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does stomach acid kill probiotics? SIBO conundrum


Senior Member
My thinking:

  1. Stomach acid (ideally) should kill any bacteria that comes through.
  2. Obviously that doesn't work 100% of the time because food poisoning/travelers diarrhea is a thing.
  3. But, is that controllable? Like, how could you force probiotics through the stomach unharmed?
  4. Maybe by taking them first thing in the morning in a liquid solution that will pass through the stomach quickly.
  5. But, does doing it that way leave you open to SIBO since you're basically pumping your upper GI full of live bugs in large quantities?
  6. If SIBO is a risk from oral probiotics, is a probiotic enema the better delivery method?
  7. With enema it seems hard to deliver the bacteria to all parts of the large bowel.

Just thinking through these things. Any input would be welcome. I know the GAPS diet book suggests probiotic enema. But it also suggests fermented foods, which are way more packed with bugs than a capsule.


Senior Member
In theory, you could try taking your probiotics on an empty stomach (eg, first thing in the morning), and with a ¼ teaspoon of bicarbonate of soda; the bicarbonate may help neutralize any stomach acid still present, giving the bacteria more chance to reach the intestines alive.

However, I have not seen any studies indicating whether such an approach actually does deliver more live probiotic bacteria to your bowels, so its just an idea, rather than a proven concept.

This article suggests the reverse:
Take your probiotics immediately before or during your meal. Eating a meal temporarily reduces the acidity of your stomach and makes it easier for the probiotics to pass through. This means that more will survive the journey through to your intestines.

This article suggests that consuming probiotics in milk or yogurt helps protect them from stomach acid.

This article says that high-temperature foods or drinks can kill probiotics, so you'd want to avoid adding your probiotics to hot items. Possibly you might also want to avoid drinking hot liquids like coffee immediately after taking probiotics.

Don't forget prebiotics (the food for the probiotic bacteria). I have had more success with prebiotics than probiotics, in term of improving my gut health. Prebiotic supplements include inulin and fructooligosaccharides (FOS).


Senior Member
Common probiotic bacteria like lactobacillus do survive stomach acid quite well from what I have read, and that's one reason why almost every commercial probiotic on the market contains lactobacillus or bifidobacteria, since most other strains have much lower rate of survival through stomach.

The problem I have with probiotic supplements like lactobacillus is that they rarely form a permanent colony in the gut, so you would have to keep taking the probiotic supplement forever to maintain the benefits, and even then it can be questioned if the particular strains you take are doing any good. I agree that prebiotics and probiotics that have proven to have actual benefits (check for example this blog) are a better approach.

Regarding SIBO, I have had some probiotics and prebiotics cause it, others not, so for me it was a hit and miss and depended on the strain rather than on the quantity.
Many food poisoning bacteria poison you through toxins. Some of these are endotoxins released from the cell when they are digested.

Generally microorganisms can survive the stomach acid otherwise we wouldn't have a gut flora at all. The issue is "viable ph" to allow them to grow and become established. Each genus has its preferred environment for optimum growth in terms of ph. There is also the environmental pressure of other more virulent species "crowding others out".

Taking probiotics per se doesn't Gurentee that it will become established in the right place. This is the main reason why commercial probiotics can't make claims other than "scientifically proven to survive". That could mean one cell. It doesn't mean it will do anything, if it is shocked and non viable due to the many conditions it needs to grow being sub optimal.

An example would be food preservation. You can have the food spoilage bacterial or fungal cells cells or spores there, but as long as you stop them from growing they pose no risk. This is mainly achieved via ph water activity and lack of oxygen and sometimes a chemical preservative (smoke, salt, potassium sorbate etc).

Food poisoning microorganisms have different lines of defence but food spoilage collanisation is more akin to what you want to achieve in the gut.

The biggest issue is species competition and ph in the gut


Senior Member

1st I think I should mention that I found GAPS a real problem. It effectively switched my brain off.

2) probiotics can be an issue, they can make things worse I strongly suggest that you look at ken lasessen's blog https://cfsremission.com/ because he reads the microbiome research and collects data from readers with CFS.

3) With SIBO of SIFO (f for fungal) the issue is infection in the upper gut. The upper gut is not normally sterile, but a healthy upper gut is relatively sterile.

This sterility is maintained by bile and digestive enzymes. In healthy people these are released into the upper gut when acidic chime enters the duodenum.

I found that taking betaine HCL + oxbile + digestive enzymes (3 x creon 25,000 per meal) seemed to do it, but I spent years playing around with protocols that were meant to help people without CFS/ME before I got there, and some of those things may have helped.

4) I have been strongly influenced by this video

As you probably know there has been research showing that pwcfs/me have problems with bacteria getting from the gut into the blood, particularly with PEM.

In the video Bagnulo covers two topics that I think are particularly important. One is that some substances like gliadin, MCTs and long chain fish oils have been shown to increase the paracellular permeability of the gut. And that others like zinc, vitamin D, vitamin A, quercetin and ECGC reduce permeability.

The other is that in a healthy gut the food we eat and the bacteria that live on it are mostly in the centre of the passage, there is a mucosal layer that reduces contact between that food and bacteria and the gut. In rodent experiments it has been shown that eating acellular carbs thins this mucosal layer and brings the food and bacteria into contact with the gut wall.

So I would think that part of the solution to SIBO and gut issues more generally would be avoiding acellular carbs and things that increase permeability and taking things that decrease permeability.

5) I haven't the time to search for it at the moment, but I also read an interview last year in which a microbiologist explained that in the oral microbiome (the best studied one) the right (or wrong) environment can cause usually commensal bacteria to become pathogenic.

They adjust to changes in their environment by upregulating and downregulating genes. And I do not know if it works but I have been trying something like Michael Maes's protocol to try to reduce inflammation in the hope that this will also shift the behaviour of my gut bacteria.

Acid and Bile tolerance

As to your specific questions: well there is a lot of research on it you can look up info on specific strains to see how acid and bile tolerant they are

There are also companies that produce delivery systems that are designed to bypass all of this. Mutaflor has a capsule that is designed to open just before the colon.

And of course if you take 10 billion CFUs and 90% are killed off that is still 1 billion CFUs where you want them.


Senior Member
2) probiotics can be an issue, they can make things worse I strongly suggest that you look at ken lasessen's blog https://cfsremission.com/ because he reads the microbiome research and collects data from readers with CFS.

Thanks for the thorough post. It's actually that blog that got me back thinking about probiotics again. I had given up on them as dangerous and/or ineffective a few years ago. I've been eating Bubbie's sauerkraut recently and it has definite effects. So, I'm going about this slowly with much research. No diving in.
Kings College London and UCL did some studies on probiotic (brand products). They found Symprove (brand) to be good at surviving stomach acid . it's a probitoic in liquid form which claims to have a good delivery system ..reaching the gut

greetings ~