Some doctors are now recommending that people with Crohn’s and Colitis NOT take probiotics. They are saying that people with IBD do not have a normal response to beneficial bacteria and therefore probiotics can aggravate these conditions.

Back when I was diagnosed with Crohn’s (1984), the medical establishment maintained that Crohn’s  was an autoimmune disorder rather than an immunodeficiency. In contrast to this, a friend (who is also a scientist) recently said: “I had noted that those I knew who had Crohn’s tended to be more vulnerable to certain types of bacterial infections, but had assumed that this is due to the drugs they are on. However, after looking into the matter – it seems that a faulty immune system is actually an inherent characteristic of the condition. Is this something that you have noticed with those you help? It seems quite a tight walk to expose oneself to “good bacteria” and trusting the immune system to respond appropriately. I want to suggest this route (i.e. the probiotic route), but given the tendency to pathogenesis to organisms that would normally not be problematic for most others – I don’t want to add fuel to the fire….”

This approach is actually not new, it is just becoming more prolific in the literature. Here are some excerpts from Listen To Your Gut (2006) where I talk about factors pertaining to this:

“It’s also important to ingest the right strain of each probiotic species. Different strains of acidophilus (for example) can produce completely different results. Out of 200 different strains of acidophilus, only 13 have potent antibiotic and antiviral capabilities. If you have IBS or IBD, you need to ingest potent strains that are capable of wiping out the bad bacteria in your gut, strong enough to protect against re-infection, and capable of restoring your mucosal lining and helping to balance your immune system.”

“Some species that are routinely included in commercial probiotic blends simply do not have a long-term record of human safety and not enough is known about their actions/ramification in the gut under varying conditions. For example, a study on immunodeficient mice found that supplementing with a certain strain of L. reuteri (used in many probiotic blends) caused some of the mice to die, leading the researchers to recommend “the need to proceed cautiously when using high doses of this strain in neonatal, immunocompromised hosts.”(10) Therefore, you only want to purchase a probiotic supplement that contains species and strains with a proven, long-term record of human safety.”

“So, you need to be very careful when choosing a probiotic brand to supplement with as the field of misinformation in this arena is vast. In my opinion, probiotics are so powerful, they should be stringently regulated and undergo routine, independent testing. Swallowing live microorganisms, which are highly adaptive, intelligent beings, should be undertaken with great caution and safety should always be paramount. Unfortunately, currently probiotics are not regulated at all, and many probiotic manufacturers do not even comply with labeling guidelines. In addition, when I refer to ‘probiotics’ I’m referring to food-cultured beneficial bacteria only.”

“When I first began recommending Natren probiotics to my readers, I did so for one reason only; they worked. At that time, I knew a fraction of what I know now about probiotic strain selection, manufacturing, storage, and other factors effecting potency and efficacy. I had experimented with different brands of probiotics off and on for seven years and each time I tried supplementing, my symptoms (gas, bloating, bleeding) worsened. Although the science behind probiotics and why they should benefit me seemed sound, my experience proved contrary. When I was nearly ready to give up on the whole subject, my naturopathic physician Dr. David Wang, convinced me to try Natren brand probiotics. He insisted they were the best brand he knew of and that I would see good results from them. I started with just Natren’s Bifido Factor powder (Bifidobacterium bifidum Malyoth strain) and for the first time, experienced an improvement as a result.

Prior to taking Natren’s B. bifidum, the only thing that had worked to stem my chronic diarrhea was L-Glutamine (on an empty stomach only). However, within three doses of Natren’s bifidobacteria, my stools began to firm up and excess water was reabsorbed. I tried Natren’s Megadophilus (Lactobacillus acidophilus DDS-1) next but did not tolerate that as well as the bifidum. In searching for reasons why, I came across this bit of research that showed that in states of inflammation the overall tolerance to bacterial flora is greatly reduced:

“It is possible that the products of the commensal flora promote inflammation in the presence of an impaired mucosal barrier or injury to the mucosa… These results indicate that, in health, there is tolerance to autologous [your own] but not allogeneic [foreign source] intestinal flora, and tolerance is lost during inflammation. Evidence also exists that animals are tolerant to their own flora in health but not after colitis develops.”(13)

