I would like to know how to get the good bacteria to colonize more permanently. I have been having trouble for the past 3 years with taking probiotics. I get very bloated and gas that is pretty painful. I used to be able to tolerate a 5 billion cfu capsule daily and now can only tolerate about 1/4 of a capsule every other day. I have cleared myself of yeast. I had a stool test done and it showed no yeast and no other pathogenic bacteria. It also showed that I tested a level 1 for lactobacillus and 3 for bifidobacteria. 4 is ideal. So I know exactly what I need but I'm not sure how to get it to take over when I can't tolerate that much. 

Original Post

Hi there Michelle,

If you are unable to tolerate any probiotic capsules, I would guess you are sensitive to the pre-biotic (inulin) that is packaged in the capsule as a filler and as food for the bacteria once arrived at it's destination (your intestines).

Though Whole Approach does not carry it, you might find a probiotic powder that has only rice maltodextrin as a filler. I've seen it and you just add the powder to water or even just eat it. 

You can also experiment to see how you feel with sauerkraut or kimchi as one food source of probiotics. Kombucha is also good though the supplements are much more concentrated and so, if you can find a source that you can tolerate well, it will more quickly raise your levels.

Good luck and sorry we don't have the product you need. Take good care,


I should have clarified that. These are probiotics with out the prebiotic inulin in them. Probiotics alone bother me. I was always somewhat sensitive to them, but I could take at least one capsule daily. Then about 3 years ago they started to bother me more and more. I started having to take less and less of them.

I have since cleared myself of yeast and other pathogens, backed by a stool test. So right now I am just in the process of building up the good bacteria. Since I can't take that much of them, I would like to know how to optimize the little I can take.

What is the best way to get them to stick around permanently and/or multiply. Should I try to take some sort of prebiotic, or should I just try and eat well, lots of raw veggies, and create a good environment for them. Is it possible to get them to colonize without taking prebiotics?

Do CRC folks have to take probiotics for the rest of their lives or is it possible to replace what you've lost?




Hi Michelle,

Thanks for clarifying. I have only seen probiotics with malto dextrin or inulin in them. Are you sure the ones you are taking do not have any pre-biotic fiber? This is an important but not essential ingredient. Have you tried this amazing probiotic? SBX has a different formula and, though it contains a small amount of lactic acid bacteria, it is mostly soil based microorganisms. These are not indigenous to our gut but they are necessary for health and originally were sourced from soil grown foods. Modern diets contain very little, if any for many reasons. Having these bacteria in the gut help create an environment for the lactic acid bacteria to thrive so may make it easier for you to repopulate them.

Yes, people who have candida overgrowth and do this program along with a new awareness, can reduce candida levels to normal and increase probiotic levels. 

It's an unusual experience to be sensitive to a bacteria that is naturally colonized in our body. But, if your observations are accurate (not somehow being confounded by an unknown), then you could try eating/drinking unpasteurized fermented foods instead of, or in addition to supplementing with probiotics. Fermented foods have small amounts of bacteria in them that include sauerkraut, kimchi, miso, and kombucha, natto (look up how to enjoy this odd food but be sure not to cook it if you want the good bacteria), kvas, brine olives and pickles (no vinegar - also if you want the bacteria).

I hope this helps. Feel free to ask me anything else.


Yes, they do have malodextrin in them. I did not realize that this was a prebiotic fiber!!! Would potato starch be considered prebiotic also, and cause the same sensitivity? So if I find one that has rice malodextrin in them, I might be able to tolerate that better??

I have heard of the the soil based organisms before, I will look into adding those.

I have tried very small amounts of fermented foods before, they do scare me a little.....I had heard they contain trillions of bacteria, so I was afraid to try more, are you saying they contain small amounts of bacteria?


Prebiotic fibre is usually fine for most people but a very small few have trouble with the inulin type. I think the starches (maltodextrin) are not fibres and not prebiotic- just filler. 

No, fermented foods are full of bacteria, not likely as many as supplements per dose but still very good for you and should be very 'relatable' to your gut. 


