SCD Probiotics – What You Really Need to Know

A few months ago I was listening to a podcast by Chris Kresser and he said something that shook my “etch-a-sketch.”

You know what I mean right?

I use that term whenever I learn something that erases everything I thought I knew and leaves behind a blank slate…

Here’s what he said (paraphrased):

“Humans have ten times more bacteria than human cells in their body. So a common saying is: we’re more bacteria than we are human.”

Crazy right? What if our bodies are just puppets to carry bacteria around?

Yeah I know – I’m coming back to earth, but it’s something to think about for a minute…

If we have 10x more bacteria growing inside us than human cells, maybe we should become better friends with them.

They might play just as big of a role in our health as food, air, and water. Some people refer to this as “tending our bacteria gardens.” It can be one of the easiest ways to feel better faster other than changing your diet.

Is Leaky Gut Making You Sicker?


And that’s why I put this post together about SCD Probiotics and what you really need to know.

For Starters, There Are Three KINDS of Bacteria

Each of these three types of bacteria has a different role in our body and there’s some that are more important than others.

For the sake of making it simple, they can be separated by how they interact with each other. With that said, here’s the best explanation I’ve seen about the different bacteria types:

1. Essential or Beneficial Flora (AKA the good guys): that’s the friendly bacteria we’re always talking about, like Bifidobacteria, Lactobacteria, and E-Coli.

(Yes, some strands of E-Coli can be friendly.)

2. Opportunistic Flora (AKA the bad guys): there’s around 500 various species of microbes in your gut that fall in this category.  And they’re actually controlled by the beneficial flora, so they keep them in check.

They can cause problems once they overgrow… this is the “bad bacteria.”

3. Transitional Flora (AKA the drifters): these are microbes from the outside environment, the ones you take in through food and drink or just living and breathing in the environment.

They can take hold and damage our guts and even cause disease. In this case, beneficial bacteria (the good guys) usually keep those in check and prevent that from happening.

All these types have a place and a purpose, and when they start doing something other than that is when they wreak digestive havoc in our bodies.

But Probiotics Are Something Different Altogether…

Probiotics are strains of beneficial bacteria that, when we take them, support our native beneficial bacteria.

They also help control the opportunistic bacteria from getting out of control and protect us so that the transitional bacteria and pathogenic organisms can’t take hold inside our damaged guts.

But the supplemental forms that we take are “transient” and don’t stay in our bodies for very long… something like two weeks.

So they aren’t really “replacing” what we’re already missing in that sense…

Which is a bummer, because research shows that the guts of IBD patients contain 25% fewer species of bacteria (on average) than healthy people.

So we’re already at a disadvantage…

So Who Needs Probiotics?

Well, symptoms like diarrhea and constipation are signs of “Gut Dysbiosis” AKA “really screwed up gut bacteria” – which probiotics will help with.

Remember that anywhere from 50 to 80% of the dry weight of a bowel movement is dead bacteria.

And most people with digestive disease or high inflammation are going to see a benefit from taking probiotics. As I said above, we’re running on 75% of the gut bacteria a healthy person has so any little bit helps, in my opinion.

It reminds me of our friend Jay Baluk (Chrohnsboy), who has this “burnt lawn” analogy that I have to share with you.

He says (paraphrased):

“Imagine you have a big, beautiful green lawn but you have this big circle in the middle that’s burnt to a crisp and dead. Would you just let all the weeds grow so you have this beautiful lawn and in the middle you have a big giant circle with all these weeds and nasty stuff growing out of it? Or would you do what you needed to do to re-plant the seeds and let everything re-grow?”

The Bad Side of Probiotics

Before we get into the good stuff we have to touch on Bifidobacteria. It’s a hot topic in the SCD community for the reason that it can “take over” and cause health problems in some cases.

It is a beneficial bacteria, but the problem is, it’s just not a good neighbor at times. So, sometimes it can overgrow in and of itself.

So just to be on the safe side we usually recommend avoiding it in the beginning of the healing journey, but later on it can really help…

Now onto the important part – how to get started using them.

How to Start Using Probiotics… the Right Way

Fermented food has been used for tens of thousands of years and getting Probiotics from naturally fermented foods is going to be the best bet long term…

That’s why I think Elaine was so emphatic about using SCD yogurt if you’re starting SCD. It really can change lives and heal people fast, but it has its own draw backs.

Fermenting SCD Yogurt for 24-32 hours does remove 99% of the lactose sugars, BUT… it still contains the casein protein.

And we’ve seen too many people start SCD eating the yogurt, DCCC, aged cheeses, etc. and never start feeling better…but those same people try cutting it out for a little while and notice an immediate improvement.

The best non-dairy option would be making your own sauerkraut. But if that’s not an option…

So our current thinking on it is: once you’ve been on the diet about 30 days and you’re starting to feel better, go ahead and test SCD legal fermented yogurt slowly…

In the meantime – probiotics can help you heal start healing in the absence of these other sources.

Here’s Two Steps to Get Started Today:

Step 1) Your safest bet to start healing is Lactobacillus acidophilus. GI Pro “Scdophilus” is great because it’s non-dairy, SCD legal, very high quality, and has a long shelf life.

