Saturday, November 16, 2013

HOW TO CURE SIBO, Small Intestinal Bowel Overgrowth: Step #3 Eat Soil-Based Probiotics

Step #3:  Soil-based probiotic 1-2 daily if not severely immune compromised (Prescript Assist, Bacillus licheniformis, Clostridium butyricum, etc)

Or eat soil-based organisms (SBOs) from ancestrally prepared fermented foods: KOREAN PEPPER PASTE (GOCHUJANG), Thai shrimp paste, natto, fermented black beans, etc.

See prior animal pharm: Kochujang, [B licheniformis, B subtilis] fermented soybean-based red pepper paste, decreases visceral fat and improves blood lipid profiles in overweight adults

B pumilus

Today we'd like to talk about step 3 in Dr. BG's 7-Steps Paleo* Gastro IQ SIBO Protocol.  I came here as a bit of a know-it-all on resistant starch [RS3 from legumes, lentils, whole GF grains and roasted heirloom tubers/roots], but quickly realized that while RS3 was somewhat of a missing-link on a paleo diet, soil-based organisms (SBOs) are missing even more-so.  Luckily, combining RS and SBOs is the quickest route to restoring harmony in the gut.  In a few email exchanges with Dr. BG, she mentioned SBOs several times.  I was totally unfamiliar with the term.   I thought to myself, 'wow--she is so dumb, she can't even spell 'SIBO'.  Boy was I in for a surprise!  After sending me 200 links to read, I quickly became a believer in Soil Based Organisms.  

Also known as Homeostatic Soil Organisms (HSOs), these microbes have been flying under the radar for decades.  All throughout our evolutionary history, SBOs were there with us.  When we started cleverly sanitizing our hands, sterilizing our eating utensils, and homogenizing everything we ate SBOs were no longer our faithful ally.  
L plantarium
Soil Based Organisms are microbes which normally live in dirt, but can also live happily in our digestive tract.  Approximately 30 different strains have been successfully isolated and are commonly put into probiotic supplements.  There are hundreds of articles available concerning SBOs, but most of them are advertisements from the supplement industry designed to sell you their favorite formulations.  I managed to find a few papers that were reviewed by the National Institute of Health such as this one on SBOs and Immune Function.  The article describes using SBOs to successfully treat Chronic Fatigue System and cancers and they had "...proven successful in restarting the immune systems of persons with allergies, lung cancer and TB."  

clinical study was done with 25 sufferers of IBS using a commercial SBO probiotic.  The study concluded: " This study identified 3 subsyndromic factors of IBS: general ill feelings/nausea, indigestion/flatulence, and colitis. In this methodologically oriented double-blind study in patients with IBS, combined probiotic-prebiotic treatment with Prescript-Assist was associated with significant reductions in these factors."  

I looked at the formulations of several SBO supplements recommended by Dr. BG and found they all contained a variety of microbes.  The first one I looked at is called Probiotic-3 from iHerb.  It contains Streptococcus faecalisClostridium butyricum, and Bacillus mesentericus.  Each one of these are well known probiotics found in the soil and in humans and convey protective properties when in the human digestive tract.  

S faecalis

WHOA!  HOLD ON...Dr. BG wants us to swallow a pill containing Streptococcus faecalis?  [Grace: YESSSS]  It's commonly found in 'diseased teeth needing or having had root canal treatment' and 'Some diseases caused E. Faecalis are endocarditis..., urinary tract infections, pneumonia or meningitis.'  WTF?  Well, it turns out that this microbe is also a powerful 'lactic acid [producing ] bacteria and it can help reduce symptoms when a person is lactose intolerant. The products created with this bacteria are useful for clearing diarrhea and for stimulating the immune system. Products fermented with this bacteria help to balance the intestinal microflora.'  Almost every one of the SBOs has a similar story!  OK, maybe Dr. BG is not totally crazy, but the jury is still out.   [Grace: Demented, no debate~!]

(NOTE: this is not an advertisement!)

Click the links to learn more:

Bifidobacteria and Lactobacillus are some of our most ancient enviromental and soil based microflora that our ancestors co-evolved with.

Lactobacillus acidophilusLactobacillus caseiBifidobacterium longum
Lactobacillus rhamnosusLactobacillus brevisBacillus subtilis
Lactobacillus salivariusBifidobacterium bifidumSaccharomyces boulardii
Lactobacillus plantarumBifidobacterium breve
Lactobacillus paracaseiBifidobacterium lactis

If anyone is as interested in gut microbes as Dr. BG and I, please click each link above...these are links that I personally searched for, they were not hand-fed to me by manufacturer.   For instance, the link on Lactobacillus paracasei will lead you to an article by the American Society for Microbiology concerning this microbe and it's relationship to mucosal immune response.  I will leave it to you to look into these, as each one alone could fill several blogs!

Here is the takeaway for this blog:  If you are severely immune-compromised, do not take any probiotics.  They are alive or spores (except for the killed ones). Like a live (attenuated) vaccine, probiotics are contraindicated in a severely immune-compromised individual, someone on or after chemo/radiation, low WBC or suppressed bone marrow.

If not, and you want to treat SIBO or just improve your gut microbiome, consider taking supplements like these in your therapeutic plan along with RS3-rich foods and Bionic Fiber (version A, B, C):  

Prescript Assist
AOR Probiotic-3
Body Biotic 
Primal Defense
MegaSpore (practitioners' offices only)
Primal Flora

There is no magic in using these brands, but the supplement you choose should  have a similar composition.  These supplements don't need to be taken for life, just until you kick-start your gut flora--when properly fed, these microbes will set up shop and help keep you healthy and happy.  Proper feeding of microbes relies on resistant starch and some other prebiotics we will talk about next...


Naomi Devlin said...

Look forward to your article on pre-biotics. In my experience, formulas containing these tend to exacerbate the reflux symptoms of SIBO.

Totally on board with the soil bacteria though! I try to encourage consumption of foods fermented with soil bacteria such as Natto, kimchi and sauerkraut rather than large doses of probiotics. As some people experience huge die off crises from high dose probiotics.

X x x

The Natural said...

Hi Tim,
I have read some where else(maybe on FTA) that pro-biotics in supplement form may not make it past the harsh acidic environment present in our stomachs. Even if they do, only a fraction of them make it to the gut. What is your take on this. Is it even a valid concern? Do enteric coated pro-biotics have a better shot at making it past the stomach? Or as suggested in FTA, should they be taken along with RS so the they can hitch a ride to the distal gut by attaching themselves to the RS?

Another question I have is, could we introduce these SBO to the fermenting media so we could get them from the foods instead of in a pill form?(such as the water used to soak the beans, or just throw a capsule in the sauerkraut or Russian Beet Kvass while they are fermenting)

Thanks for all the links on SBO...there goes my weekend ;-)

BTW, I cannot see the article when I click on the SBO Improve Immune Function (Pubmed) link you provided in this article.


Dr. B G said...


Thanks for your comments. I agree -- prebiotics can exacerbate symptoms depending on what organisms are growing in the small intestines and to what degree. I certainly experienced that! Even 'safe' vegetables made me bloated. When the 'load' of overgrowths is that high, then I believe a course or two charcoal/betonite clay should help lower the burden. If not then consideration for parasite, protozoa or pathogenic overgrowth herbal treatments is necessary.

The SBO are super effective at killing off candida. They are also bionic BIOFILM BUSTERS. ;) This is so crucial as these growths live behind a heavy fortress of slimy matrixes that our immune system cannot reach.


The shelf stable spore ones should make it past natural environments like the acidic gastric pH. Also those with SIBO often have more of an alkaline stomach, so no problem LOL. The SBO are not fragile.

We think alike! I've already fermented my kraut with C butyricum and B lichineformis but honestly (Tim and I had this dicussion) really there is no evidence they would ferment and thrive there.

From my research the SBO strains are found Korean ferments of soybeans. Traditional kim chee is often made with raw squid or other seafood which may mimic an organic protein/fat substrate (similar to soy) that may support SBO strains, I strongly suspect. Kraut with bits of Stinky Flipper, anybody?

Have fun!

Here's that fun article (it's a fun tertiary source)

Posit Health News. 1998 Spring;(No 16):16-8.

SRL 172, a protein derived from a soil-based organism, is advertised for being able to restart the immune systems of persons with allergies, lung cancer, and tuberculosis. SRL 172 also appears to shift the cytokine profile in persons with Gulf War Syndrome and Chronic Fatigue Syndrome from TH2 back to the more effective TH1 profile. One patient reports improved DTH skin responses to topical DNCB after using Nature's Biotics Soil-based Organisms (SBOs). There also appeared to be improved immunity response indicating a shift from a weaker TH2 to a TH1 cytokine profile. The patient explains his successful use of SBOs and reveals that all but 1 out of 100 other patients who have used the product for a variety of ailments cite successful outcomes. Among the ailments whose symptoms the SBOs have helped relieve are foot sores from diabetes, Chronic Fatigue Syndrome, insomnia, and genital herpes. Recent use of SBOs by HIV-infected patients has had positive results in energy and weight gain and improvements in some types of chronic conditions indicating an improvement of cell mediated immunity and antibody production.

