that this article seems to confirm much of what I’ve observed and experienced throughout my own life.

  19. says

    I started using InLiven two years ago and definitely noticed some major health improvements – namely, no more yeast infections (used to struggle with them chronically), was negative on the strep test with my 4th baby (had been positive with the first 3), and overall just fewer bouts of illness.

    I have tried homemade milk and water kefir and other ferments, and just personally, still have a hard time with the taste. I still make them for my hubby and kids, just don’t care for them myself – except some batches of water kefir that turn out exceptionally good. And I do like homemade yogurt, but I’m not real big on dairy (even though we do the raw Jersey milk – just limit it for myself).

    So anyway, I really liked that InLiven is just certified organic fermented foods – with all the other food nutrient benefits but in a concentrated powder form and without the ferment taste. Simple and convenient.

    The other big perk was the 20% off all the time option offered by the company and then the option also to become a rep to get my products free. I had three friends who wanted to become monthly customers, and so I’ve gotten my probiotics (and other organic products) free every month since. In this day and age, I really appreciated a no-hype, no pressure way to trade a little referral work for free product. Sharing a great product find with people I knew would dig it, and getting my stuff free.

    Can’t beat free! :)

    (In the spirit of full disclosure – since getting my products free, I have chosen to continue working with the company for income as a WAHM beyond just our household product savings.)

    • Katie Kimball @ Kitchen Stewardship says

      Nice! That’s a great testimonial – I’ve been Strep B pos too, so that’s a huge bonus to hear about…TU! :) Katie

  20. says

    Great post! I am a HUGE fan of fermented foods. I, too am half Polish, but I have always loved sauerkraut, pickles, yogurt, etc. my whole life. It wasn’t until recently, though, that I started eating more probiotic-rich foods. Kombucha is a favorite of mine (next to yogurt and sauerkraut of course) but it is expensive if you buy it pre-made. Do you know of a good place I can buy a kombucha mushroom?

  21. says

    I take probiotics only when I have persistent diarrhea or constipation or gas, when I start eating again after an illness that stopped me eating for 18 hours or more, or when I have just finished taking antibiotics. I don’t seem to need probiotics the rest of the time. I average about 1 cup a day of active culture yogurt, and I eat a mostly vegetarian diet with lots of grains including wheat. I have never seen any sign that grains are problematic for me; I think they are for some people but not all.

    The one thing that made a big difference in pooping for me was eating less meat. I grew up eating meat about twice a day and was usually mildly constipated. When I quit meat I began eating more beans, so overall I get more fiber than I used to.

  22. Beka says

    Hi Katie, thanks for this great post … I will definitely need to do some more research on the probiotics my family is currently taking.

    However, when I tried to click on the “which probiotics are best” link at the bottom of the post, I was redirected to a suspicious looking website that my anti-virus software immediately blocked as a threat … Hmmm … not sure what’s going on there, but thought you might want to know.

    • says

      I am sorry about that. I am the owner of that site and I have been guaranteed that there is nothing wrong w/ my site. Something is throwing off security software and I am removing ads and other things to find out what it is. But you are safe. I promise. Katie herself told me she got the warning w/ one browser but not w/ another. Thanks for the heads up though and sorry!

  23. Tiffany says

    I just got a box from Vitacost with probiotics, how can I tell if they are SBO or not? Do I just need to email them?

    • Katie Kimball @ Kitchen Stewardship says

      Any bottle should list the kind of probiotics contained within…
      :) Katie

  24. Nav says

    eep! So the Culturelle Kids my 3 yo is taking aren’t that great since they’re from the unrefrigerated shelf in the supermarket (we keep them in the fridge..)??

    • Katie Kimball @ Kitchen Stewardship says

      I’m not sure about particular brands – my naturopath just told me to get one in the cold section… ?? Katie

  25. joy2all1000 says

    I thought I’d mention that the blogs I’ve read from people who take and profit from SBO’s state clearly that they can set off seemingly negative results in people who severely need them due to the presence of parasites and pathogens. Those organisms may try to get away from the SBO’s.Also a person often incurs a die-off of pathogens, and in the process of dying off they excrete toxins. This information is widely recognized. In those cases the person has a choice to make for themselves, whether to heavily load the SBO’s to attack the critters and/or pathhogens outright, or whether to slow way down and sneak up on them slowly. The latter is more comfortable, though I’m not sure if anyone knows for sure which is more effective. The ones who have chosen the 1st route report that the discomfort passes and they do very well.