Unfortunately, this bit of research doesn’t specify which species of bacteria the body loses tolerance for, and which strains of which species – perhaps all of them? Nevertheless, it provided me with a clue by which to proceed, and I stayed on just the B. bifidum bacteria for another three months before trying the L. acidophilus again and I then tolerated it well. By that time (I surmise) the B. bifidum and other supplements I was taking had healed my intestine to the point where it was able to tolerate – and benefit from – additional probiotic supplementation. About a month after that, I added Natren’s L. bulgaricus and tolerated that successfully as well. I have since continued to recommend the same conservative course of action to my readers.

However, in March 2005, Gastroenterology journal published results of a human trial on 75 people with IBS, supplementing with 10 billion cfu of B. infantis, once per day in a malted milk drink. Now, Bifidobacterium infantis is, as the title suggests, a strain typically used for infants. But as Dr. Quigley and his colleagues note in their paper, the symptom relief achieved with B. infantis in the trial was comparable to that seen with Zelnorm (tegaserod) and Lotronex (alosetron) – two drugs used in the treatment of Irritable Bowel Syndrome.(14)

B. Infantis is the predominant bacteria found in the bowel of healthy breastfed infants. As the infant begins to eat solid foods, the more ‘adult’ strains like B. bifidum come to dominate. However, what if you never had a healthy bacterial flora as an infant? Then maybe it would be best for you to start with what was missing from the very beginning and work up from there? This approach makes sense to me both logically and intuitively. Interestingly, I had a bottle of Natren’s Life Start (B. infantis) in my fridge (that I had given to my daughter) and about six months before this research came out I had begun taking it myself (along with the three adult species/strains) just because I intuitively felt like trying it.

In light of this research, you may want to consider beginning probiotic supplementation with B. infantis, especially if you try B. bifidum and can’t tolerate it. And just to confuse you even more, I have talked with readers who couldn’t tolerate B. bifidum at first, but could tolerate L. acidophilus. So, essentially, I’ve provided you with a guideline, but within that you may need to experiment and find what works best for your particular body and gut environment. The only thing I can tell you for sure is: Don’t give up! You do need to establish a healthy bacterial flora (consisting of all three species) to enjoy long-term, lasting health.

I know many people have experienced good results from more aggressive supplementation and also from beginning supplementation immediately (with ulceration and bleeding still present). Feedback from hundreds of readers has confirmed the effectiveness of the slower approach (as outlined above), but it certainly does take more time to see results since you’re proceeding so slowly. However, if your gut is really toxic, proceeding slowly helps minimize the die-off effect (Herxheimer Reaction), so while it takes longer to see any results, at least you don’t have the nausea, bloating, headaches, etc. that can result from a rapid die-off of pathogens in the gut. As in all things, please follow your own gut instinct first. If you feel you should pursue aggressive supplementation, then please do so. I know of a colon clinic in Sydney, Australia that treats people with active, bleeding Crohn’s with high doses of Natren brand probiotics orally and also via retention enemas and they have had good success with this approach.”

Experiential Knowledge

Now, having said all that, over the years we have also found that people get the BEST results from starting with Jini’s Wild Oregano Oil Protocol (which has you taking wild oregano all day and then one dose of probiotics before bed). And then from there (once infection is under control and the mucosal lining strengthened) transitioning onto high dose oral probiotic supplementation three times per day. Some also do Jini’s Probiotic Retention Enema too at that point. If you are interested in just those protocols (without the rest of the book), we sell the eBook here:

BUT when we tested with people ONLY using the pathogen killer (wild oregano oil) without the daily dose of probiotics, many people couldn’t tolerate the protocol and results were not as good.

Likewise, my new experimental Intestinal StrictureHeal protocol also involves killing pathogens first, and then one dose of probiotics before bed.

At the end of the day, research results can swing all over the place, but the bottom line is WHAT WORKS? Hence I keep stressing to people that you have to use a multi-pronged approach (see the 8 Steps To Healing on my homepage) to get the best results.