You can find out more about it here:

Step 2) Start low and work your way up.  For example, if you go with “Scdophilus” from GI Pro Health, they have a 3 Billion CFU pill and a 10 Billion CFU pill. So you could start by taking 1 of their 3 Billion CFU pills per day and work up slowly to 30 to 40 billion CFU’s per day by moving up to the 10 Billion CFU pills.

(For best results: take them 30 minutes before breakfast right when you wake up or atleast two hours after a meal right before bed.  That’s the best odds to get live cultures past the stomach pH and into the intestines.)

Taking Probiotics Long Term…

Those two steps will get us started, but it’s a long road we’re headed down.

In Dr. Natasha Campbell-McBride’s book, Gut and Psychology Syndrome, she states:

“A good probiotic should have as many different species of beneficial bacteria as possible. A human gut contains hundreds of different species of bacteria. We should try and get as close to that as we can.”

She goes on to say, “Making sure there are strains from different groups of probiotic bacteria is more beneficial than just one group.”

So if you’ve been cruising along for a while taking 30-40 Billion CFU’s of Lactobacillus Acidophilus and you’re feeling kind of “stuck,” consider testing a multi-strain probiotic.

It might be the next missing piece of your healing journey…

The other obvious choice here is to start testing fermented foods like Sauerkraut (Wild Fermentation is a great book to get started) OR introduce SCD 24-Hour Yogurt.

After you start feeling better on SCD + Probiotics, give SCD legal yogurt a shot…

Either one is just another step along the way.

All I do know is: Gut Bacteria is like outer space – there’s still a whole lot we don’t know about it.

In good health,


Jordan Reasoner

About Jordan Reasoner

Jordan Reasoner is a health engineer and author. He was diagnosed with celiac disease in 2007 and almost gave up hope when a gluten-free diet didn’t work. Since then, he transformed his health using the SCD Diet and started to help others naturally heal stomach problems. You can check out his story here and find him on Google+, Facebook or Twitter.

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105 thoughts on “SCD Probiotics – What You Really Need to Know

  1. Avatar

    I’m wondering what you guys are recommending for probiotics these days? I’ve been on Klaire Labs Therbiotic Complete since 2012, but it’s been getting increasingly expensive in Canada.

  2. Avatar


    Love your site. Used it to start my healing journey before hooking up w my naturopath.

    I just went to a farmers market and noticed someone selling goat milk yogurt- which i have made w raw goat milk many time, the scd way. The vendor said her yogurt was runny because to strain it in order to make it thicker would remove the probiotics. I dont’t believe her as I found nothing in a quick internet search that suggests removing the whey removes probiotics. Any evidence to back up either of our theories? I have read removing the whey removes some of the sugars, carbs, and calcium.



    • Avatar

      HI Lara – straining often removes the liquid on top which is the whey protein. (this is what they do to greek yogurt to make it thicker).. I don’t have any research that shows the straining process is removing the probiotics:)

    • Avatar

      HI Lara – straining often removes the liquid on top which is the whey protein. (this is what they do to greek yogurt to make it thicker).. I don’t have any research that shows the straining process is removing the probiotics:)

  3. Avatar

    Your site has been so helpful since Celiac diagnosis 5 years ago. Thank you! Have been making coconut yogurt in a Hotpot pressure cooker for probiotics. Easy and delicious w no milk products of any kind. Danielle Walker of Against All Grains developed the recipe for anyone interested. just google for recipe.

  4. Avatar

    Hi guys,

    I’ve been healing through diet (scd, low fodmap, etc) for over a year now. I haven’t taken any probiotics (except for eating sauerkraut) for ten months after learning that I had a SIBO issue. Now I’m very scared about re-introducing any probiotics but I think it could be a missing piece for me. Yogurt isn’t an option for me right now. My naturopath recommends Apex Sibiotica and it’s apparently specially formulated for SIBO however I’m confused because it contains lactobacillus caei, bifidobacterium breve and lactobacillus plantarum and these are not what’s recommended here. I see this post is from 2011…. I’m wondering if you have any new/updated information on probiotics for SIBO/ibs-d?

  5. Avatar

    I’ve been hearing so much about the importance of pre-biotics and was wondering what the SCD world has to say about it. Prebiotic supplements all seem to be starches that we can’t eat on our diet. Also…have been taking prescript assist
    for a few months now, but haven’t noticed any change and am wondering if we should switch to something else. We have ASD issues and SCD diet has been very helpful! Thanks!

    • Avatar

      HI Jolene, thanks for reaching out. There is a time and place for prebiotics. For example, they can exacerbate certain things like SIBO or a FODMAP intolerance. You can test out a small amount of prebiotics (garlic, onion, banana) and see how you do. MOre research is needed to on the topic of how prebiotics affect symptoms, but it is clear that they increase our beneficial bacteria.

  6. Avatar

    I have severe ibs and constipation and have tried nearly everything. A lot of times probiotics make things worse. So sometimes it will help w constipation but make the bloating and pain worse. So more recently I wanted to try something more simple so I would know which strains I was reacting to. My diet is extremely limited and I can’t do any of the fermented foods.