    Since HBO’s don’t live very long, as you say, in the body, it seems questionable that they actually take over. In any case a person should always be taking other probiotics with them, as are formulated in all of the Garden of Life products. Another web site that features a lot of info on probiotics always incorporates into their formulas both permanent and transitory probiotics. All all the experts above agree that eating cultured foods is far the most effective way to take in a wide variety of probiotics. It is, after all, the natural way.

    Just one more comment: I hear/see people stating that eating dirt is healthy. Actually, it puts a person in danger of flesh-eating bacteria and other pathogens, unless the dirt has been pre-cleaned and conditioned, which I don’t think exists at the moment. Jordan himself practices extreme hygiene, and certainly does not eat dirt or recommend it. A little good sense should be employed, and this advice for children to be allowed to eat dirt could be vastly more dangerous than someone taking HBO’s as part of their probiotic diet.

    I hope this adds to the overall information, as I think it can greatly change the context and understanding of the info you already had.
    All best–

    • Katie Kimball @ Kitchen Stewardship says

      The naturopath who shared this information with me has worked with clients who got worse (and stayed worse) after starting SBOs. She is well aware, I am sure, of die-off symptoms and the idea of toxins leaving the body. I definitely don’t claim to be an expert on probiotics of any kind. In fact, I have never noticed a difference whatsoever when I took them or stopped taking them.

      I don’t think I advocated eating dirt, though, just not freaking out quite so much when babies put things in their mouths. I was exploring the idea of WHY in the world God would create that instinct that seems so dangerous to me, to put things in their mouths. But maybe you weren’t saying that I did, just that some do. No, I don’t want to actually grab a handful of dirt and eat it, but I guess some exposure to dirt is important for our systems.

      Thanks so much for your thoughtful comment!
      :) Katie

  26. Bebe says

    I’m so glad to hear you are learning to enjoy fermented foods. I am still trying to incorporate the process of making our own on a *regular* basis… I just get overwhelmed with being in the kitchen or or reading/watching about what to do once I get back in the kitchen! Kombucha has become a regular occupant on my counter, I am working on making kefir that I like the taste of now that I’ve got the grains rehydrated and I’ve made kraut and kimchee… but not enough to keep us in good supply for long. My whole family loves fermented foods though (well, except for the kefir… what am I doing wrong?) and I am committed to stepping up production this summer. Just do it is my motto!

    • Katie Kimball @ Kitchen Stewardship says

      Good for you! I know, keeping up on it all is crazy overwhelming sometimes. I wish I was a kefir expert…but I’m soooo not. :(

      Good luck! :) Katie

  27. says

    Thanks for the informative post. I typically recommend “soil-based probiotics” to my patients because they just seem logical. But accurate information on this topic is lacking.

    Your article warns of dangers from SBO running amok in the digestive tract, but that part of the article has no references. Do you have more specific information about that?

  28. Rachelle says

    Katie, Thanks for this awesome post! Very informative. I read something a while back that your article reminded me of – it said that the probiotics in kefir actually populate the gut, while the probiotics in yogurt are beneficial, but pass through eventually. I thought that was exciting in light of your topic. Here’s an article I found when I searched today if you want to look at it –

    • Katie Kimball @ Kitchen Stewardship says

      Thanks for sharing that link! Very interesting article, and I’m just about ready to get some kefir grains, now that I’m understanding how important it is to get a variety of different strains of probiotics going.

      I wonder what the source is for the article you sent though… 😉 Katie

  29. says

    Hey Katie.

    Funny enough, there was just some discussion this past week on the Miessence Reps forum about SBO’s.

    The guy who formulated InLiven said he would never use SBO’s and wrote a good, short article on the subject. If you (or anyone else) would like to see the article, let me know and I can send it to you. :)

    He also talked about the importance of avoiding capsules and pills.

    Lacey :)

  30. Janette says

    A little off topic maybe, but does anyone know anything about giving probiotics to babies? Was thinking of giving my 4-week old some to help relieve her gas and help with more frequent bowel movements. Thanks!

    • says

      I just got a sample of probiotics for vaccinations: and there are some other brands for infants/children out there too (try at However, if your 4-week-old is breastfed exclusively, the bowel movements should be regular unless she’s sensitive or allergic to something in your own diet. ??? I say that as a mom who talks to a lot of other moms, not as a health professional. Might be worth eliminating some common triggers like dairy and gluten for a few days to see what happens.