Doctors Say No Probiotics For IBD Patients

31 thoughts on “Doctors Say No Probiotics For IBD Patients

  • I think your methods sounds awesome and amazing. If we had enough funds, I would be doing all of it. Unfortunately, we have nothing available, so I wait. I hope for a day soon when I can begin to heal my body more actively. Currently, I’m focusing on cleaner eating and just completed a 5 day fast, which seems to have really impacted my stool formation VERY positively. We’ll see in a few days if what seems to be continues….

  • This is an excellent overview of the current developments of our understanding of various gut inflammatory disorders – which all have different roots and triggers despite our attempts at lumping them all simplistically under one umbrella. I have had the fortune to work with various doctors (PhD’s as opposed to MD’s – so a lot of their curiosity is driven by a desire to understand mechanism as opposed to pharmaceutical dogma which are prevalent in the latter group – especially in industrialized nations). At the molecular level – for a group of Crohn’s patients there have been pathways that are supposed to respond to certain types of microbes (through intracellular molecules called NOD receptors) that are dysfunctional – and this was found to lead to barrier dysfunction. One scientist explained it beautifully that the immune system communicates constantly with our “friendly” bacteria – but if the communication system breaks down – then the ability to tell the friends from the foe and to maintain a friendly border is destroyed and this leads to the chronic inflammation that really takes a toll on health. Remarkably – and you have probably heard of this therapy, Jini – other organisms – such as the Helminth (a type of worm) can replace this need to communicate with the immune system in some people with Crohn’s (if you type into PubMed “helminth and Crohn’s treatment” you will come across all the research that has gone into the area). For mainstream medical doctors – who still seem to be ignorant of the fact that a sterile gut is a contributor to immune dysfunction given their fondness of antibiotics – the idea of inoculating someone with a parasite to treat a gut disorder is beyond comprehension. However, this is the best time for gut health as the study of micobes as a focus in health has never been greater, and we are now finally recognizing their importance. It was, in fact, recently published by resarechers from UBC that antibiotic use during infancy was directly associated with chronic immune disorders such as asthma. Thus, I am highly optimistic that the tides are turning.

  • Yes, but it’s bizarre that the med world has lagged so much in this area – if you talk to any doc, I believe they are aware of the high risk of secondary or opportunistic infection following hospital IV antibiotic therapy… and yet…

    Your helminth example is also the likely reason people see good results *initially* from ingesting bacterial soil organisms (spore-formers).

    The other thing that people lose sight of is that due to antibiotics overuse and misuse, these intelligent critters have evolved into much stronger pathogens than we’ve seen before. Yet another reason we need to have a gut teeming with beneficial organisms.

  • Ah, dear Jini, your surprise with the lack of adherence to evidence by most of the medical community likely comes from the fact that you are an innovator who doesn’t seek approval from traditional authoritarian heirarchies that are both blinded by dogma and beholden to alternative conflicts of interest. Both the ability to heal and discover how things work are to a great degree an innate skill (which I liken to any aptitude one may be gifted with – such as musical talent, teaching, or athletics). You can go to medical school, pass your exams and still be a substandard – but “good enough” healer – just like you can learn how to play the piano. Most of our doctors lack true intuition of how the body or life works – and worse – lack curiosity and a drive to understand. They just follow their limited manual and look at the print out to see if your levels of such and such a measure are within the normal range.

    Congruent with the detrimental effects of antibiotic abuse – I think we will soon realize the consequences of the same overuse problem with vaccines. A highly contentious subject.

  • Hi Jini
    I know that you only recommend Natren probiotics and I did take them for about five months but when I finished my six week Absorb Plus diet I started SCD. Unfortunately I had to stop taking Natren as it contained SCD illegals and have been using Klaire Labs Acidophilus as well as making my own yoghurt. Are there any SCD legal probiotics you would recommend or do you feel none are as good as Natren? I have also start using Interphase Plus which is used to break up the biofilm containing yeasts and bacteria in the gut and was wondering do you rate this product?

    Thanks again

  • REBECCA – the Natren Healthy Trinity capsules do not contain any culturing medium and therefore are SCD compliant.