    So recently I started now acidophilus and I tried pearls also. They are all acidophilus bifidous strains and I got the most disgusting taste ever in my mouth. I thought maybe it was the rebalancing of bacteria but it’s so bad I am going to have to stop taking it and I don’t know that it’s working that well anyway. I upped my dose last night and woke up with tons of canker sores in my mouth, the skin behind my ears is raw and the post nasal drip I always have is significantly worse. The taste in my mouth is like I licked toxic waste. I actually woke up and had to brush my teeth and scrape my tongue numerous times during the night.

    How do I know what to take and what my body is missing. I overdid hydrocolon therapy and laxatives due to being unable to move my bowels and antibiotics I believe are what messed me up for go. I’ve done tons of candida cleanses and parasite cleanses etc to no avail. Recent tests say I’m clear of all that which surprised me but I really think I need good bacteria. But I have no way of knowing what kind. I’ve heard of probiotics helping breath but mine is now so bad there is no way I can continue another day. I’ve tried about ten kinds now with mixed results but none the results I wanted.

    • Avatar

      It sounds like you’re having a negative reaction to this probiotic.

      Steve and Jordan recommend you spend about 30 days focusing on the diet before introducing probiotics. This gives your gut some time to heal before introducing new strains – if your gut is really in bad shape (you’re a Tough Case) you might not be ready for probiotics just yet.

      You can start addressing your diet using this free guide:

  7. Avatar
    helene wishnev says:

    My husband is suffering from UC. He has been on the diet for 7 weeks now and has shown some mild improvement although the diarrhea is still present. Our health care advisor has advised taking Saccharomyces Boulardii (probiotic 3 billion C.F.U. 2x daily) in addition to his regular probiotic with 12 billion lactobacillus acidophilus and other strains. Is this OK to take with the diet?

  8. Avatar

    Hi, I’m thinking of adding sauerkraut juice to help boost probiotics in my diet. I’m already taking GIProHealth SCDophilus which seems to work fine. I’m in a flare right now and have had to go back to the intro diet. How much sauerkraut juice would it be best to start with per day?

    • Avatar

      Hey Eve, its great to supplement your probiotics with fermented foods. However, we don’t recommend introducing fermented foods when you’re experiencing a flare-up. We suggest you wait until your symptoms have stabilized and you’ve experienced some improvement to introduce fermented foods like yogurt or sauerkraut – usually between 2-4 weeks into the diet. Then we recommend introducing sauerkraut very slowly to see how your body responds. I hope that helps Eve 🙂

  9. Avatar

    I have been trying to take probiotics for leaky gut and colon issues, and every time I take them, they cause burning to my stomach. Multi-strains, blends of Acidophilus and Bifodo, different strengths, all cause burning, some more than others. The really sad thing is that they help my overall condition and colon. I have not tried a single strain like Acidophilus yet. Why do probiotics cause stomach burning? I am eating some yogurt to get a bit of probiotic, but I think I may have an allergy to it and will to stop eating it. Any clue as to why probiotics cause stomach issues?

  10. Avatar

    So what’s the consensus on acidophillus vs bifido strains? Chris Kresser warned about taking acidophillus if you suspect SIBO. Also, Low Histamine Chef and Chris Kresser both posted that bifido strains lower histamine levels in the body.

    Dear Steven and Jordan, does any of you have research papers that support your statement about bifido overgrowth activity? As far as I know, your website and Breaking the Vicious Cycle website are the only one suggesting potential downfall of consuming bifido strains. I would sincerely appreciate your response.

  11. Avatar

    I’m new to the SCD but a I’ve had IBD for about 10 years. It has more recently progressed which is the reason I am now here. All that to say,
    I’ve been reading through the (SCD) website(s) and have some confusion. I was just reading the article about probiotics. I have been taking pretty high doses of these for years. But more recently, I realized my Brand (New Chapter) may not always be as free of things that could be harmful to me as I would like. So I’ve stopped using them. Since, I’ve stated a new brand that seems to be free and clear of potentially confounding things. But because I’m starting the SCD diet, I’ve stopped all of my supplements to reintroduce. This is pretty scary for me actually because, I’m so deficient but I’m trying to do this right.
    But my main question, I suppose, is about the probiotic issue. I do wonder why dairy is so heavily promoted for the SCD yogurt when it seems that non-dairy yogurt could be just as, if not, more beneficial because we aren’t suffering from the dairy itself. I haven’t seen this addressed anywhere. But I’m sure that doesn’t mean it doesn’t exist. I am very curious about your feedback on this. I would like to try the yogurt hopefully in the not too distant future, but (dairy) milk having been a problem for me almost since birth, I am not very keen on the idea of pushing that issue. At the same time, I don’t want to be left out of all of this healing I hear about from the SCD. I am at this point still left out of eggs and nuts too. I do have to wonder when/if I will be able to get this healing when I can’t take advantage, it seems, of much of the diet.
    Again, I would greatly appreciate whatever feedback you might be able to offer. I thank you in advance.
    Kind regards,

    • Avatar

      Hi Naima, thank you for reaching out! The yogurt provides powerful inoculation of healthy bacteria to your gut, which is necessary for the gut to heal. For those that can not tolerate cow dairy, you can try goat yogurt. And certainly, if you can not tolerate that, don’t consume that either right away. If you try either of the yogurts and can’t tolerate them, you can always try later as the gut has had more time to heal.