*Fatigue Syndrome, Chronic/IMMUNOLOGY *Persian Gulf Syndrome/IMMUNOLOGY *Soil Microbiology *Th1 Cells/IMMUNOLOGY *Th2 Cells/IMMUNOLOGY


Dr. B G said...

T-Nat ~~ Don't want to make your eyes glaze over but SRL 172 is cool stuff, it's the protein from a soil based organism known as saprophytic mycobacteria. It enhances success in chemotherapy oncology protocols. Here is a Phase II trial and III trial, respectively.

Have you read the Old Friends theory about our co-evolutionary friends, the saprophytic mycobacteria? CUUUL STUFF.


The Natural said...

Dr. Grace, Thank you so much for the quick reply and the links you shared.

I posted this comment for you on another post about charcoal. Could you please give me your take on charcoal?

Dr. B G,
Your mentioning of the clay and charcoal in the comments above caught my attention. A while ago, I followed a protocol that recommends fiber + charcoal + bunch of supplements.
The idea behind the protocol was to get rid of any excess estrogen with the help of DIM (an extract from cruciferous veg like broccoli) then flush out the free estrogen and other toxins from your system with 1T x 3 a day + lime juice and charcoal before bed. After this phase 1 for a week, super saturate your body with some vitamins and minerals. I felt very good within the first week and the first positive sign was the my eyes stopped hurting and vision improved. However, I could not tell if the positive effects were due to caffeine elimination or fiber increase or activated charcoal so I never repeated this protocol as it was quite an ordeal to drink a lot of fiber and charcoal before bed time.

Anyway, I was just wondering how you used charcoal and to treat what? What were your results? Were you able to pin point any of your results specifically to charcoal?

I have a lot of charcoal sitting around and would love to put it to good use!

PS: I will email you in a few days about the GI FX and ONE testing. Like I said, I will have to wait until after Thanksgiving to move forward with that.

Tim Steele said...
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Tim Steele said...
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Keith Bell said...

Particularly interesting is Probiotic-3 as this appears to be the only product on the shelf containing butyric-belching clostridium. Might these clostridium clusters (IV, etc.) be the underlying beauty behind success of fecal transplant? I believe butyric acid explains the French Paradox and possibly longevity (one strain of clostridium was found 15x higher in centenarians). Clostridium has a nasty reputation due to botulism and C. diff, but this is a large family of microbes with taxonomy still up in the air regarding gram-negative vs. gram-positive status.

Here's some recent science, rationale for clostridium based-probiotics, maybe the next best thing to the new pills made with human feces. It's about IL-10 producing macrophages protecting against colitis via Treg cells:

This still newer research illustrates how the process works via the clostridium's butryric acid in producing Treg cells:

Treg cell deficiency no more! But why are so many people apparently deficiency? What happened to their good clostridium?

1) They were born imbalanced from imbalanced mothers, a matter of poor microbial predisposition. Colonization begins in the womb, yet modern science still largely believes it takes place during the birthing process without a lick of evidence.

2) Vaccination and antibiotic abuse. There are no comprehensive studies about collateral damage to flora by vaccination. Can you say vaccine injury? Vaccine-induced autism, a gut-brain phenomenon?

3) Toxic pollution in air soil and water. Mercury pollution is a perfect example where some microbes are sensitive (certain clostridium strains, gram-positive lactobacillus and bifidobacteria), allowing resistant gram-negaitves to flourish (e. coli, "bad" clostridium clusters) along with rampant, opportunistic fungal overgrowth seen in every major disease, both physical and mental illness.

Mercury adjuvants in vaccines may have similar effect in infants, allowing mercury-resistant microbes to flourish. This new molecular study about earthworms details flora shift possibly consistent with known flora imbalances in autism. Many types of bacteria are known to be resistant to mercury, studied for use in environmental remediation. But other microbes are sensitive to mercury. Clostridia known high in autism may have mercury-resistant clusters (via hydrogen sulfide), but also sensitive clusters crucial for balance, such as the cluster IV butyrate producers.

Tim Steele said...
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Keith Bell said...

Fascinating stuff, Tim. No, I don't know much at all until now about RS co-feeders and keystone species, but that paper you shared would make a lovely audio book for that certain someone.

Interesting to note that Ruminoccus bromii and Eubacterium rectale are both clostridial species. As my mom used to say quite often, "It takes two to tango."

Where are the clostridia? And where are the lactobacillus and bifidobacteria which would normally control fungi?

The Hygiene Hypothesis can KMBA as it promotes poor sanitation, giving a huge pass to the idea that it's ok to defecate in water. In wastewater treatment we trust. But the activated sludge process purposely multiplies ciliate protozoans to reduce bacteria, making sludge legal for disposal. What happens when these voracious protozoans find their way to our livers and intestines? Oops.

Kate said...

I'm wondering if I bought some of the Korean pepper paste Dr. BG covered in a previous post, would that be a viable source of b. lichenformis?

Tim Steele said...
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Kate said...

Ha, Ha, Tater, I think I'll pass on licking ducks, although I do occasionally see a Mallard hereabouts. I ask, because I believe only 2 of the listed probiotics in your post contain lichenformis, body biotic and megaspore, and the latter is only available through medical professionals. I already have some Prescript Assist, but am wondering if lichenformis might be the key to rein in the gas.

Tim Steele said...
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Kate said...

Tim Thanks, not to worry. Its not a huge problem, I think I am slowy getting it under control. I've been pretty strict with the PHD for two years now. I think my diet is pretty dialed in, except fermented foods give me big headaches, even migraines. That is the main reason I began this admittedly speculative foray into gut remodeling. I have taken various amounts of potato starch since June, and have been experimenting with various probiotics. SBOs are definitely helpful. Even if I never solve the headache issue, RS is worth it for me because of excellent TMI and terrific energy levels. I read over at Kresser's blog that you received your American Gut Project results. Congrats! Sounds like you are in good shape. I was slow to take my sample and return it, but am looking forward to getting results as well.

Tim Steele said...
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The Natural said...

Can't wait to read about your American Gut Project results.

Another question for you; My son is scheduled for a minor surgery next week. I am sure the docs will be giving him a lot a antibiotics. What would you suggest I do proactively to protect his gut bacteria from getting destroyed by the antibiotics. If I just wanted to put him on one probiotic - which one would that be? He is 12.


Tim Steele said...
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The Natural said...

Thanks Tim.
We make yogurt at home and have a lot of PS. So we are all set!

Jason said...


I love this blog and I think these series on SIBO are really important

I have some serious histamine intolerance AND - I suspect- some IBS/SIBO.

Having histamine intolerance means that I react strongly to fermented (fatigued, migraine, hives) foods and to nightshades like potatoes and lentils. Tomatoes and Spinach in green powders like the one you recommend are also causing me some reactions.

What can I do to get rid of at least one of the two problems?

Thank you!!

Dr. B G said...


Any further questions? Would love to hear your progress and thoughts later


Did you see Mark's Daily Apply on fermented foods?

If you buy the fermented Gochujang or other sources that are made the ancestral way and without perservatives, I believe you'll be getting a great source of B licheniformis. It is a spore so probiotics and food that contain it do not need refridgeration.

I don't know if it will be the 'cure' for gas as you're asking but certainly I have seen numerous cases of gut problems improved with just a few days worth of B licheniformis!

For me, I was able to tolerate gluten and dairy after two SBOs C butyricum and B licheniformis. Not bad, eh? Power is in the pudding. I would love to hear your results and progress later.

We didn't add this link to the post -- which is my oversight. Sorry. Lists the foods that naturally contain fermented B licheniformis. Tim naturally gets a boatload from the chicken coop! He doesn't need to worry...

If you've had antibiotics, I suspect you've wipe this niche out.

Anonymous said...

Tim/Grace, I put my aunt on the PS regimen. She has severe iron-deficiency anemia and has some kind of long-standing IBS (alternating diarrhea and constipation), along with PCOS.

It's been 2 weeks and she's only doing 2 tbsp but she's complaining about gas and indigestion. Any caution do you see for someone who might be iron deficient and on iron supplements and is PCOS? Thanks. Namby

Dr. B G said...


If the symptoms of gas and indigestion are moderate to severe for someone adding any fiber -- metamucil, inulin, or RS, then it is likely prudent to consider that that dose is probably too much. The colonies have to shift and it can be definitely done more gently and and with ease.

Does that help? Her gut sounds pretty f*kcered. PCOS is a candida condition and involves microbial translocation to ovarian tissue. Gut or vaginal mucosa can be breached by permeability.