    Sorry, I don’t know anything about Interphase Plus. Did you do Jini’s Wild Oregano Oil Protocol when you were on the IBD Remission Diet? Keeping in mind, that most have to cycle on and off the Protocol for 2 – 3 years to clear all the pathogens. This accomplishes the same thing – but is also anti-inflammatory.

  • Hi Jini

    Thanks again I was using oregano oil but stopped because I didnt know whether it broke down biofilms so thats why I start using interphase. I am delighted to know that I can use Natren again as I have not been sucessful with yoghurt and any of the other probiotics I have used are not up to standard. I have only found out I am pregnant which is the whole reason I done the diets while I still have D a lot I have gained weight. Hopefully proper probiotics will help me stabilise along with oregano oil.
    Thanks for all your help again

  • Hi Jini,

    You mentioned a colon clinic in Sydney Australia that specializes in probiotic enema’s and supplies natren products. Could you please provide the details of the clinic?

    Thank you


  • The article said you took B.infantis. Can you please elaborate on the time, empty stomach or not, with what, about your dosage, etc.

  • I have been using Custom Probiotics Six Strain Probiotic Powder as it was available in NZ. I did this because I was concerned at the travel time and the fact you require Natren to be refrigerated. I have been taking 2 scoops mixed with water before bed and results probably exacerbated bleeding. Have reduced to 1 scoop and now waiting for the effect. Am I using the wrong probiotic and can Natren be shipped successfully to NZ?

    1. Hi Gary,

      We can’t comment on that particular product as we haven’t tested it, unfortunately. We certainly can (and do) ship to NZ but it is expensive. You can visit the probiotics section of our shoppe here:

      If cost is a major factor, you might want to check around locally and see if there are any other probiotics available. If you would like to use the same criteria Jini uses to evaluate probiotics, click the link below to read her methodology in detail:

      Kind regards,
      Customer Care

  • Alas you might deliver to New Zealand and Australia, but when it gets here eventually, it is probably no good and your customer service staff are very unhelpful. I spent many hours on phone with your deliver company’s which to get to Australia they have 3 branches was a night mare.

    1. Hi Ben,

      I’m sorry to hear that you had a bad experience with the FedEx and your order. Most of our customers in Australia and New Zealand receive their orders without issue and we’re happy to do everything we can on our end to expedite the delivery process if an issue does arise. Unfortunately we don’t have very much influence over local delivery practices in foreign countries and are at the mercy of FedEx when it comes to that. However, over the 10+ years we’ve been offering our products worldwide, we’ve found that FedEx does a better job at delivering our customers’ orders efficiently and safely than any other carrier we’ve tested. If you ever have questions or concerns please don’t hesitate to email use at, give us a call at 888-866-7745, or visit the live chat in the blue box on the bottom right edge of this page. Thanks so much for your business and we hope Jini’s protocols work well for you!

      Kind regards,
      Customer Care

  • I started the half elemental diet three days ago. I also started the Wild Oregano Protocol three days ago as well. I start out with one tsp. each of the natrens powder probiotics in the morning, wait two hours then have five drops of the wild oregano with water. I am having a least two shakes a day plus tolerated food. Then about 7 p.m. have the mucosheal then five more drops of the oil of oregano. Then right before bed around 10 have one capsule of the Natrens Healthy Trinity Probiotic.

    1. Hi Amy,

      Thanks for sharing a little about your regimen. We’d love to hear more about your progress later on as well and wish you all the best. If you ever have any questions, please don’t hesitate to contact us here, via email at, on live chat at the little blue box on the bottom right of this page, or give us a call at 888-866-7745.

      Kind regards,
      Customer Care

  • Hi Jini,

    I was just diagnosed with Crohn’s in Feb and have recently been to two doctors for a second opinion of medication and then I came across your book. I have ordered it and bought the wild oregano oil and the three probiotic powders. I have currently been in a flare since Feb and I am slowly getting better the disease is in the small bowel. I tried to start the probiotics before bed last night and ended up vomitting. I have a horrible gag reflex and do not do well with liquids. Is there any other way I can mix these powders I have ordered with something else to get them down?