      Good luck! :) Katie

        • says

          I asked the maker of the probiotic fermented foods product I use and just got this response…

          “Hi Lacey, I am not familiar with human strains of probiotics. Be interesting to see where in the human they source it from, fecal matter maybe? That is the only place I can think of since human bacteria exist from mouth to anal and I can not see how they would scrape it out of a human to culture???

          Also I quote from their web site: “All other probiotics are made from animal or dairy strains”… This is not a true statement since we source ours from fruits, veggies and grains. So it shows me that they really do not know their probiotics. In addition I noticed they are not certified organic nor do they have the nutrients of 26 living whole foods that have been fermented….”

          Yeah, I don’t know. “Human derived strains” sounds like something I’d prefer to avoid, but would be good to get clarification from the company on what exactly that means… ??

          Cheers! :)

            • says

              Huh, interesting. From a healthy live human intestine… I don’t know, I guess I go back to ‘how does nature do it?’ Our intestines don’t *manufacture* probiotic strains; they colonize our guts from the types of foods we eat – fermented/cultured foods being the best source. We wouldn’t be sourcing and ingesting bacteria straight from a friend’s intestine, but maybe from her jar of ferments… It’s an interesting theory that these are somehow better supposedly, but personally, I would stick to food sourced probiotic strains. Just my opinion. :)

                • says

                  Hi Kris. I haven’t seen very many to be honest. And the ones that I’ve seen in passing that might even come close to qualifying as such generally have other additives and such. Always ingredient lists and ask deeper questions. :)

                  The one we use in our house is called InLiven, and I love it because it is just certified organic fermented food in powdered form. Nothing added. It also gave me noticeable differences in my health – fewer and less intense bouts of illness, more regularity, negative on my strep culture with my 4th baby after having been consistently positive with babies 1-3, and getting rid of chronic yeast infections.

                  In the spirit of full disclosure, I am now also a Rep for the company and sell it. But, I’m first and foremost a happy customer and married to principles not a brand. If I found one that was better, I would switch. But this one is excellent on so many levels and is sought out by many naturopaths and practitioners once they are aware of it. It comes in a single tub, or in a 3-pack.


                  It’s not cheap, but compared to other high quality probiotics (many of which, however, I don’t think are as good as this one), the price point even at full retail is competitive. I know people who spend ~$75/month on other probiotics. And customers can get 20% off all Miessence products, so the price point with the discount is quite good for this type of product. (If you’d like info on how to get the 20% off, let me know.)

                  If you have any other brands you’d like a second opinion on, happy to look at them. I’m always happy to give thumbs up where thumbs up are due, regardless of the brand.

                  Cheers! :)

                    • says

                      Hi Allison,

                      Miessence gives a free Lifestyle Membership for 20% off with an initial qualifying order value of $150+. In other words, a one time order of $150+ value gets you 20% off that order, plus 20% off all future orders of any size – with no monthly ordering commitment (there are other perks available for people who do want to do a monthly order, but with the LM there is no monthly commitment).

                      If you’re ready to order, simply go to and add $150 worth of product to your cart. Once it hits $150 in value, you’ll see the 20% come off. Then, with just an email and password at checkout, you can log back in any time in the future for 20% off any sized order (within a year – if past a year, you have to do the initial $150 again; but if you order at least once a year, you never have to do the $150 again).

                      If you need any guidance with product selections, just let me know – happy to help. You can email me directly at laceyswartz (at) verizon (dot) net.

                      Lacey :)

  31. daniella says

    Hi Katie,

    I typed in google “Soil Based Probiotics” and found this post of your blog. I am SO glad I did. It answered a lot of my lingering questions. My 3 year old son who has a neurological disorder is doing a treatment for the elimination of parasites, fungus, bacteria and pathogens in general. The program states that ONLY soil based probiotics are allowed because the parasites feed off of all the other kind, and that he needs one with the highest strain possible to repopulate his unhealthy bowel and gut. Any thoughts? Can I still give him SBP? He’s 3. I ask this because I noticed that you give your baby the ones from Garden of Life. Hope you can shed some light on this for me. I know you’re not a medical professional but you seem to know more than me :-) Thank you!

    • Katie Kimball @ Kitchen Stewardship says

      It seems prudent to speak with whomever you’re working with to determine this regimen for your son…I’ve never done a parasite cleanse, but I actually have some of the supplies to do it. That one doesn’t include anything about probiotics.