Constipation IBS is dominated by methanogenic species. Lots of GAS! And in all the wrong places-- small intestines instead of large intestines. Is she gluten-free and dairy-free? Probiotics?

I wish her improved gut health soon!

Anonymous said...

Thanks Dr. BG. Yes, definitely everyone's tolerance for gas is different. She has Sjogren's and Sjogren's renal tubular disease, so she has many issues. I'm gonna have her start slowly with maybe a teaspoon everyday until gas subsides. Btw, do you normally store your protiobics in the fridge? I usually don't but it's a bit overheated in my apartment and I put them in the fridge for safekeeping. Primal Defense and ORAC seem to harden a little bit. That should be still good, right?

You were right about reversing autoimmune issues, Dr. BG. That seems to have happened with me with Sjogren's. People don't realize the magnitude of this finding. Seriously, you can cure leaky gut + gut dysbiosis with probiotics and RS, thereby reversing autoimmunity. I'm talking about being antibody-free. Isn't that supposed to be impossible? Worthy of a write up in the New England Journal of Medicine.


Dr. B G said...


So your aunt has at least 2 autoimmune conditions:Sjogrens and PCOS. Personally I feel that C-IBS is another autoimmune disorder, but we just haven't figured out the consortium of auto-antibodies produced (is it against the MMC? the smooth muscle for peristalsis?).

So you saw Anonymous's remarkable reversal of both Sjogren's (SSB-LA) and Chromatin (lupus) autoantibodies to negative and reduction in ANA+ titers, IN ONLY 3 WEEKS?

I'm not the only one! Thx for your kind words though. For me, Robb Wolf is the one that really began this bad-health reversal trend and revolution with his vocal introduction of the paleo diet!

WIth you and others, however, I believe we can MOVE MOUNTAINS and ameliorate as many root causes as we can. I certainly cannot do it alone, but with you and others, my big hope and dream is that we can enjoy harmony again between the heavens, soil and humans... Is that fantasizing too large??

So your signs of Sjogrens are 100% in remission? Did Sjogrens appear after children or after hypothyroidism/adrenal dysregulation?

No dry mouth or eyes? Did you ck antibodies pre- and post- interventions? What can you share with me for our NEJM publication/letter? LOL. Namby -- you dream so BIGGGGG.

The wonderful thing about spore-based soil based organisms is that no refridgeration is required. I talked to the co-CEOs my buddies at Prescript Assist and they have experimental conditions where Prescript Assist has been kept at 100F (i recall) and despite one year duration, there was something crazy like 98% viability still.

ORAC powder is usually room temp storage unless you live somewhere moist or hot or both.

Phobos said...

I have been following the RS discussion over at FTA from the beginning and have attempted to use PS a few different times, but have been turned off due to bloat in the lower abdominal region. The bloat was not immediate. It seemed to show up after several days on PS, and then it would take several days to subside after stopping PS usage. Then I made my way over here and have been following several of the steps on the SIBO posts including clay usage, SBO (primal defense), fermented foods, psyllium husk, etc. The combination seems to be working in many respects.

I have some GI history, especially as a child, but something that really struck a chord with me was Tim’s experience with Cipro. Mine was not as extreme as his, but I have been on cipro twice for campylobacter, so I felt it might be necessary to repopulate the potentially empty cages prior to feeding. I must say the combination has been extraordinary. Digestion has been much better and of course sleep, but the clarity of mind that I have now is something that I have been searching for for so long.

I had noticed over the years that my ability to solve problems was not near what it used to be and always tried to track back in time to when things might have started to change with no real success because it seemed like the change was too gradual to pin on a certain event. Now, I believe the event may have been the first course of cipro in 2001! At that point I was at the top of my game. I was an undergrad student taking many mathematics, physics, and chemistry courses with no problem. Two years later I was accepted to multiple graduate schools, but I had noticed that I was not as sharp as I had been. I managed to plow through and get a masters, but it was a fight. Since then I have been playing around with diet, exercise, and rest attempting to keep myself healthy and regain that mental edge. Nothing I tried (every kind of paleo) gave me the mental edge I once had, till now. Over the last couple of days I have had moments of clarity that take me back to those days. I am so thankful for Grace and Tim and all of the work they have done. What an amazing find!

Now to my question. My wife has IBS, psoriasis, and she suffers from occasional migraines. I just read a comment over at FTA from someone that had his psoriasis flare after starting PS. He said he had not seen a flare like that for 30 years. My wife has been on humira and enbrel and I would love to help her get off those meds, but I’m apprehensive to suggest the PS protocol due to the other commenter’s issues. He states that he is not the only psoriasis sufferer who has had a flare after using PS.

Grace/Tim, do you have any thoughts on the use of PS for those who suffer from psoriasis? Would the use of SBO’s be alright SINCE she suffers from psoriasis or should they be avoided because she is compromised? I just have a feeling her cages are empty from LOTS of meds over the years. I appreciate insights you might have.

Ann said...

I have a question for those doing both RS (plantain flour) and SBOs. I have been doing RS with plantain flour for about three weeks. So far no letup on the gas, but the gas from the RS is usually lower, colon mostly, I think. Just the plantain flour by itself has never given me painful gas, or the kind that makes me feel sick. I started Primal Defense Ultra a week ago, and was feeling good and noticing better digestion, especially of fats, and my unmentionables have gone from floaters to sinkers within the week. This really suggests to me that something is improving my fat digestion.

Both yesterday and today, however, I have begun to have really painful gas in my stomach and small intestine area (middle of gut, just above my belly button) building to a feeling that my stomach is going to have to explode to relieve the pain within about two hours after eating. I haven't eaten anything out of normal for me either day, and I don't remember EVER having stomach gas this bad before in my life. Since the gas was lower and different with the RS, I can only wonder if this is caused by the Primal Defense.

Has anyone else here experienced horrible gas and bloating that commenced after beginning the SBOs? Did it pass, or did you have to stop taking them? I don't want to have to stop taking them, but if this doesn't pass it won't be something that will be worth it for me to live with to improve my gut flora. That would seem like a bargain not worth the price.

I took some charcoal in water about a half hour ago, and seem to be feeling some relief, so I'm thinking it's definitely gas of some sort.

Matt said...

Earlier in December I began the RS protocol from FTA and thought I was going to burst from the pain. I obviously didn't easy into it, downing 4 TBS.

After that, I have been taking Prescript Assist for the past 1.5 months without the any problems. I thought my SIBO was cured!

I then started to implement the Bionic RS w/ SBO and immediately found my SIBO was still around since I was experiencing bloating and pain in my lower/middle abdominal. Not to mention a complete Fibromyalgia Fiesta in my body. This was with only using small dosage of 1/4 TSP.

I then tried using activated charcoal to soak up the gases, and it actually worked.

I've incorporated RS with my meals by mixing it in my water. I've found to have less bloat and less pain in the gut.

Ann said...

Matt - I'm wondering if just the opposite is true for me. I seem to have MORE gas and bloating higher up (small intestine) when I do the RS with food. Not sure what that means.

Overall I'm feeling a lot better, but experiencing different stomach issues now. An hour or two after eating anything, I just feel so bloated in my stomach - to the point that it's hard to breathe sometimes, and I feel almost like heartburn or acid, but not quite. I'm starting to wonder if I should still be supplementing with enzymes containing betaine. I took my enzymes after lunch today, and just don't feel right. Just took some calc. carbonate antacids, and feel a little better I think. Maybe the Primal Defense and RS have improved my stomach acid? Don't know, but food seems to still be in my stomach for a long time.

Sarah Thompson said...

This is great info! Definitely seems to be an important 'missing link' in our efforts to treat my significant other's Crohn's.

He has been on the GAPS diet (not as strictly as Dr. Natasha would recommend) with a lot of symptom improvement, but seems to have hit a plateau. He still has cycles of flares, they are just milder and he has somewhat better bowel functioning ( he struggles with constipation and has a BM a few times a week now, typically)

The big hurdle that I really really want to get past: he still takes weekly Hummer shots.

From this post, I understand he likely should not begin doing SBOs while on an immune-suppresant.

But, he may not be able to benefit from RS or anything until he does that because I am SURE he has got some major dysbiosis (he's had Crohn's and eaten whatever for at least a decade).

But, he doesn't want to stop Humira until he is at a point when he won't flare badly when he does!

So, what to do?

I would love to find doctor who is on board with all this, who could walk us through a process of going off of Humira. The naturopath we were going to didn't seem knowledgable enough to me. Didn't tell me anything I didn't know and didn't know some things I do, like some of the info here.

Any suggestions of any kind GREATLY appreciated.

Thank you for all of your work,


Kim said...

Tim mentioned that people who are severely immune compromised shouldn't take SBO's. What about if you have an autoimmune condition like Hashi's? Is that considered 'immune compromised'? Looking forward to trying this SIBO protocol to heal the gut. Thanks :)

Natalya said...