  12. Avatar


    I’m also in the U.K and looking for suitable probiotics, and as I am trying to rid myself of candida too, was recommended Healthy Origins 30 Billion CFU. Is this ok? Any advise would be welcome!


    • Avatar

      I think it’s really important that you get tested, and also if you can purchase the Clean Gut book by Dr Alejandro Junger, who is a Medical Doctor practising Functional Medicine, it will open your eyes.

      There are few functional medicine practitioners in the UK but if you’d like recommendations, I would be happy to help as I know a few and they are helping me tremendously after 5 years of seeing various Gastroenterologists and nutritional therapists and being diagnosed with candidiasis… my FMP has identified the root cause through very specific tests as Leaky Gut, and I’m now finally on my way to recovery.

      I was initially on VSL #3 for years along with Udo’s Digestive enzymes, Biocare’s Oregano complex, and another EcoBalance supplement…

      I definitely improved but the committment recommended by the nutritionists of sticking to the anti-candida diet for over 3 months alongside all these supplements proved to be too much, and I failed every time.

      Find yourself a Functional Medicine Practitioner, get tested and then get on the right treatment protocol (I’m now on an anti-inflammatory diet plus BioDoph 7, saccharomyces boulardii, interenzyme, betaine HP plus, and wholly immune which you can order online from

      I know how frustrating (exhausting and depressing) this search for healing and relief can be.

      I wish you much luck.

  13. Avatar


    Do you have an opinion for Soil Based Probiotics? I have been taking various different probiotics for a few months now, without noticing much of a difference. Including home made Kefir, and Saurkraut. I still have burps after eating most food types, and occasional bloating though.

    I’ve read that SBO’s are better for the gut than Lactose based, what are your thoughts?

    Thanks for a great, and informative website.

  14. Avatar

    Why is sauerkraut ok but kefir is not? Don’t they both contain yeasts? If the kefir is fermented 48hours it has same lactose content as yogurt.. Just want clarification cuz I thought GAPS was about fermented foods and SCD was not.

  15. Avatar

    What are your thoughts on Florastor? I have been on a SCD diet for 4 months after Xifaxan for SIBO. I also have fructose malabsorption. The only probiotic prior to Florastor was raw milk yogurt (24 hr cook time) and then goat milk kefir. The goat milk kefir made some improvements.

  16. Avatar


    I’ve had severe food intolerances for over 20 years and about three months ago I started on the GAPS diet from the book Gut and Psychology Syndrome by Dr. Campbell-McBride. Things started to improve after the first few weeks and I was about to move onto the second stage when I suddenly had a lot of pain and bloating in my stomach and my symptoms worsened again. I did start taking sauerkraut and I felt it helped initially but I still have bad symptoms. I initially thought it was a stomach bug but it has been going on for over two months.

    Anyway after seeing your website I would like to start on a probiotic and Betaine Hcl + Pepsin regime. I found the HCL your site recommended but can’t find the same probiotic that you suggest as I live in the UK. I’ve found a few probiotics but am not sure if these are ok or not as I have never taken them before. Anyway here is a list of probiotics I’ve found and I just wanted to know if any of these are suitable as one does have bifidobacteria as well as Lactobacillus acidophilus.

    Sorry for the long message but if you have any suggestions at all it would be greatly appreciated.

  17. Avatar

    i have diverticulosis and was just told by my doctor to take VSL#3. I took it and it caused manjor gas, bloating, pain, and diarreah! I saw that you don’t highly recommend it, and its because it has the Bifidobacteria in it right? Which you don’t recommend during the beggining stages of healing. So my question is what do you recommend , so i can ask my doctor.

  18. Avatar

    Hi guys!

    I’ve learned so much from you:-) Was curious if you could culture soil based organisms in yogurt – like Biokult or Prescript Assist – I know they do it with beans (Natto) but my kid probably wouldn’t eat Natto – or sauerkraut -actually, thinking about it, you could probably just buy some Natto at a Japanese food place and use the slime for a probiotic – probably way more potent than Biokult anyway:-)

  19. Avatar

    I’ve been following SCD just shy of three years now, and *still* cannot tolerate probiotics or fermented foods. Not because of bowel issues though–rather, they trigger massive anxiety and panic attacks. I’ve tried to introduce them several times, and always with the same results. I never in my life experienced panic attacks before I started trying to introduce probiotics and fermented foods (SCD yogurt, beet kvass, etc.), and they always go away within about two weeks of quitting the probiotics/ferments, so I’m 100% certain there’s a correlation. Any thoughts? I feel like I will never ever be able to get back any good gut flora and my gut healing has been stagnant for ages. I’m kind of at my wits end here.

    • Steven Wright

      Hey Sarah – our gut flora communicates directly to the brain so this isn’t a surprise to me. Sounds like you still have a leaky gut, likely a leaky blood brain barrier as well. I’d focus on finding out if you have any GI infections or other chronic infections in the body.