    1. Hi Erin,

      You can certainly mix the powders with a different type of liquid if there’s something else that you find easier to drink. We’d just recommend not taking them with something that is very acidic or hot. The only other thing we’d suggest is to further dilute the powder with more water so that it goes down easier. I assume that capsules are out of the question due to your gag reflex but, if not, many people opt to use Natren’s Healthy Trinity product because you get all three strains of probiotics in one little capsule which makes it simple and easy to manage.

      Kind regards,
      Customer Care

  • Hello
    I loved that absorb plus its so good and easy to make
    But the problem is the shipping to australia is very expensive and out of my pocket is there anyway u can ship this product cheapier as it helps me a lot with my crohns thank you

    1. Hi Heba,

      We’ve tried cheaper shipping options in the past but the unfortunate thing is that we ended up dealing with a number of lost/damaged shipments and customs issues which we found unacceptable. Jini wrote some instructions about how to make your own elemental shake and you should be able to source the ingredients locally if the shipping cost is becoming too costly. Here’s a link to the instruction document:

      Another option is to integrate some common foods into your diet along with the Absorb Plus (or homemade elemental shakes) as Jini talks about here:

      Kind regards,
      Customer Care

  • I have UC (currently off all medications and following a 100% organic paleo diet)and am in Phase 2 of the Oregano Oil Protocol. I tolerated the oil very well in the first phase, and am now doing fairly well with two doses of Natren probiotics (all three) twice daily – though at half the dose in the afternoon (1/2 tsp each). I do sometimes wake in the night because of the probiotic, to use the toilet and may reduce the second dose as well if that continues for too long.

    My question is, do you personally rotate different brands of probiotics as some have suggested? I am very pleased with Natren, and happy to have found them through you; I just wonder if it will be enough to continue with the narrow strain selection considering that our guts should contain 400 or somesuch different strains of bacteria. What is my lifetime strategy?

    Also! Thank you so much for all you do and for the great book!

    1. Hello Beth,

      Thank you for the inquiry. Natren is the only brand that Jini recommends and uses through years of research and experience. It is the only one with all the requirements she feels that is needed. She believe it is crucial to use them at least during the times of during and after you’ve been on the elemental diet, or after a course of antibiotic medication, or any GI diagnostic/exploratory procedure (barium enema, colonoscopy, sigmoidoscopy, etc).

      After the 6-12 months on them she recommends to take at least 2-3 weeks to maintain the healthy gut flora. However she say you may be able to do less if you can consume fermented foods on a daily basic. The book she recommends on how to prepare these foods is Nourishing Traditions cookbook by Sally Fallon and Mary Enig PhD.

      If you have any other questions please let us know.

      Kind Regards,
      Customer Care

  • Hi I am suffering from proctitis and colitis and tried the oregano protocol for a few days. I diluted with organic olive oil and wild oregano and used re tally. I think I am having more rectal bleeding however have you heard of this has happening to people before. Not sure whether to continue the protocol or not….

    1. Hello Natasha,

      We would recommend continuing to use the wild oregano to help kill the infection, as well as using the probiotics to help build the good bacteria at the same time. We would recommend checking out these links and then let us know if you have any additional questions:

      Kind Regards,
      Customer Care

  • This is actually absolute truth that people with damaged gut should not take probiotics!! From my own experience, I tryed every probiotic there is, expensive and not, literally, everything, and in spore forms too, nothing worked and even made it much worse! I was diagnosed with IBS after taking antibiotics for 6 month and completely destroyed my gut. It’s been three years of AIP diet (elemental diet first, then FODMAP), I just started taking probiotics again, after years of not taking them and my gut is about 100% healed now, and probiotics working now!!

  • do you do (space) the probiotics, oregano protocol when you need to also be taking oxy powders, or the like, plus daily cleansing enemas, coffee enemas, for a megacolon? It is very difficult to see which are cancelling out which but don’t want to just do the oregano and colon cleanse, enemas, without supplementing w/probiotics but feel they are getting wiped out with all the other stuff?

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