Hi Grace,
I started PS in Jan, after 18 months on the GAPS diet, LC. Started other forms of RS a week or so later. Then psyllium. Intermittent diarrhea cleared w 6 TBS PS. Now at 4. Taking GutPro, was taking Body Biotics, now Prescript Assist. But the AOR 3 sends my Windage through the roof! A third of a cap is too much, we are talking uncontrollable:)Gas collects around cecum too, and exits at will (not my will!). I'm thinking to continue, but real slow, any ideas? Loving all the RS. Thanks.

Natalya said...

Sorry Tater, meant to address you too, of course. Happy for any comments about difficulty w AOR 3. I'm thinking it will be really beneficial, thus the struggle!

Webraven said...

Hi all! I would appreciate your experiences/comments/advice. I am working on correcting long-standing dysbiosis using soil based organisms and potato starch. I am experiencing a gradual and somewhat significant worsening of my pre-existing symptoms (bloating the big C, systemic inflammation, fluid retention, low mood (low serotonin?)) If it is the case that the potato starch feeds both "good" and "bad" bacteria, it does make sense that initially my symptoms would worsen as the predominating "bad " bacteria proliferate as well. If, as I've read, the potato starch predominantly feeds the "good "bacteria I would over the course of time see the levels of those bacteria increase, along with a decrease of my symptoms. I assume I could also be experiencing some degree if die-off of whatever micro-organism the SBOs are killing.

So there is my theory. Has anyone else with a significant degree of gut dysbiosis experienced something similar and/or improved their gut using soil based organisms and potato starch? How quickly were you able to proceed and heal?

Grateful for any insight!

Deb said...

I have the same questions as Kim and Webraven, namely, a) is it safe to take PS / RS and SBOs if you already have an autoimmune disease, and b) if you start to get bad symptoms, or an increase of some symptoms, how do you proceed? I am finding that some symptoms get exacerbated although I am having excellent sleep (the best in decades) and (sometimes) improving TMI after about 20 yrs of chronic diarrhea.

Webraven said...

Hi Deb,
I'm reading The Probiotics Revolution by Gary Hufnagle, PhD (in immunology), and he recommends probiotics for autoimmune conditions.

Regarding the exacerbation of symptoms, I'm still wondering, too. Logically, if you have debilitating diarrhea that will result in malnutrition in the long run, you'd have to progress so slowly that the treatment doesn't exacerbate it too much. But in my case, there is abdominal distention, that I could decide to deal with through baggy clothing and avoidance of social situations where looking pregnant migh not work in your favor (say, first dates, for example), general inflammation and fluid retention, which I could deal with in small doses and combat somewhat through anti-inflammatory herbs, and other similar symptoms. In a case such as mine, I would love to know if there would be faster improvement if I were to just decide to grin and bear it for a while, or whether an increase in these symptoms could present a sign that I'm harming myself and slowing things down.

Good luck however you decide to proceed!! <3

Dr. B G said...

Thanks for the book info. I would concur. In autoimmunity (and 99% of chronic diseases and cancer), the gut is 'broken' -- critical microbes are missing and unbalance occurs. Often parasites and pathogenic yeasts and bacteria are additionally present.

It is ideal to get GI tested with the GDX testing to determine the above.
--GI 2200 panel
--ONE optimal nutri eval

Hashi's generally is not a severely compromised condition but if the WBC (white count) is suboptimal, most probiotics except Bifidobacteria or L plantarum are contraindicated.
There are several cases of autoimmunity reversals on the blog. Did you get a chance to read about them?

Here is an updated 7 Steps for ultimate gut health

Definitely the 7 steps are the missing steps for many conditions that we see in modern healthcare where everything is linked to gut dysbiosis. Crohn's is another where tremendous absence of gut diversity has been seen in recent trials. Yeast is a big pathogen as well. The SBO probiotics including L plantarum are all yeast and pathogen busters.
Please let us know your SO's progress!

That is truly wonderful! Sorry about the late responses. AWESOME to kick the pharmaceuticals to the curb when the body kicks back in.

Awesome! I'm sorry about the Fibromyalgia Fiesta and hope to hear more progress from you soon.

Thank you for your kind words. Psoriasis requires a full gut workup, much like Crohn's to get to the root problems and potential high environmental toxin loads. The skin is always a direct reflection of 2 things -- hormones and gut function.

Dr. B G said...


How is the gas now? Have you tried decreasing both fiber and continue proceeding with low-dose probiotic, even every 2-3 days AOR probiotic-3?

Marcus said...

Hey Tim, Dr Grace

I seemingly have a similar problem to Natalya with the AOR Probiotic 3 (terrible, terrible wind, pain and oh the smell is just not conducive to remaining married).

A bit of background.

My wife was diagnosed with MS around 5 years ago. There were probably 5 years of low grade symptoms and oddities in the run up to this diagnosis which led to some larger attacks and the diagnosis (loss of vision, balance, blindess, numbness, all fairly typical).

We played with various diets for a year or so (low fat swank etc) and ultimately ended up Paleo and have been so for the last 3 years solid.

This seems to work and the disease has not progressed too much. THere have been the odd attacks but lingering symptoms have cleared up and these problems have been largely related to slip ups, big nights out, marathon training etc.

As time has gone on we have optimised the diet beyond the basic exclusions and we regularly eat organ meats, seafood (mussels etc), fermented foods and all our meat bar chicken breast is grass fed organic.

A bunch of my friends were recently 40 whilst Emma was in the midst of marathon training and had ran 60 miles taht week. After a big and drunken night out (they don't happen often) there was a new attack. This leads me to believe that whilst Paleo and lifestyle factors keep the wolf at bay the wolf is still at the gates. This is a defence rather than a cure.

Enter resistant starch which seems to be the missing part of the picture. We have started with the Primal Defence SBO and potato starch without too many problems (a bit windy for a few weeks).

This weekend just gone we tried to introduce the AOR-3 Probiotic and the results were, well, they were painful and smelly. One cap and my stomach was in a bad way, I had some loose stools, really smelly and almost constant 'fartage' and it was just generally a disaster. I tried Emma with half a cap and it was much the same.

So, this is my question - we are okay with primal defence, we are okay with other probiotics like BIO Kult and we are okay with fermented foods, Is this just that these new strains need some breaking in? The whole butyrate thing is important for us (Emma) as this offers another tool for us to control (and hopefully fix) her immune problems and keep the MS locked up.

I have taken about a 1/4 of a cap today so will see how I get on but is this a sensible strategy? Take the smallest amount possible and scale up slowly? We are in this for the long game but would value your opinion on why this one probiotic is so tough going and the best strategy to introduce it.

Loving your work. This blog, Tim, FTA and the Cooling Inflammation blog are really at the forefront of what could be a revolution for so many people.

Many thanks.

Marcus said...

Hey Tim, thanks for the response.

I have seen this before when breaking in a new probiotic and I have had a similar problem when overdosing.


- first time I had bio kult it was like IBS (stabbing pains, loose stools etc)

- once tidying up the fridge when Bio Kult was well tolerated I took several caps and had a similar problem (it was maybe 8 when usual was 2)

My only thought here is that a new strain or one not currently down there will induce some kind of war and it can be difficult. Funnily enough, I had no such problems with the Primal Defense and was able to jump right into them. Likewise, I have never had any issues with the home made fermented vegetables (we have sauerkraut most days and I also have some pickles and kimchi - I am even fortunate enough to have a buddy that brews and supplys me with kombucha).

Point being here we have plenty bacteria, almost daily from the kraut and certainly in the last month we have had RS + primal defence + kraut daily. Also a whole bunch of Kombucha and occaisonal kimchi and pickles.

Still though, one cap of the AOR Probiotic-3 gave me trouble for about 3 days. Mostly uncomfortable wind that was pretty much a fart a minute and really, really stank.

It's tough as a few other variables changed - we had white potatoes two nights on a row which can give me a bit of wind and my daughter had a bit of a stomach bug.

I took about a sixth of a cap today and had just the lightest wind after eating but nothing major. I also have a few business things the next few days that mean I can't really be Johnny Fart Pants but I will try to keep scaling it up and try half a cap on Friday and see how I get on.

I have kept up the resistant starch, sauerkraut and Primal Defence last few days and no problems there so it's seemingly not any old microbes that are causing the issue.

Thanks for taking the time to reply and I promise I will feedback. My gut tells me (see what I did there) that this is a new strain and to take it's place it is having to displace something else and that adjustment (battle?) is causing the upset. Previous experiences with Custom Probiotics (CPR1) and even Bio Kult would suggest this on a personal level.

One last thing - Prior to the whole paleo and low(er) carb thing I was always one for wind and it would be frequently smelly. Paleo pretty much fixed that and a whole bunch of other issues (IBD type issues, acid reflux etc) but was it fixing things or just subduing it - I tend to think the later and the RS is the missing piece of the puzzle.