      I wish I could help you more, but believe me, I only know a little bit. I can say that I’ve given my kids the Garden of Life soil-based probiotic. Would I do it again after learning the information I shared in this post? I don’t know…it makes me nervous, and our whole family has changed to other brands. ??? However, I also learned that Garden of Life changed their probiotic quite a bit, so who knows?!? Watch for ill reactions and follow the advice of your practitioner, to whom you can bring your research and questions.

      God bless your little one; I hope this does what you want it to for him!
      :) Katie

    • Katie Kimball @ Kitchen Stewardship says

      I can only tell you that the website and your birthing center know a lot more than I do on the subject! I didn’t see anything on the site that put up red flags…I can’t imagine figuring out how to get a probiotic into a newborn, though – it won’t go through your breastmilk? If you’re using formula, that makes sense. Wish I could help more! :) Katie

      • says

        I’m still learning myself, but it’s my understanding that if mom is eating good probiotic foods and breastfeeding, then baby is covered. If using formula, then yes, it’d make sense to me to maybe consider adding a little bit of liquid probiotic food source to the formula. ~Lacey :)

  32. Marcie says

    I just read your followup comment on biokult. What probiotic are you taking? I’m thinking I need to switch. Thanks for your help!

    • Katie Kimball @ Kitchen Stewardship says

      I have a few capsules that are mentioned here, BUT for the last 2 months I’ve been taking InLiven by Miessence…and it’s making quite a difference. I’ll be posting on it in January, but if you want to look into it:


  33. Kelly says

    Apparently you haven’t heard of Prescript-Assist, an SBO product that has three clinical studies backing up it’s effectiveness, something that can’t be said about Rubin’s product.

    No, I don’t sell the stuff, but a quick google search will turn up more information.

  34. Kris says

    Wow, now I am confused. I just purchased Prescript Assist which I believe is SBOs and I feel better after a few days some how but now read this. I also take PB8, which is not refridgerated but seems like it helps some. I do take more than the recommended dose though. Which do you recommend for a great probiotic, any as long as they are refridgerated? My daughter does take some that are refridgerated. I am so confused now on what to do, the ones that help could cause more harm then good :(
    Thanks for any assistance!

    • JB says


      Prescript Assist is the most well researched SBO based probiotic on the market, bar none. Studies done were specifically on IBS, and achieved 82-100% remissions within 2 weeks of use – without any side effects. This was also the case at the 1 year clinical extension.

      That said, much of the info put forth on this post is inaccurate and does not reflect current research. Micrbiology is an incredibly complex field, and to offer a parallel analogy – there are beneficial forms of E Coli (e.g. Nissle 1917 strain, et al). Products on the market like Garden of Life Primal Defense may as well not even be called an SBO product since it only has one organism that is an SBO. In any case, rest assured you are using the best probiotic currently on the market.

      • Katie Kimball @ Kitchen Stewardship says

        This article was definitely simply an exploration of the article I read, which is over 8 months old. Thanks for linking to current research; I really appreciate how it helps the post stay up to date (and hopefully get rid of any inaccuracies). :) Katie

    • Katie Kimball @ Kitchen Stewardship says

      Nothing is easy in the natural health world! I appreciate JB’s helps on this one, since I didn’t know much more than I read in the one article I sourced. I usually say that if something works for you, that’s a huge good sign…
      :) Katie

  35. Kris says

    Thank you for your replies! I did read about Prescript Assist and did look over the studies, which prompted me to try it. But when I read spore-forming and could become pathogenic I was imagining a bad bacteria take over and did was not sure this was an okay product to use after that. I want what works, but do not want to pay a price for it :( JB, it sounds like you have good experience of this product and approve, thank you for your research!

  36. Gina Love 17 says

    I have been taking the Lady Soma Probiotics for about 1 year now and I can’t belive the difference it makes in my digestive health! My OB/GYM reccomended Lady Soma. I have had stomach/instestinal problems my whole life and I have diagnosed with IBS. since taking the probiotics I have seen alot of improvement.

  37. Gemma says

    No mention that I could see, about taking care to be sure WHATEVER probiotic one chooses, that it be GMO free. If certified organic, then should be GMO free.

    Many supplements, especially the cheaper ones, can easily be cultured on GMO base. NOW brands is one that does not guarantee that their products are GMO free.

