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Feeling Worse After Taking Probiotics When You Have SIBO and IBS? Learn Why

Feeling worse after taking probiotics? 5 Reasons Why you felt worse and The Best ways to take probiotics.

I’m Dr Hagmeyer and welcome to my YouTube channel. We are continuing my SIBO video series titled “Everything you want to know about SIBO”

Today’s video is on the topic of probiotics and why many people feel worse after taking them.

As we learn more and more about the microbiome, we are learning about the importance various strains play in keeping our body healthy and this is especially true- when it comes to SIBO.

It is also super important to understand that probiotics are very case and condition specific.

People who have Crohns, Ulcerative colitis, SIBO or IBS…. when they first start taking probiotics especially the Right probiotics- will find that probiotics were one of the missing pieces in their health puzzle, others, they don’t notice any change whatsoever (which isn’t necessary a problem).

If you don’t feel a change as long as you are taking the right strains- then I recommend that you just give it more time.

All too often, I find too many people fall into this mindset- that if they don’t feel better- it’s not working. That’s not the case-

Now a small percentage of people who take probitoics- Unfortunately, feel worse- they have more bloating, more gas, more diarrhea and constipation and more pain.

And this is unfortunate because probiotic, especially the right probiotic at the right time taken for the right purpose- in my opinion is absolutely essential to reset your microbiome.

The Missing Piece in Treating SIBO- Prokinetics 1

If you started taking probiotics and you felt worse then I want to share with 5 reason why you had a bad experience and how you should take your probiotics. and I hope that with this new

information that you won’t give up on them.

In another video, I will talk about the specific probiotics for SIBO and IBS I have found to be incredible helpful based on the hours of research I have done and which ones I recommend.

“5 Reasons You Feel Worse When You Take Probiotics 

Reason #1 People Feel Worse When Taking Probiotics-

The specific strain within your probiotic formula, is the wrong kind or you already have too much of that strain in your gut.

Remember that the bacteria and the bacterial diversity found in your microbiome is highly unique to you. There is no one size fits all. We all have a different microbial blueprint.

Unfortunaly there is no way of knowing it is the wrong strain for you unless you test. So my best suggestion here is to Start with a very small dose. A lot of probiotics contain billions of microorganisms per dose.

If you still have a reaction even after taking a very small dose then I suggest that you open up one of the capsules and sprinkle it on some food or try taking it at a different time of the day- so- instead of in the morning take it at night before bed.

Reason #2 You Feel Worse When You Take Probiotics- Die off.

There are handful of reasons for “die off” but – The changes that might cause die-off are usually:

1. Switching from processed food to a real food diet (death of pathogens by starving)
2. Starting or increasing probiotic dosage (death of pathogens by good soldiers)
3. Starting or increasing dosage of antiparasitic, anti-yeast or antibiotic (death of pathogens by bombing)

In each of these scenarios, the change in treatment will cause substantial changes in gut flora and knock out a big portion of the bad guys.

When that happens, they release toxins that need to be excreted by the body. So, can you see how each of the major changes above actually causes a release of toxins?

So if you suspect die off my suggestion is to try and push through the process within 3-7 days your diet off symptoms will subside- if it becomes unbearable- discontinue for a day or two and then try again at half dosage. Symptoms that make me think of die off include typical flu-like or cold-like symptoms

Your whole body is becomes increasing sluggish and it usually feels as if your body is working harder any symptoms that you currently have become magnified.

Reason #3 You Feel Worse When You Take Probiotics-MMC

You have a problem with your MMC (Migrating motor complex) otherwise known as the cleansing waves –

The Migrating motor complex clears bacteria in the small intestines between meals and is one of the major pieces of people suffering with SIBO.

If someone has a very slow MMC, adding more of the wrong kind of bacteria can just fuel to the fire.

In cases like this you want to focus on improving the MMC and improving GI motility before introducing the specific kinds of probiotics. If you suspect this is the problem, I suggest you

Go back and watch a video I did titled, “11 reasons Why SIBO treatments often Fail Part 1″ this is a two part video series that I talk quite a bit about the MMC, why it slows down some of the causes, etc.

MMC and its connection to SIBO 

Reason #4 and 5 You Feel Worse When You Take Probiotics- Prebiotics

The Fourth and 5th reason, you feel worse when you take probiotics is that your probiotics contain prebiotics and you have damage to the brush border enzymes.