Starve the bad, feed the good, eat clean.

Will report back when we get back into it. :)

Natalya said...

Hi Marcus, Tim, Grace,
A bit of a coincidence Marcus. I too was diagnosed w MS, 23 yrs ago, at 30. Also spent some time on the Swank Diet. Have generally been aware of my diet since then. Probably drank too much, for me, over the years. Had gut issues since I was a child.
But I have done incredibly well over the yrs. Have issues w numbness, and have had several bouts of optic neuritis.
My carb digestion shut down 3 yrs ago, and then I developed an arrhythmia, still have it, super motivating!
I got into ferments big time, gave up drink, coffee, sugar, everything that might be an issue. Was on the GAPS diet 18 months. Consider myself still GAPS, w RS! Digestion so much better. Used to tend to constipation, on GAPS had intermittent diarrhea. w RS just about perfect. PS, Green bananas, rice, potatoes. All eaten w/out issue. Although some gut rumbling and gas at first. Body Biotics, I noticed a mild kinda chestiness, for a few days, worked up to 3/day. Prescript Assist, more gas, took 2/day and gas started to taper lots, felt my lungs clearing a little. AOR 3, didn't take any for 4 days, gas tapered. Took a SPRINKLE yesterday, today guts all gurgly and farty. Some gas discomfort around ileocecal valve, guts quicker a tad. I discovered an amoeba, stool test, about 5 months ago, took mega garlic, turmeric, spices, but may still have it. Iodamoeba butschlli. I imagine the AOR 3 starts a war in my gut, I will continue to take a sprinkle every few days. To keep it at a skirmish, not a full blown battle! (did u see Alien? The scene where the guys gut explodes and a critter charges out?)My feeling is that the AOR3 is a really good thing, but I obviously do not know. And I have been wrong before:) All insight welcome!
Grace...I haven't tried cutting back on the fiber, take about 2 tsp psyllium, and ~ 4 tsp mix of flax, chia, coconut, bean/seed sprouts (Garden of Life Raw Fiber). w/o the AOR 3 fiber seems OK, maybe I'll see what happens w less fiber.

Ann said...

Dr. Grace and/or Tim - I'm wondering how many others you have heard from that have chest issues and congestion, seemingly from the probiotics, and if so, how long it lasted. I'm having a rough go of it with something I'm taking, and I can't seem to figure out what. I have this constant phlegm in my throat where my larynx joins my esophogus, and I can't seem to cough it around or clear my throat. It just sits there. All day. Sometimes, when it catches me off guard, the feeling can make me a little panicky for a second because it's a little choking feeling. I've stopped the AOR 3 for two days. I figure I'll use a process of elimination for with all three - AOR 3, Primal Defense Ultra, and Prescript Assist. I'm pretty sure it's one of the three because this didn't start until I began to take all three of these about eight weeks ago. It's taken me this long to suspect the probiotics because it's been allergy season (Pacific Northwest is allergy central) and we've had some spring colds. Now that others are starting to feel better, and get some relief of their allergies, I'm wondering why I don't.

Anyone else mentioned this? Could this be some kind of gut-healing thing?



Natalya said...

w the AOR 3 my experience is that there is a cumulative effect: Day 1 w a bit of a cap is OK, day 2 OK too, but by day 3, w just a little, it is too much. Yea, lots of farts, totally uncontrollable and smelly. And then it takes several days to subside.
I too ferment veg, beet kvass, kombucha, and sometimes ginger beer. Have kefired coconut water in the past. The ferments don't have the same effect.

Dr. B G said...


Has your wife had a functional medicine workout to get at the root cause? Wahls talks about mercury and chelation. I wish she was into the gut but her approach for toxins is sound.

What is in Emma's guts? Vipers? What's missing, obviously the AOR 3 strains.

As Natalya says, keep at it. It will break thru. Titrate slower if uncomfortable and painful. Reduce the fiber. What RS and fiber are y'll taking?

At some point you need to broaden the fiber spectrum to get the ultimate benefit from probiotics, fermented foods and the native indigenous gut flora.

Dr. B G said...

Thx Tim,

Yes you eat plenty of dirt -- shoveling chicken poop, hauling dirt covered wood, etc -- which are rich in Bacteroidetes but the Lacto in frozen (dead) sauerkraut may explain why the Lacto is not as high as good/should be on the GDX stool testing.

For urban folks like me, we all struggle to get it all in.

I'm so grateful that technology allows high quality supplements like the current SBO probiotics on the market and other tools to achieve ultimate gut health and longevity.

Dr. B G said...


Thanks for your comment! I dunno! "I have this constant phlegm in my throat where my larynx joins my esophogus, and I can't seem to cough it around or clear my throat." It sounds like a shift in immunity is occurring or an allergic reaction (hyperimmunity).

Did you have a reaction with potato starch as well? More joint aches?

If so, this indicates to me likely Klebsiella have overgrown in the small intestines, and likely other 'vipers'.

Dr. B G said...


Thx so much for your story. Fiber can't feed what isn't there, no?

I love the advanced testing available because so many guts are wrecked by antibiotics, stress, poor diets and pharmaceuticals/mercury.

Everyone is affected. I'm sorry you had MS at age 30. That is unacceptable.

Hate to tell you but flaxseed and chiaseed may cause gut problems. i don't know if it's the lectins or what. A lot of people don't tolerate well.

Consider a spectrum of fiber:
--modified citrus pectin

I appreciate you sharing the AOR-3 info and experiences. I think when a vital 'niche' returns to a dysbiotic gut, there is rumbling and minor unhappiness until things settle out! Please continue to report your progress.

Ann said...

Dr Grace, what do you mean by broadening the fiber spectrum? Am I doing myself any good with Acacia fiber? Sometimes the psyllium husk seems a little harsh, and gives me some IBS type symptoms.

Yes, the potato starch makes me achey all over. Makes me schizo for a day as well. Weird thoughts and feelings. I feel "safer" using plantain or green banana.

How do I deal with Klebsiella? Other vipers?

Thanks Dr. G.!

Webraven said...

Dr BG-
Would you please expound on what you said about Klebsiella above? My RS experiment lead to just that- I went from my " normal" state of bloated and C'd to very inflamed and achy, joints, especially ( gave me a LOT more compassion for my old, achy clients)!) with lots of fluid retention, and with an exacerbation of my pre-existing Sxs in just a week of 1/2-1 tsp of PS and later plantain flour. Achyness slowly decreasing after stopping RS supplementation and SBOs. Does this change how I should oh about it at all?

Dr. B G said...

Ann and Webraven,

There are many wonderful ways to weed out the vipers until the ecosystem can recover appropriately.

--introduction of viper-predators (eg SBO probiotics -- L plantarum, AOR, RxAssist, PrimalD Ultra, etc)
--bentonite clay
--activated charcoal
--oligosaccharide and soluble fiber (arabinogalactan, inulin, pectin, etc)
--g banana flour
--walking/exercising 20 min after meals

Have you read my story?

Acacia is not a food I believe our ancestors commonly consumed, neither is the seed that psyllium is made from -- therefore it's been nixed out of the protocol in favor of more whole food substrates. Acacia is a gum as well and I believe there is research that may implicate it exacerbating lectin toxicity.

Ann said...

Dr BG. -

You mentioned Kebsiella, but that didn't show up on my MM GI Effects 2200. What was high was Fusobacter. Can this be treated with the botannicals?

I am interested in using some of the botannicals you mentioned. Berberine, for one, but I'm also curious about Grapefruit Seed Extract and Olive Leaf Extract. I'm reading that the GSE doesn't have a huge impact on good bacteria.

I've tried Oregano, and won't use it again.

How do I schedule a consult with you? I am going to have another Cortisol Stress test done soon, and hope to do food allergies at the same time. Would love to consult about my MM GI Effects 2200 results, and hopefully the results of the adrenal and allergy tests as well.

Thank you Wise Goddess!!


Marcus said...

Hey Natalya, Tim, Dr BG

We have tried to follow the basic protocol from FTA / your healing the gut post and are taking about 3 Tbs of RS and 1 Tbs of Psyllium. We are also eating a lot of fermented vegetables (almost daily) and taking Primal Defence.

Few more details

Emma runs a good bit. She has just done a marathon and previous big attacks have been around this level of running but usual levels of around 30 to 60 mins 5 times a week seems to be health supporting.

Emma also walks a lot - no driving licence and three kids so the walking part of the equation should be well covered (on her part at least).

Emma had lots of nasty fillings - they are all gone now and have been for years. There was also a lot of gum inflammation but again, with the removal of the fillings and our paleo lifestyle that has been much improved for years now. I had hoped that all the sweating from lots of running would deal with the metal problems.

Historically Emma had terrible blood sugar control and would crash badly if had not eaten every three hours or less. Paleo, higher fat style eating seemed to deal with that mostly though so that has been okay for a good while now.