    • Avatar

      This is me! I have been on probiotics for a decade now… and have had horrible racing thoughts and irrational fears the entire time. A lightbulb went off that I was acne free and more mentally stable (just constipated with stomach pain) prior to the probiotics. Well – I finally took a week off of them and instantly regained clarity. The only catch 22 is the pain returned with the constipation and my dust allergies came back. So after a week I said screw it and went back on. The racing thoughts are horrible though. How on earth can I do this? I’ve tried all sorts of did probiorics allergen free, l-glutamine, stomach acid tablets etc. Maybe there is something else going on but I’ve done hummaworm and strict candida cleanses! Maybe TRG treating leaky gut again :/

      • Avatar

        Lisa, I have been reading post and came across yours. I also have the same thing happen 🙁 But, what I have found out is that my liver becomes toxic and as long as I keep my liver flushed with dandelion tea or milk thistle drops or drops with milk thistle, dandelion and artichoke, the panic attacks stop within 10 minutes. I now have been able to catch them coming on. I am not on probiotics as I am still detoxifying. And they did make everything worse but I think these attacks have more to do with our livers. I am currently looking for a doctor who can tell me if there is more going on with my liver but I do think I am just very toxic and it is going to take sometime to clear this out…..

  20. Avatar

    hi.thank you for a lot of help and support. ive had croghs for 28 55 cm. 1or 2 bowel movementsper 24. ive weighed 52 kilo for years and have been following scd for 4 months. i feel great eat mountains of food but still have absorbstion problems as i cant get above 48 kilos ion scd and i am looking really scraggy. the last 2 weeks i stopped scd ate loads of bread.little milk product.felt okay back to 51 kilos.but ive got terrible impertigo on my guess what
    im starting back today. whats your advise to drag me through the weight problem.i eat eggs.cheese dutch. of soup.i have your avacado shake nearly every day put dates in it. i eat at keast 4000 cal. a day. when im ons scd i have to much e
    nergy and sleep to little but im never tired. now im in bed exhausted after 2 weeks of bad foid.testing myself was goid but im going thriuh hell.
    im in a bad periode because of a divorce and its useing up alm my reserves.
    thank you for being there.your more helf than my crohnsoecialist.

  21. Avatar

    What is another source than GI PRO’s scodoffilis (which Ive been using for 30 days at full stregnth) to get MULTI strains of acidofillis and still get no Bifidus). I seem to be having trouble find one. I saw culturelle, but then saw it on the illegal list. I don’t have any issues with the SCD yogurt and have been using the GI Pro health Starter. ANY ideas or links?

  22. Avatar

    Hi Jordan and Steve. I’m sort of new to the SCD lifestyle. And lately I’ve been taking Phillips Colon Health Probiotic caps daily. They were working pretty good but now I’m not seeing the improvement I had at the beginning. I’m disappointed because I finally found something that was working and now I’m right back where I started. Do I need to switch to a different one, like one made specifically for SCD (i.e. the one you mentioned above)? Because the Phillips Colon health has potato startch in it. Thanks in advance, Claudia.

  23. Avatar

    When I developed food intolerances I went straight to Paleo. A few months in I added Dr. Ohirra original gormula probiotics and ended up with green fatty and loose stools for over two months.

    I am going to be switching to SCD.

    My auestions: I have a small ulcer at the base of my esophagus. I found out that I have low pancreatic enzymes and assuming low stomach acid as well. When I take enzyme supplements with high levels of protease, apparently it aggravates the ulcer. I have had 2 episodes where the large supplement capsule burst and I coughed up mucous and blood. I read that hcl and protease shoud not be taken if an ulcer is present.

    How can I best digest my food, and will the SCD help my ulcer heal? Any recommendations? Thank you so very much 🙂

  24. Avatar

    Great post on probiotics. I have a suspected histamine intolerance: I have all the symptoms. I know that probiotics make it much worse(I was my own guinea pig with homemade yogurt and sauerkraut). Sooooo, what’s a gal to do? It’s really a catch-22 because probiotics will strengthen my gut, but it makes my allergies much worse!!! Any advice?

  25. Avatar
    Melanie Ciccone says:

    I thought everyone in this community would be interested to read the recent NY Times article, “Do You Have the Guts for Gluten”, published Feb 23, 2013. The author has a remarkably interesting book called An Epidemic of Absence which is kind of a manifesto
    about a new way of understanding the root causes behind allergies and asthma. it feels like the picture is beginning to come into focus a tiny bit, in that folks are beginning to appreciate that this disease/s is/are multi-factoral: what is your DNA portrait; what do you eat; your biome look like (quality and quantity); how many antibiotics have you taken in the course of your life; how about your mom; what was her health like when she was pregnant with you: were you breast feed (how long); were you delivered vaginally; what is the quality of your emotional life; inflammation anyone….. it seems that a combination of a few of these is a perfect storm for a lifelong debilitating gut.

    grateful for the work of SCD and GAPS scientists and community!!!

    wonder what the general consensus to probiotic product VSL3 is?

    new to this site, not new to SCD.


  26. Avatar
    Margaret Pellegrini says:

    People with gut flora damaged by Celiac or other problems often can’t digest casein. One way around this is to take protein-digesting enzymes with dairy products. Trypsin is one of these enzymes but the general term for them is proteases. Pancreatin is one type of enzyme product which contains proteases.