  38. Tammy says

    I’ll be honest, there is no way I would eat anything that contained “soil-based organisms” to include soil-based bacteria. That is where botulism comes from. Yuck! I won’t even can non-acidic foods for that very reason – well, that and having children, I figure something would happen that they would determine they needed my immediate attention while pressure canning and I’d wind up with a lovely new sky light in my ceiling where the lid went through. For non-acidic vegetables, we either eat them as we can or put them in the deep freeze.
    I did read an interesting article that pointed out that sugar is important in controlling botulism. Apparently a company in the UK was trying to reduce calories in a yogurt (specifically a hazelnut yogurt – sounds yummy) by using aspertame for a sweetener instead of sugar. They had 27 patients and one death from that. – under the “Outbreaks” section.

  39. Matt says

    Hi, I was wondering if you could provide the specific strains that have been shown to be pathogenic in Primal Defense Ultra. I have reviewed all of the strains stated to be in this product and the only complications that I have been able to find in reputable medical journals would be cases where complications arose in patients that were in immunocompromised risk groups, patients using immunosuppressing drugs, or in infants. B. subtilis seems to be the one that folks are pointing their fingers towards since it is the only one that states to be a spore-producing bacterium. But, this bacteria has been shown to be safe in many areas of the world, including the United States, Canada, and Europe. It is used in joint medicine, GI tract medicine, and used in some food products. So, if you could provide me with the specific strain that I should be concerned about, I would appreciate it.

    • says

      I’m so sorry, I really don’t know how to answer your question. (also my apologies that your comment was lost in the shuffle for so long!)

      The info from the post was largely from conversations with a naturopath, not independent research. The Primal Defense has changed its formula recently, so it might not even still have the same issue – aren’t most of the SBOs (or all) removed now? Also, the naturopath was specifically mentioning people with Crohn’s and such, so that would probably count as immunocompromised…maybe? Thanks for visiting, Katie

  40. Holli says

    Great article! I’ve searched the web trying to find more info on sbo’s because I react so badly to them. 5 months ago I started primal defense ultra and became constipated. I continued for 30 days but had to stop because I would get so sick. I had horrible cold sore break-outs and a case of shingles came up (which I’ve had before). I finally gave up on them but I’m still horrible constipated. Health trinity doesn’t seem to help either. I don’t have any auto immune disorders but I’ve had gut problems for years with multiple food sensitivities. I’ve done antibiotic and anti fungals on more than one ocassion as well as extended anti candida diet protocols. I’m convinced that my gut bacteria adapt within 2 days to any food or supplement or medication. Its downright creepy. I can’t find any info to support that either, but I know what i experience. I truly believe there is no cure for me until we better understand the human microbiota and how to manipulate it. :(

      • Holli says

        Thanks so much for your comment, Katie! I find GAPS too difficult to stick to. Instead I do the auto-immune version of the paleo diet which is very similar, but better addresses my sensitivities. I know I don’t have parasites, but I’m starting to wonder if I have a lingering virus of some sort. I’ve started high doses of l-lysine to see what I can knock out. Wish me luck!

  41. claire says

    Thanks for this info. I still have no idea which probiotic is good. We’ve used bio-kult but to be honest haven’t noticed any benefits.
    I would only poop every other day since childhood. But since 3 years ago I would poop more often since starting eating fermented foods and later doing GAPS diet fr about 1 year.
    I now go usually daily (rarely more, sometimes I miss a day), so not perfect. I just can’t figure out how to improve my digestion further.
    It saddens me that my children don’t poop more than once daily either. My 5 yr old doesn’t even go daily.
    I’ve tried so hard with GAPS and they eat fermented foods daily usually with every meal and sometimes in between too, including sauerkraut, raw , kefir, sour cream, yogurt, occasionally others like beet kvass and fermented carrots, pickles etc..

    Anyone have any ideas what we could do t increase our bowel movements further?? Any suggestions would be much appreciated! :-)

    • says

      boy, if you’re doing all that fermented foods, GAPS, I’m sure plenty of bone broth… I can’t imagine what else could help! The grain-free diet that would be part and parcel for GAPS always gets me going. The only thing I wonder about – and I’ve only read about stuff like this – is an enema or colonic to really clean out any built up gunk in there and maybe get things moving once and for all? Again, it sounds like you’re doing everything right! I wouldn’t get too worked up about it; maybe this is just your family’s “normal.” (But remember that I’m just a mom too, nobody special and with no medical training, so I’m just guessing here too…) :) Katie

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