So, my plan was to shoot for the obvious and continue the RS + probiotics + fibre and introduce the AOR Probiotic 3 and then the Prescript Assist but AOR P3 ended up being a bit of a bump in the road.

The experience for both of us was much as described and we could actually hear our stomachs gurgling after taking the P3.

My plan now is to continue with the PS + Psyllium + Primal Defence and to slowly add in the P3 till it is manageable. If that takes weeks to add a bit in, back off and add it back in again then so be it.

When that one is well established / tolerated I will add in the prescript assist and hopefully by then that will be an easier job.

Long term I would hope we could just take a couple of these probiotics a week to make sure everything stays topped up with daily fermented vegetables and potato starch.

We are in the UK so the whole functional medicine thing is not so easy to do here. We have managed to keep the MS at bay with Paleo but this seems to add up for us. If the MS is due to the gut and a lack of butyrate and repopulating the gut with this strategy will fix that then... well, it offers great hope and is worth a few uncomfortable (and smelly) weekends experimenting. I am prepared to give this 6 months to a year but if we get stuck or dont see results then I guess it's time to look into a functional medicine doc or evaluation.

As a side note I also have an autoimmune disease - only psoriasis but I have found it a useful marker for self experimentation. That is also much improved on Paleo but not 100% gone. A simple bit of soy sauce or alcohol will make the remaining tiny patches on my ankles tingle and redden.

A few questions and clarifications:

Is 1 Tbs of Psyllium - is this enough fibre?
Do we need the green powders you recommend?
Should we try clay or charcoal?
Should we try any anti fungals etc?

I like to try and get the easy wins out the way first but am happy to take any guidance you can offer for simple tweaks.

Thanks all - glad to be part of this wonderful meta experiment! :)


Webraven said...

Thanks for sharing your story, dr BG,
I've had Merametrix done and like yours it shows pancreatic hypofunction ( perhaps due to hypochlorhydria?) . No pathogens, but lots of fungi, taxonomy unknown. Whether that's worse or better than C. albicans, I don't know. Clostridial overgrowth. Terrible reaction to SBO/RS. Symptomatically, i clearly have Very Screwed Up Gut Syndrome, no doubt. Either that, or I'm pregnant through immaculate conception :-/..

Like many here I'm a bit unclear on whether you recommend antimicrobials first ( for how long approx.?)
or used concurrently with SBOs?

Thanks for your thoughts!

Deb said...

Hey there,

Well, I am here to report I have a low WBC and am tolerating Primal Defense Ultra, AOR Probiotics-3 and Prescript-Assist. I also have 2 other probiotics in the mix (mostly bifidos) and take 1 per day, along with 1T PS. So far so good, but is there anything I should be on the lookout for? I would love to see the stories of autoimmune disease turned around, if you have the link!


Natalya said...

Hi Grace,
Appreciate the pointers about fiber. I'll try some of those others.
In the mean time I have Aloe vera growing outside, not sure if the main fiber in that is "Aloemannan", and therefore related to "Glucomannan"? Do you have any experience w using fresh Aloe vera? Some people call it a laxative, but others say it is a gut adaptogen.
I can also easily get the red algae, Irish Moss, which I know is rich in carrageenan. Any thoughts on Irish Moss?
The Genova 2200 is fascinating. I had Biohealth 401H done, which is basically a parasite screening, apart from the amoeba Iodamoeba butschlli, the only thing the test noted was that I have a high concentration of E. coli. But I believe it is from the German probiotic, "Mutaflor". Which is a single species, E. coli Nissle 1917. For awhile I cultured yogurt w Mutaflor.
I'm not in the States, but I think the 2200 is still doable. I see you can 'self test' it through Direct Labs. Course you also have to 'self pay'.
Thought I'd try just a tiny bit of the AOR 3, slight rumbling and happily hot-farting away!
Thanks Grace.

Natalya said...

Hi Marcus,
Personally the AOR 3 has been the only probiotic that made me back off big time. Not sure what this means. I did however notice an effect from both Body Biotics, as well as Prescript Assist. Nothing like the gut rumbling and gas of the AOR 3. With the Body Biotics I had an ever so mild flu like feeling for 4-5 days. I didn't notice anything w the PA until I cleaned up my diet. Then the 1st time I took it I was extremely nauseous, but now it is no problem. So, u may want to try a tad of the PA, it might be easier than the AOR3, but still offer something.
Speaking of psoriasis, did you read Mr. Heisenbug's post about psoriasis and L. plantarum? I used to have psoriasis too, it is mostly gone, but I thought I'd add L. plantarum to the mix. Although I think it is in Body Biotics.

witteband said...

Thanks for sharing this information, it' awesome.

I'm currently taking Prescript Asist, Primal Defense Ultra and Primal Defense (wrong order). I'm still waiting for AOR-3.

The 'problem' i experience is: I get a sore throat, snotty nose and start sneezing after taking this pro-biotics. From your comments I understand this can be vipers.

What I don't understand is it smart to keep taking the pro-biotics and let my immune system figure it out? Or stop and start taking some activated charcoal to combat the vipers?

Thanks :)

witteband said...
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Tim Steele said...
This comment has been removed by the author.
Dan P said...

How can aor probiotic-3 be recommended three times daily on the bottle if it causes such a strong reaction? I have added 2 a day to 1 rx assist, and after a couple days I seem to have strong die off. I get real bad blood shot eyes with some ab distention. Is this from the die off and biofilms release of bad guys?

Dan P said...

Update. Three bowel movements this morning in about an hour. 1st well formed, 2nd slightly loose, third very loose. Urinated about 5 times. Stomach is completely flat. Any thoughts? Is war being won on biofilms and continue slower. Is there any histamine connection with either probiotic as a cause of blood shot eyes, but with no nasal congestion would have me believe toxin release from biofilms.

Dan P said...

Dr. BG

I just saw that you have a Pharm D. I do as well but have not taken NAPLEX as I discovered late in the game my extreme philosophical difference with allopathic medicine and pharm industry in their approach to treating diseases with drugs and not diet and lifestyle modifications. Most scary and alarming is the use of multiple classes of drugs for treatment of mental health conditions.
Any suggestions with a career path for a Pharm D without board certification. Should I take the time to study and get licensed, and I opened an integrative functional medicine pharmacy where would prescription drugs even play a role?
Thank you!

Kyle said...


I've been to a number of doctors over the past year, and I've had many tests done, all leaving me clueless and hopeless. Initially suspecting SIBO, I had requested that my GI send me for a lactulose breath test. I requested it.. not him, despite my symptoms similar to SIBO - bloating after eating, belching, stomach pains, and muscle weakness primarily in my thighs when walking (not sure if the last is related to SIBO, but I have thigh pain only when walking that goes away at rest).

I don't have the results in front of me, as I took the breath test last August, but I was told it was negative for SIBO. I don't recall the levels, but I can get those. I also went to see an ND who suggested I take the Metametrix stool test (the comprehensive one) to check for parasites, candida, etc. My levels came back normal, with the exception of a +3 yeast, but it didn't specify what yeast.

We moved to another state, so I took these results to a Chiropractor/Chinese Medicine Doctor who said I may have Candida. I then took another stool test using Diagnos-techs (Expanded GI Panel). Got results this week and although most levels were in normal range, and it showed no yeast isolated/no parasites (I was sure I had something), it said there was mixed flora consisting predominantly of Nontoxigenic E.Coli (Heavy Growth) and Enterococcus faecalis (Moderate Growth). Also, my intestinal lysozyme was a 7, with the normal being below 6. Elevated lysozyme indicates an ongoing colonic inflammation. Not sure what all of this means, but we went back tonight to discuss and he suggested that I may have SIBO.

Based on the results I just stated, are these indicative of SIBO? I'm sorry, but I don't know how to interpret this stuff, and he didn't seem 100% confident when saying I had SIBO. As I mentioned earlier, I've been to a number of physicians, including GI specialists, and no one has been able to help me. I've become very depressed and hopeless not knowing what is wrong with me and how to fix it. My wife and I began eating Paleo/Primal last year, we make our own kefir, we try to eat primarily grass-fed and pasture-raised meats, grass-fed butter, lots of vegetables, fruits, nuts, non-gmo foods, etc, yet we haven't seen great results. She also had a stool test done and our results are very similar, but my comments above pertain only to me.

If I do have SIBO, I plan to follow the 7 step protocol in hopes that I can regain my life. Thank you very much for your help.

Debbie said...

So, Tim. How do we know when we no longer need to take the SBOs? I have been using Dr. BG's protocol - mixed in homemade kefir - for awhile, and my constipation is pretty much gone, which is a miracle. I've had it big time for years - since I lost 80 pounds - which was a good thing, but I stopped going to the bathroom. I'm still not really thin, so I keep hoping healing my gut will magically - along with my pretty excellent paleo/perfect health diet - will cause me to drop those 10 more pounds. Since I'm 58 and of the sturdy build type I have a feeling this is as good as it's going to get, but still I hope.