  27. Avatar

    Hi all,
    Just discovered this site. I am on SCD at week 7 now. I have found it has reduced my symptoms but increased the frequency of bleeding and so the need for medication. I also find the diet, at least at first, is quiote constiapating due to its lack of fibre.

    For context I suffer from ulcerative proctitis for 21 years well controlled by saloflak enemas. My next plan of attack was to stick with the SCD and drop dairy since I suspect dairy is causing the ongoing bleeding issue. Before SCD I didn’t eat a lot of dairy while on SCD I eat a ton (cheddar + yogurt). And though dairy has never given me any perceivable issue in the past this is more than I normally eat (I ate paleo before trying SCD and basically still eat paleo but net the difference between the two diets – that is if its banned on either diet I don’t eat it). I was also going to take some anti-biofilm enzymes from Klaire labs and then VSl #3.

    But after reading this article I may change that up to taking the enzyme and 3+ gihealth and when that runs out move to 10+ and when that’s gone move on to VSL #3 (assuming all is OK up to this point). Do you think this is a good plan? Anything I maybe missing?

    My issue is if I cant eat yogurt and probiotics are all transitory how will I replace/replenish bacteria permanently? I guess its not the end of the world if I had to take a probiotic permanently if I I don’t have to take anything else. But I just want to get as much information as possible so I know what I am in for and set my expectations appropriately.

    Ultimately if this all fails I plan on trying FMT but that’s my last (non medical) resort.

  28. Avatar

    I have been on the SCD diet for two years now. I have been med free for one year. I have mostly good days but occasionally have minor cramping and slightly loose stools( not really diarrhea) I am going to try the prozymes from gi pro health and wanted to try the digestive bitters but the one you recommend has some illegal scd ingredients-such as grain alchohol. Is there a digestive bitter that is legal on SCD diet? Also, my doctor(who highly recommends the SCD diet) told me to try apple polyphenols because clinical trials have shown good results with apple polyphenols greatly reducing inflammation and symptoms of ulcerative colitis. (google it-you will find it. Love your site!

  29. Avatar

    Hi Steve
    Thanks for your advice I will try and buy Klaire Labs lactobacillus if you think they are better then Kirkman as I think they are also available from Nutricentre. When I ordered Natren products they always came in an icepack to keep probiotics cool but the Kirkman products just came in a package which made me think would they even work. I have been on the diet five months and only really start eating dairy yoghurt the last few weeks but am having D throughout the night. I am not sure whether it is dairy or bacteria I am having a problem with as I had problems with nut yogurt too. Is it ok to just use acidophilus or do you need a broader range of bacteria.
    Thanks again

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    I just wrote a whole post but I don’t see if it went through.
    Short post, I have Short Bowel Syndrome, 135 cm of small bowel left and no iliocecal valve. I was recommended protiotics by my Holitstic doctor ProbioMax Plus DF which contains both Lactobicillus acidophilus an bifidobacteria but after reading an article that probiotics and acidophilus are contradicted in patients with short bowel syndrome especially with no iliocecal valve I used it for 3 days and stopped. I have bloating, bad smelling gasses and stomach growling plus costipation. I am so confused. My GI/surgeon says that probiotics are better than antibiotics and no to read so much stuff in the internet.! I am so confused. I am 27 years old and don’t know what to do. Is the SCD diet good even for short gut patients like me? Should I not take probiotics? Please help! Very depressed living with my condition and the special diet I am in.

    • Steven Wright

      @Angie – I’m so glad your searching out more advice and opinons. That tells me right there that your going to figure your health out! Keep it up. SCD will help short bowel people and from time to time we get emails from people like yourself reporting great success. BUT the big cavate is that they do our “tough case” version. Which is no dairy, no legumes, no nuts and limited fruits. I would highly suggest you try that and check for low stomach acid. We have several posts on our blog about stomach acid and the tough cases as well as meal plans to help.

    • Avatar

      I’ve been following the “tough case” plan with reading and using the tips and tweaks in the guys SCD Lifestyle Guide; Surviving to Thriving e-book and am better than I’ve been in years. I’ve struggled with #1 bristol stools -constipation- almost my whole life. I’m on day 8 of the diet and have been having #4-5 stools since day 3 without taking anything or enemas!:) Their book really is sooo helpful in getting started and getting a plan set for your needs. I know depression can be when you feel like crap, you can do this! I feel sooo much better mentally and physically. Some die off, but the guys discuss pushing through and keeping on keeping on… I would try the diet to start. The book will help you step by step….

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    Hi, I’m not completely following the SCD diet however I’m highly interested in the whole restoring the good bacterias in my body through probiotics. I have been researching my heart out before ordering anything but the more information i get, the more confused i get.
    On the sight you recommend Pure Encapsulations Digestive Enzymes Ultra – 180 capsules from, however on this page you recommend ProZymes from GI Pro Health.
    Are they the same? Which would you recommend more?
    On the other hand, I was also looking into VSL#3 as i was recommended it years ago by a doctor, but when i asked my specialist, he told me it was a waste of time.
    You also recommend the scdophilus so i looked into that, i am at the point where i really want to get my life on track. scdophilus seems worth a shot.
    I was going to buy the digestive enzymes from amazon, and then get the yoghurt starter and scdophilus from GI Pro Health when i stumbled across the starter pack which includes the ProZymes, scdophilus 10+, and SCD Complete. Is it worth getting the SCD complete?? What benefit does it give?
    Also if i accidentally have something wrong when out, or travelling, (i usually feel quite sick within 15mins whenever i eat anything oily, fatty, or high sugar) would the digestive enzymes help with ‘feeling ill’ afterwards?