Many probiotic formulas from some of the best manufactures – contain prebiotics and while these prebiotics are of great benefit for many kinds of GI issues, they are not always great for people suffering with SIBO.

If you are taking probiotics right now, I want you to grab your bottle and look at the ingredients,

if you see something that says inulin, or chicory or Arabinogalactan or GOS or FOS.

These are all prebiotics and you may need to avoid these for a time being. If you are drinking tea- some teas contain inulin and chicory- both are prebiotics.  If you are noticing more bloating- you may need to take a probiotic without the Prebiotics and start reading labels.

Many people suffering with SIBO- often have injury or damage to the cells that make the Brush Border Enzymes.

These Brush Border enzymes are needed to help break down sugars (Sucrose, Lactose, Maltose) and starches. Without these enzymes doing their job- sugars and starches sit in the small intestines, ferment, and cause SIBO.

Feeling Worse After Taking Probiotics When You Have SIBO and IBS? Learn Why


If you want more information on Probiotics and Prebiotics- you can watch a video I did titled, “The Best kind of Probiotics for SIBO and IBS”– where I go into much more detail about the specific strains that have been studied when it comes to SIBO.

Points To Remember About Today’s Video

1. Probiotics should be specific to the person and testing of the microbiome is incredibly helpful in this area.
2. If your Facebook friend who has GI problems, took a probiotic and he had a bad reaction- does not mean that you are going to have a bad reaction.
3. If you don’t get a test that looks and quantifies the strains in your microbiome- it is going to be a bit of trial and error.
4. Timing can make the difference. If you had a problem when you take your probiotics in the morning try taking them at night. If you had problems when you take them at night- take them in the morning.
5. Some people just may not be able to tolerate probiotics at the beginning of treatment where they tend to be the most sensitive. Don’t give up!
6. When you get your gut under control a bit more and gut motility is functioning better you can test again in small amounts to see if they are helpful.

When To Get tested for SIBO-10 Most Common Signs of SIBO (Small Intestinal Bacterial Overgrowth) 2

How to Take Probiotics for SIBO

  1. Probiotics are very case specific in SIBO patients. Some people may find them super helpful, others will have no change, and some people will get worse when using probiotics. I often recommend stool testing when incorporating probiotics
  2. Avoid probiotics that contain prebiotics as a main ingredient. Prebiotics to look out for are FOS, GOS, MOS, Inulin, and Arabinogalactan. In people with SIBO, prebiotics can aggravate the gut since they feed all bacteria including the overgrowth.
  3. Experiment for 1-2 weeks and evaluate results. You should be able to tell after 1-2 weeks if there has been benefit, no benefit, or regression in your symptoms.
  4. Test one at a time. It’s important to test one brand or strain at a time so you can monitor the effects of that particular type of probiotic. There is no way to determine which probiotic helps you if you don’t isolate the brand.
  5. Be aware of reaction within first 3 hours. When testing a probiotic start small and stay aware of initial negative reactions within the first 1-3 hours. If you have a negative reaction you may need to stop and try another probiotic that doesn’t cause bad side effects.
  6. Timing Matters. Some people may not be able to tolerate probiotics at the beginning of treatment or when they are more sensitive. When you get your gut under control a bit more and gut motility is functioning better you can test again in small amounts to see if they are helpful. Personally, I have found this important.

Our Personal SIBO Recovery Program is a great place to start

The Personal Program IBS/SIBO/SIFO Recovery Program is a Natural Treatment for IBS and other GI related problems.
Our office implements Advanced Functional lab Testing, Natural Medicine/supplements as well as nutritional counseling tailored specifically to you.

  • To See If a Free 15 minute consult is right for you start here
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  • Not Sure Where to Start? Have a more complex GI problem you need help with? Have seen several other doctors and still suffering? Consider purchasing an in depth Case Review.

We’re here to listen and help you through this frustrating and confusing time.

The Missing Piece in Treating SIBO- Prokinetics 1

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  5. Why SIBO Treatments Fail Most Of The Time-Part I
  6. Part 2 Why SIBO Treatments Fail Most Of The Time-Part II
  7. 4 Common Mistakes Made On Low FODMAP and SIBO Diet
  8. Feeling Worse After Taking Probiotics ? Learn Why
  9. Best Probiotics To take When You Have SIBO and When To Introduce Them 
  10. How Food Poisoning Triggers Autoimmune IBS-D
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  19. Studies Now Connect Fibromyalgia and Chronic Pain to Bacterial Overgrowth (SIBO)

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