If one feels generally pretty good and the digestion is pretty good, is that it? Should those SBOs be in there, so that the PS and lots of vegetables, including fermented, will do the trick going forward? Thanks so much.

Tim Steele said...
This comment has been removed by the author.
Debbie said...

Thanks, Tim. One thing I didn't mention - my energy levels plummet when my weight drops past a certain number, and that just happened. I thought healing my gut might prevent that; I'm wondering if this has to do with stomach acid and digestive enzymes and stuff I'll never know about. I thought the fermented vegetables would be enough to spur the stomach acid. We're not talking skinny here - I still look fat (here in New York, anyway). I wonder if I am not properly digesting protein? I make my own kefir, but buy the fermented vegetables. I will start making my own soon. Thanks again. Your niceness is really nice - much appreciated.

Debbie said...

Oh, one my question, Tim. I've been doing the protocol with kefir - about 8 ounces - instead of water, and then drinking a lot of water after. So, the drink is pretty thick. Is that okay? would plain water work better? The protocol has been my breakfast for about two months.

Debbie said...

Tim, I was reading some of your earlier posts here, and am wondering why, if you don't make kefir daily for the lactobacillus?

lisao said...

Acacia is high in arabinogalactan and has studies showing it to help bowel disorders

Lily W. said...

hi Tim and Dr BG,
First off I can not thank you enough for sharing this wealth of information.

My temps went up from 97.7 (for many years) to 98.6+ immediately after starting potato starch with psyllium husk powder. The BEST PART is every other approach (including coconut oil and sauerkraut) I have taken that upped my temps up also drained my adrenals to such a degree that I required a boatload of supplements to keep everything from crashing and none of that has been necessary this time. Whoo Hoo!

I do have a couple questions and I MUST APOLOGIZE because I am betting somewhere these have already been answered, but after reading all of your posts on different blogs on RS my brain is mush.

First off, I am currently on Prescript Assist and I just bought Probiotic 3, Primal Defense, and Body Biotic.

Rest assured I will not start them all at once, but is it ok to add them one at a time to the other SBOs I am acclimated to or do they compete in the gut?

Also, like Dr BG, I had my amalgams removed and did a ton of chelation. Chronic fatigue has been my overriding issue all of these years so I am REALLY EAGER to try the strain that was mentioned above in the article that had success with Chronic Fatigue.

I might be confused but is the strain called "saprophytic mycobacteria/SRL 172" and if so, do you know what product includes this??

Thank you again SO MUCH for being pioneers in a field that is so ripe for discovery and might hold a lot of healing for many of us.


Dr. B G said...


I'm so glad to hear of your adrenal and gut successes! You've noticed they do indeed go hand in hand for many. the gut surface area is soooooo immense and drains the adrenal function when inflamed and consistently broken.

I see actually many people taking several brands together. I think this mimics natural exposures but any route can be beneficial -- rotating, resting, staggered, etc. See what works for you in the beginning but it may all be dynamic and keep shifting.

saprophytic mycobacteria/SRL 172 -- not familiar with a brand or product yet. Let me know if you find anything. Dirt carries a load of saprophytic mycobacteria, which classic gut researchers refer to as 'ye old friends' lol.

It is great you targeting optimal gut health because this will help to chelate in the end as well. controlling yeasts and pathogens can be a pivot point for many as well.

Please let me know your progress. Would luuuurve to hear your updates, questions or further challenges!

Lily W. said...

I DEFINITELY WILL keep you updated!!

A rather curious detail, I was told to try Prescript Assist 7 months ago and one day the capsule broke open in my mouth and it tasted like the sweetest dirt in the world. From then on I broke open the capsules because the flavor was so delicious to me.

A couple weeks after starting this habit I remembered reading about pregnant woman craving dirt.

I am ALWAYS ASTOUNDED at how much our body's impulses are TRUSTWORTHY and still shines through after so many years of poor choices. Long ago I lost faith in my hunger after eating a bag of Cheetos and other crap foods loaded with things that pull us astray. :)

Seriously if Prescript Assist was in my back yard, I would make myself a bowl full and smile like it was candy!!!

I wonder if the dirt our feet are exposed to makes its way to our gut in any real fashion. I always read how we can get bugs through our feet and should always wear socks, which I never do.

Thanks again! And if anyone figures out what brand/strain was used in that reviewed paper for Chronic Fatigue Syndrome that is mentioned in this article above PLEASE share. I need to give it a ride.

THANKS AGAIN AND AGAIN for your generosity of information!!!


Anonymous said...

Thanks for sharing your knowledge I need help living in the modern world of hygiene and keeping healthy guts
I cant stop thinking that when I drink my morning bionic smoothie Im whisking some of the minty fresh commercial toothpaste deep into my body. Would Xylitol or just salt water be a good tooth/mouth protocol? Im just looking for kind of a rule of thumb on this. Thanks again.

Paul Ennis said...

I have just purchased PA for myself and my young kids (after a dose of antibiotics for our 16 month old). I decided to get it after all the rave reviews it has been getting but delving into it further I have become a little anxious about following through with the kids. A fellow by the name of John Brisson has been advocating not to go near it I would love to know your take on his view of PA esp. the the idea that the strains present in PA are not native to our gut, the potential for a microbial coup d'etat and the establishment of a mini evil empire that may lead to us requiring the equivalent of antibiotic napalm to rid us of the takeover. Many thanks!

Tim Steele said...
This comment has been removed by the author.
Dr. B G said...

HI Paul,

Thanks Tim for your deep thoughts and ideas.

I like John Brisson and his protocol. I like also GAPS, SCD, VLC and paleo because they all have immense roles in healing the gut in different ways.

Did you watch the AHS14 talk about the ancestral core? No, none of the ancestral core are in the PA probiotics however in terms of functionality, about half of our gut is Bacteroides and PA contains several strains of healthy Bacteroides. This is why it has been so effective for many with broken guts -- it literally mimics our ancestral gut. Bacteroides actually shares functionality with Clostridia as well -- so in some folks I suspect this one probiotic PA can impact the entire gut because it is 29 strains of a collaborative community of probiotics, ones that mimic our ancestral core.

The contraindications for all probiotics (except perhaps bifidobacteria), raw foods, live cultures, uncooked meat are
--low white count (WBC)
--immuno compromised state (like Tim mentioned ICU, HIV, cancer, etc)

Paul Ennis said...

Thanks Tim and thanks Dr BG your response is very much appreciated! I really respect your opinion it's just that I had a little bit of a speed wobble when I came across John Brissons info.

I myself have no problems at all taking PA, I'd eat Kiviak if I thought it would help my gut, it's just that I do not want to take any unnecessary risks with my children. Would you guy's have any concerns giving a 16 month old, lump of a chap, PA? He has just finished 7 days on an antibiotic and I would like to give him a decent probiotic. Should I begin with the usual Lactobacillus & Bifidobacterium strains first or does it matter?

I would also like to bolster my other two kids immunity now that school has started (young kids swapping snot and sharing food from off the floor plus the cold damp weather is coming). I live in Ireland btw.

I have to say that you guys have a great resource and I am delighted I stumbled across it, thank you for sharing your knowledge, Paul.

Tim Steele said...
This comment has been removed by the author.
Dr. B G said...

Hi Paul

You're welcome. My kids are much older 13 and 15 but my best gal pal gives part of capsule of PA to her 16 month daughter with great results. She used also the children's lacto (sorry -- don't remember which strain), a standard one. Now her daughter can tolerate dairy! previously any milk, cheese or yogurt my friend would consume, her baby via breastfeeding would get rashes and skin breakouts. All gone! I don't know which probiotic did it. She also did more fiber -- bananas, fruits, yams, and raw potato starch (just a smidgen on her finger daily). Mom took probiotics too.

Antibiotics can really wipe out the immunity via destroying our good commensals. C difficile is a potential renegade. One study show Bio-K (lactobacillius acidiphilus + casei) prevented C diff by almost 20-fold.

S boulardii is also 'proven' to maintain more of the baseline flora and fights candida which often flourishes after antibiotics wipe out our good symbionts.

Dr. B G said...


You're awesome. Nice new avatar lol!!

Tim Steele said...
This comment has been removed by the author.
Dr. B G said...


Looks familiar... ahah like my grand uncle

Hey I've heard of bacon juice being used the same way. But it wouldn't be as a great a synbiotic as the dirt off the E. potato and microbes from mom's mouth!

Paul Ennis said...

Thanks guys for your advice. The info you presented is great, very reassuring.

I just watched the AHS14 talk, fantastic info.

I will look into S boulardii and my little ones already get plenty of homemade yogurt and play outside. I let my smallest fella eat dirt, just a little (can't stop him really lol).