    • Steven Wright

      @ Suellan – Great questions We recommend both Gi Pro Prozymes and Pure Encapsulations ultra enzymes. If I had to pick one with a gun to my head I’d choose the GI Pro Health brand but both are seriously very good. VSL #3 has helped many but also hurt and not helped many. We are skeptical of it until your well on your way to feeling better. We see better results faster with less complications using only L. Acidophilus and like the GI Pro Health brand because it’s dairy free. SCD complete is a great SCD multivitamin, a multivitamin should be part of everyone’s healing plan until there digestion is back working. If your properly absorbing your foods, you will end up nutritionally deficient it is just a matter of time.

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    I have been searching for legal probiotics as I live in Ireland and to have them shipped from GIpro health would be to expensive so to anyone else searching I have found Kirkman Labs acidophilus which is sold on in England. I was also wondering does anyone use Natren probiotics as I have used them in the past but have stopped because the dairy free version contains potato starch and chickpea extract.
    Thank you

    • Steven Wright

      @ Rebecca – If you tried them and they were working, don’t just stop because they have some illegals. It’s one of those don’t break what’s not broken things. It might not be ideal but if it works don’t stop. Also see if you can find Klaire labs L. Acidophilus.

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      Hi Rebecca,

      I realise your post is quite old (2012!) so you might not read this, but would love to hear from you if you do. I am also from the UK and trying to find UK-based SCD legal supplements (probiotics and multi-vits especially) and struggling to do so. GIPro Health shipping is so expensive. Did you find any UK-based supplements? Would you recommend the Kirkman Labs acidophilus? I also came across the Natren website but I thought this was also US-based so the shipping rates would be as high as GIProHealth? I will take another look. If you have any advice it would be much appreciated.

      Many thanks,

      Kate x
      – See more at:

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    I am also wondering about digestive enzymes – which products are good, how much to take, etc. Also, I’ve been told that the VSL#3 probiotic pills are really good, but they don’t specifically detail on the bottle which probiotics are present – Just “Lactic acid bacteria.” And finally, I’ve heard of a strain called Lactobacillus plantarum299v, which is found in Good Belly – and that strain supposedly works miracles – unfortunately Good Belly contains gluten. Any thoughts/guidance on this would be appreciated – thanks.

    • Steven Wright
      Steven Wright says:

      @ Shannon we don’t recommend VSL #3 if your symptoms are present because it contains Bifidus stains of bacteria. We like single strains of Acidophilus. Gi Pro health makes a great version and we also like their prozymes I would start there.

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    jodie Ivanecky says:

    Hi guys.
    I was diagnosed 5 years ago with SIBO. Have done the scdiet on and off for years now, supplementing the entire time with bifidobacterium probiotics. Its only recently that I read about the possibility of it actually CAUSING overgrowth of the small intestine with bifidobac.
    I now cannot tollerate any fodmaps, and have felt all along I have been getting worse. I am on an entirely protein diet with supplements.
    If this is what has happened to me then what the hell can I do now? I am desperate!

    • Steven Wright
      Steven Wright says:

      @ Jodie – I’m confused so did you stop taking Bifido species and your symptoms got better or worse? We suggest using on Lacto. Acidohilus and really like GI Pro Health’s version. I would start there and try some digestive enzymes as well. Are you following a plan like we lay out in our book? We cover all of this in there in an easy to understand format.

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      Jodie, I feel for you. I’ve struggled for years too. I just recently bought the guys SCD Lifestyle Guide; Surving to Thriving. I also bought their book of “Hard Cases” Meal Plans. On day 8 and feeling better than ever. (Yes, some die off but that’s good.) Success is going to come along with the right mindset. The guys helped me to see this, because I was having such a hard time just getting started, because I was afraid it wasn’t going to work– Like sooo many other things I’ve tried. There is HOPE! Don’t give up! You’re on your way, you can do this. Start with baby steps; let things (bacteria) calm down for awhile. I’m not doing any fruit or sugars, just the broth, meat and pureed veggies for now. The book is really valuable and the guys have been very supportive and are truly concerned:) My prayers are with you….

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    How do digestive enzymes play into this? And bile salts? Can one safely take all three — probiotics, digestive enzymes and bile salts? And in what order?

    I’ve been taking Now Super Food enzymes, which now I realize from other comments was not at a high enough dose. What is the maximum dose if I want to use up what I have first?

    • Steven Wright

      @Jill – yes you can safely take all 3. We don’t like super enzymes because while it covers all the bases it’s weak in everything. Better to buy them all separately and adjust the dosages accordingly. We see much better results in all our clients.