Well that's great. Digging in it yes, and eating from the garden too. Though I know food can have dangerous pathogens from birds or ground dwelling creatures, I still eat a lot of food from the garden before washing it. I figure it's likely I will get more of the good than the bad Maybe I'm overly optimistic but it feels right to me.

Would SIBO be a reason I can't tolerate probiotics?  I have had inconclusive results with SIBO testing. I tested positive on an Organic Acids test, then negative with the breath test for SIBO and it was a possibility with the stool test.

Because of those results I did treat for SIBO for about 6 months and thought that would be a good amount of treatment time. I did not have the money to have any retesting done.

Certain foods bother me now too that didn't before like onions and broccoli. Maybe I need to treat further for SIBO? 

Hi Michelle,

I wish I could help you with that. I don't have enough experience with SIBO to give you a useful answer.  

You might be interested in a couple of new books. The Hidden Half of Nature and The Secret Life of your Microbiome.

The Whole Approach Candida diet supports the health of your microbiome. Just we called it an anti-fungal diet, and an intestinal ecology reset or rehabilitation but not a Microbiome Diet as researchers have begun to speak of it now.

The Secret Life of Your Microbiome

Why Nature and Biodiversity are Essential to Health and Happiness

by Susan L. Prescott & Alan C. Logan

A local publisher just released this book. I can' t wait to read it!

For too long our bodies have been viewed as capsules, sealed off and protected from "bugs" by our immune systems and an arsenal of antibiotics, pesticides, processed foods, and anti-bacterial soaps. The more insulated from nature, the better.

The Secret Life of Your Microbiome shatters this deeply held myth, presenting a revolutionary new paradigm, backed by vast science; we're deeply connected to the biodiversity of nature through our microbiomes — the rich microbial ecosystem of our guts and skin — and this connection is essential to health and happiness.

From sugar-rich diets wiping out good gut bacteria and exacerbating depression, to microbes mediating phytonutrient absorption in the brain, to inflammation and cancer, the influence of biodiversity on our bodies is everywhere. The great communicator is our immune system, a "mobile brain" that interacts with micro-organisms in and around us with profound health consequences.

Written with pace, clarity, and humor by world-renowned scientists in immunology, nutrition, and environmental health, The Secret Life of Your Microbiome makes the irrefutable case that health and happiness depends fundamentally on the health of biodiversity, and shows how we can nurture this nature.

The Hidden Half of Nature

I'm not sure why this book calls it the hidden half. I've not read it yet but my understanding is that humans are at least 90% other cells so I'd call it the "hidden 90% of nature. " This book goes beyond humans and our micro biomes though.

A riveting exploration of how microbes are transforming the way we see nature and ourselves—and could revolutionize agriculture and medicine.

Prepare to set aside what you think you know about yourself and microbes. Good health—for people and for plants—depends on Earth’s smallest creatures. The Hidden Half of Nature tells the story of our tangled relationship with microbes and their potential to revolutionize agriculture and medicine, from garden to gut.

When David R. Montgomery and Anne Biklé decide to restore life into their barren yard by creating a garden, dead dirt threatens their dream. As a cure, they feed their soil a steady diet of organic matter. The results impress them. In short order, the much-maligned microbes transform their bleak yard into a flourishing Eden. Beneath their feet, beneficial microbes and plant roots continuously exchange a vast array of essential compounds. The authors soon learn that this miniaturized commerce is central to botanical life’s master strategy for defense and health.

They are abruptly plunged further into investigating microbes when Biklé is diagnosed with cancer. Here, they discover an unsettling truth. An armada of bacteria (our microbiome) sails the seas of our gut, enabling our immune system to sort microbial friends from foes. But when our gut microbiome goes awry, our health can go with it. The authors also discover startling insights into the similarities between plant roots and the human gut. We are not what we eat. We are all—for better or worse—the product of what our microbes eat.

This leads to a radical reconceptualization of our relationship to the natural world: by cultivating beneficial microbes, we can rebuild soil fertility and help turn back the modern plague of chronic diseases. The Hidden Half of Naturereveals how to transform agriculture and medicine—by merging the mind of an ecologist with the care of a gardener and the skill of a doctor.

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