For anyone else interested I contacted the PA website and here is their recommendation "After a round of antibiotics, our practitioner's are suggesting one capsule with breakfast and one with dinner for thirty days, and then just one capsule for dinner for the next thirty days. And yes, you can give it to your four and six year old. If it is just for maintenance, then one capsule with dinner is fine. If they experience any gas, bloating, diarrhea or constipation, it will be short-lived, and is simply the PA getting rid of bad bacteria".

I'll probably just give half a capsule in some yogurt.

I will be starting the bionic fibre regimen soon and I will let you know how I get on. Thanks again guys, you have a new fan!

Dr. B G said...

HI Paul

Thx for your viewing! Tim just posted an essay about the devastating effects of antibiotics:

Good luck in your gut health forays and adventures!

Allan Folz and his family started potato starch in locally sourced, I think, ancestrally made yogurt.

He's got a great blog about the experiment with his children.

For my 13 and 15 yo, I have to do stool and urine testing. Just looking at them, seeing their behavior or poops, sadly, don't tell me enuf about their gut optimization. We've all had boatloads of antibiotics. Just a bad legacy I passed on to them and I think being a pharmacist, I overused pharmaceuticals.

Fortunately we are lucky to have Prescript assist, local organic farms and wonderful produce around in California that make the gut recovery much easier. Hope Ireland has these sources open and accessible to you as well. We adopted this farm! I do hope you can find a great FARM-acy too!

Aaron Kaskowitz said...

Doc! Can you suggest something to help me get my levels of prevotella up? I was tested last year, using a uBiome kit, and my prevotella was .34% compared to average healthy omnivores at 7%. HUGE difference.
Think this is related to my multiple sclerosis? Any other suggestions for me?

I'm having a tough time. My mouth gets sore and inflamed when I take potato starch and probiotic 3. I believe they're linked to this reaction, at least.

I'm trying to take prescript assist. Hoping that and the 7 steps diet will help.

No sugar. No starch. No fruit other than a little bit of berries. Sound good so far?



Dr. B G said...


MS is distinct gut profile
-- missing bifido, good soil probiotics
-- excess vipers: yersinia klebsiella enterobacter candia and/or others

Have you read this? Potato starch throws fire on this profile above. Starches can too -- that is probably why you are faring well but it doesn't fix the root problems (mercury, vipers, missing gut allies).

Dr. B G said...

(also there may be no advantage to Prevotella -- I was wrong. It is just an enterotype. In fact, high prevotella in the face of suboptimal gut health may be overgrowth.)

Aaron Kaskowitz said...

Thank you so much! Your thoughtful response makes a huge difference for me.

Follow your 7 steps
Take Prescript Assist and Primal Defense
Add in more inulin sources: garlic, onion, chicory
Eat a bunch of cooked-cooled potatoes


Rebecca said...

I am strictly on the Paleo Approach AIP diet (7 weeks now), with good starches that you recommend. 2 weeks ago I switched from my ND recommended Lacto bacillus/Bifidum probiotic to Prescript Assist (SBO). Bloating has increased and gas is so so so much and smelly. What can this mean? I keep thinking I'll wait it out and keep taking it but I don't want to hurt myself and my family is suffering so much with my gas. Not sure how to proceed since my ND wasn't keen on me switching probiotics. I have advanced Hashimoto's and seem to lean toward TH2 immunity. Thanks.

Dr. B G said...


Sometimes the shifting is just gas. What does your stool testing and urine show? IN autoimmunity various opportunistic growths are implicated and the good symbionts including soil probiotics are missing. Did you read the autoimmunity post yet?

Helping the opportunistic growths to exit the upper gut will speed recovery. Some people with Hashi's have Proteus, others Yersinia. I probably had Prevotella when I had Hashi's -- because it still shows up on my testing! Candida is typically indicated too. Prevotella feeds on potato starch, regular starches and grains, that is why AIP is helpful until these populations are improved.

Don't forget gut support -- acid, digestive enzymes, etc (step #7). These are important to initiate the flush of overgrowths from the upper gut.

Good luck!

muppet said...

Could one use the amazing grass chocolate instead of the high ORAC? It's just that the chocolate tastes so much better. I know that the antioxidant part is less but wouldn't the chocolate blend also be considered an antioxidant?

Dr. B G said...


Certainly of course! Chocolate powder is a prebiotic also for bifidobacteria and other symbionts!

AG is just one flavoring agent because psyllium tastes like cr@p to me. Id love to hear how it works out for you

muppet said...

Thank you! So after doing more reading and listening to your interview with Asrey, I realize I need a more general probiotic to go with my SBO probiotic. I know it should have b. Longum in it. Are there any you recommend? Should I go with one with a lot of strains or one with a few strains? Thank you!

muppet said...

And yes psyllium tastes horrible. I just got the acacia gum to use. I was a faithful PS user for almost a year! It super helped with constipation but now that I have stopped using it, I am having problems again. I am going to weed and seed ala your seven steps. I was raised by two doctors so I have been raised with a lot of abx. Plus just a bad diet.

Dr. B G said...


I'm like you -- carpet bombed gut.

Have you done any GDX or ubiome gut testing?

This is working wonderfully for a friend

It's B longum BB536 10 B per cap.

Constipation is multifactoria -- too many methanogens, not enough inulin/OS rich foods in the diet, sometimes a mineral/magnesium deficiency

When the gut is broken, mag isn't absorbed via the gut. Need to go topical with mag oil or sprays or Epsom salt baths. Very super soothing too!!

Sulfur rich vegetables will shift out methanogens. (some people report great gut results and resuming gut acidity with Opti MSM (hat tip Christie!))
--all brassica family
--garlic, onions, leeks (also inulin rich of course)

Let me know what works for you.

Tayleepoo said...

Doc BG-
Youre such a kind soul for all that you do. Youre saving lives, gad damn it :)
Like the hundreds of people youve helped, ive been on vlc for literally 6 sugar, no fruit, no starches, literally eaves and hardly any roots either. :(
Ive had constipation my whole life, i think mainly due to having a strong uncomfortablity issue with pooping when i was younger. I always had to wait for family to be asleep or not home.. Id hold it for a week or longer! Anyways, had ezema and lactose intolerance at a young age, dealt with bloating and all that for years. Anyways, about 6 months ago, after being put on prilosecfor two months.. i hate conventional doctors for this and hate that i was ignorant at the time.. I lost all enzyme, acid, bile output.. went on gaps for month then vlc from there. Eventually not even able to eat meat, still scared to try fruit.. btw, i take enzymes, ox bile and hcl every meal..
My liver is having issues, ive developed histamine intolerance, recently found tapeworm infestation, and sibo. I have hypothyroidism and AF im sure due to stress ans vlc... and built up homocyctine, lack of methylation and glutathione! I noticed when i eat sulfur foods i get crazy sulfur gas.. is this possibly due to sulfur reducing bacteria or methylation issues? I need sulfur in my life! My meals are so damn bland. So my biggest question is, due to too much lactate forming bacteria, I cant do fermented foods plus i have a histamine reaction.. Im feel Im pretty immune compromised with the liver, adrenals, and thyroid issues.. I'm nervous to start SBOs. Should I try a bifido? Should take them orally or enema? I actually just started incorporating rutabaga and parsnip a couple days ago and ive had a bm every day since! A little on the soft side, but with the anti parasitic and anti microbials, i think its much needed. Please, give me any advice you can. Im a lost 22 year old who's read waaaaaaay too much info on this and of course, conflicted between 20 sources. Although, you and PHD seem to be most suiting. :)
Thank you.

Dr. B G said...


Have you had gut testing (urine and stools)? It's great if you know what you're targeting. Hang in there. Your story is all too common. Why don't you post on a newer thread and hopefully people can chime in! I love Paul and Shou-ching and PHD!! You're in the right frame of mind I believe

Anonymous said...

Hello, I'm a mom of two autistic young women (21 and 17). Everyone in our family experiences IBS. I don't tolerate folate well and interestingly enough, my dog was recently diagnosed with SIBO (exocrine pancreatic insufficiency) and he had high levels of folate, which is an indicator of SIBO. He was unable to absorb proteins and fats and is now on antibiotics and a low carb diet and he's greatly improving.
I've been reading as much as I can about how to deal with SIBO for our family so I'm grateful to have found this blog and comments. Diet is going to be challenging for my ASD daughter since she's highly picky and also 17 and she loves junk and there is no way I can ensure any dietary compliance outside our home. However, I do plan to follow suggestions on here with great hope. I was also kicked into perimenopause at age 36 and wonder if there were any relationship to SIBO.
Is exocrine pancreatic insufficiency and SIBO a chicken/egg thing? Does SIBO cause pancreatic insufficiency or vice/versa? Does anyone know if the SIBO is cured then does the pancreas recover? Thanks for reading.