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    Pamela Suzanne Brazle says:

    My Dr. asked me to take florastor (“probiotic (friendly yeast-based) not attenuated by antibiotics”). It worked for six months then my problems came back. Should I get back on them? I am totally off the GF diet because I was still having bad stomach trouble and losing too much weight. I’m going to try this. Thanks for the info!

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    Brian MacEachern says:

    This blog post has one thing that appears to be wrong. The GI pro health probiotics instructions say to take WITH food. I also thought that probiotics were to be taken on an empty stomach so when I recieved my shipment from GI Pro Health and read this, I emailed them to clarify, they said that their research had said it was better to take with meals.

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    Have you heard or read anything about the VSL#3 probiotic? I currently take that one, but it is fairly expensive and I am unsure if it is doing what it is supposed to…

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      Ruth Buchweitz says:

      VSL #3 has a sugar (I do not remember which one. but if you Google VSL #3 you can find what is in it.) VSL #3 gave me terrible diarrhea. I was improving steadily on SCD until my doctor wanted me to try VSL #3. It was a disaster.

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        i also get terrible diarrhea with VSL3. my doctor told me to take it but I could not tolerate it at all. i have been ill a very long time, with CFS/Lyme and have IBS and SIBO.

        i wonder why some are helped by VSL3 and some get worse?

        incidentally, i also get diarrhea with other very powerful probiotics such as ultimate flora.

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    Amen on being careful with bifidobacteria. I am suspecting the flare I am currently in may have been caused by taking probiotics with bifidum in it. Back to Acidophilus it is!

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      Actually, I’m stunned that you’re recommending acidophilus, as it’s the strain that is SPECIFICALLY linked with high d-lactate levels and lactic acidosis. Multiple studies back this up.

      A bifidus-only strain will clear up FODMAPs issues.

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        I would also like to know the answer to this poster’s question. I just read Steve’s podcast with Chris Kresser ( (search D-lactate) where Chris says specifically to NOT take L.Acidophilus if you have SIBO, but you guys are specifically recommending TO take it (and therefore I’ve been taking it for the last month). Would you mind please explaining your and Chris’s differing views on it? I’m going to order Prescript Assist next since you both seem to agree on that one as helpful, but would still like to understand the differing perspectives. Thank you!

        • Avatar

          I think that Elaine Gottschall (author of the SCD book Breaking the Vicious Cycle) recommended starting with L.Acidophilus & I think that is probably because at the time it was the most researched & safest probiotic around. L. Acidophilus is about as community-minded a bacterial strain as you will find.

          Also, I have just found this:-

          “Elaine spent a year doing library research on probiotics and realised that the whole area is very iffy. The one conclusion that she came out with is: “That Lactobacillus acidophilus had been shown to be very helpful for many schizophrenics, bowel patients, etc. over a period of 100 years.”

          However, a report was published in the New England Journal of Medicine by a gastroenterologist that stated that one doctor found that all his Crohn’s patients had an OVERGROWTH of Lactobacillus acidophilus which he felt was contributing to the disease. Unfortunately this found its way into the reference books that pharmacies use.

          Elaine feels that we should keep our probiotic ingestion to a minimum and get helpful bacteria from our SCD yoghurt and so displace the harmful bacteria.”

          Taken from

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        I agree with your comment Kelly. The more I’m reading about acidophilus the more I read that people say it is a lactic acid-producing bacteria and not to take it, especially for those like me who have CFS/fibromyalgia.

        I know your comment is from a while back Kelly but do you have any references to your comment on FODMAPs and Bifidus clearing this up? I’m fascinated by the possibility of this as I’m beginning to think I have FODMAP issues.

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    Hi Jordan and Steve
    I’m from the UK and I have looked into buying probiotics and multi vitamins from giprohealth but working out quite expensive for shipping. I would like to be able to buy something similar over here, but other than looking for tablets without sugar starch yeast wheat soy and whey is there anything else I should be looking out for. And of course if poss. is there anywhere you can recommend where I may purchase these.

    Have bought your ebooks and still keeping with the diet. I started off just reading Elaines book and tried to do it from that without total success after 3 months so decided to buy yours and I am now using the 5 phases, on the end of number 1 right now, unfortunately I have lost a lot of weight and probably only weigh about 7 stone right now. However I can eat bananas and yoghurt so I’m trying to pump as much into me as poss. including all meats fish and eggs.

    Many thanks.

    Barbara X

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      Hi Barbara,

      I realise your post is quite old (2011!) so you might not read this, but would love to hear from you if you do. I am also from the UK and trying to find UK-based SCD legal supplements (probiotics and multi-vits especially) and struggling to do so. GIPro Health shipping is so expensive. Did you find any UK-based supplements?

      Many thanks,

      Kate x

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        Try Bio-Kult! 14 strains, formulated by the author of the GAPS diet…I really like it, and use it to make yoghurt so it multiplies the 2 billion in the capsules and goes a lot further.

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    I ran out of the probiotics from GI Pro Health this summer and hated to spend the money. After a little time though, I was having a lot more trouble, and I wasn’t sure what was different. I was eating the same things. I finally realized it could be the probiotics and ordered more. I have been feeling great again after taking them for awhile. I am going to make sure I don’t ever run out again!!

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