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

5 Reasons Why You Feel Worse When You Take Probiotics

We are continuing my SIBO series titled “Everything You Want To Know About SIBO.” Today I’m reviewing the the reasons why so many people who have SIBO, yeast overgrowth and gut dysbiosis feel worse when they start taking probiotics.

As we learn more and more about the microbiome, we are learning about the importance that various bacterial strains (probiotics) play in keeping our body healthy.  Probiotics are very case and condition specific. People who have Crohns, Ulcerative Colitis, SIBO or IBS often find that probiotics are missing pieces in their health puzzle. But unfortunately for many people with gut problems, take probiotics causes them to feel worse. These people experience more bloating, more gas, more diarrhea and more constipation and more pain. I see so many people give up on probiotics because of a bad experience. This is so unfortunate because probiotics, especially the right probiotic, at the right time, taken for the right purpose- is absolutely essential to reset your microbiome. So let’s get into some of the reasons this happens but also some of the things you can do to minimize a bad experience with probiotics.


Reason #1 Your Taking The Wrong Kind of Probiotic.

Treating SIBO requires a multi-step, multi pronged approach. The first step is to remove the foods that feed it. This is where implementing A Low FODMAP/SIBO diet comes into the picture. A Low FODMAP diet eliminates sugar, alcohol, and many different carbohydrates or FODMAPS. FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides and polyols, which are short-chain carbohydrates (sugars) that the small intestine cant do a a great job at absorbing. People with SIBO, SIFO and Inflammatory bowel disease often experience digestive distress after eating them.

Second, you need to attack the bad bacteria or reduce number of good bacteria. Depending on the type of gas produced by your gut organisms (hydrogen or methane).

Third step is to restore the beneficial bacteria with SIBO probiotics. Notice I said the 3rd step! But this is what everyone jumps to when they first find out they have SIBO. They begin taking probiotics and the problem with many probiotics on the market is that they simply don’t work for SIBO. Taking the wrong probiotics often make the overgrowth and the symptoms of SIBO worse.

When bacteria are present in the small intestine, they are often of the lactobacillus or bifidobacterium species. The majority of probiotic supplements contain lactobacillus or bifidobacterium, so using this type of probiotic increases the bacteria in your small intestine and adds fuel to the fire. For these reasons, I believe soil-based probiotics for SIBO are the best probiotics to START with, when it’s time to introduce probiotics into your treatment plan.

Soil-based probiotics have a natural, seed-like structure that makes them hardier than lacto-based probiotics. Therefore, soil-based probiotics survive the journey through the stomach with the help of far fewer colony-forming units (CFUs) than lactobacillus-based supplements. This is due to the formation of endospores, which can withstand stomach acid, bile salts, and pancreatic enzymes that would normally destroy the bacteria

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.

Reason #2 Die off also known as Herxheimer Reaction

When you start taking a probiotic supplement, what happens over times is you being to change your microbiome. This can be a good thing. There are trillions of bacteria in your gut, some of these bacteria are good and some of these bacteria are harmful or pathogenic.

Probiotics start their health-driving benefits by killing off the pathogenic bacteria so that the good bacteria can reclaim their home.  When those pathogens (bad bacteria) die off, they burst open and in the process of bursting open they begin to release toxins. These toxins are highly immune reactive. Your immune system goes to work clearing out these dead and dying bacteria and the toxic debris they leave behind. This die-off is sometimes called a Herxheimer reaction.  Herxheimer or Herx Reactions are a short-term (from days to a few weeks) detoxification reaction in the body.

Herxheimer Reaction or Die off Symptoms

  • Gas
  • Bloating
  • Diarrhea
  • Constipation
  • Abdominal discomfort
  • Nausea
  • Flu-like symptoms
  • Fatigue
  • Headaches
  • Rashes

Reason #3- Migrating Motor Complex

Several studies have demonstrated that abnormalities in the migrating motor complex may predispose to the development of SIBO. (1, 2, 3). The migrating motor complex (MMC) is a system of electrical waves that “migrate” throughout the small intestine, serving to propel food from the stomach to the ileum over a period of 113 to 230 minutes. The MMC doesn’t just sweep food waste into the large intestine, but it also sweeps the small intestines clean of bacteria throughout the day. This is how our body naturally keeps the majority of our gut bacteria in our large intestine and only a minority of our gut bacteria in our small intestine, therefore preventing bacterial overgrowth in the small intestine (SIBO).

Ways to Improve The Migrating Motor Complex

The MMC is vital in keeping bacterial levels low in the small intestine and in moving food particles into the colon before they become material for bacterial fermentation in the small intestine.  This is a very important mechanism in preventing the overgrowth of bacteria in the small intestine and preventing relapse of SIBO post treatment. There are several things you can do to help support your MMC.

  1. Fasting. The migrating motor complex only occurs when the upper GI tract (stomach/small intestine) is empty. If there is food in your stomach or upper portion of your small intestine the MMC won’t be triggered and consequently, undigested food and bacteria won’t be flushed from the small intestine. Keep in mind that MMC is a neurological reflex that starts around 3 hours after a meal and lasts for 90 – 120 minutes. Grazing or snacking between meals will impede your MMC process. Meals should be kept to three a day with a period of ideally 5-6 hours between them, with no snacking.
  2. Vagus Nerve Exercises – The Vagus nerve is probably one of the most important nerves you need to become familiar with if you have SIBO. The vagus nerve is activated when the body is in “rest and digest” state (also known as the parasympathetic state).  Stress, anxiety, fear, worry also shut down your digestive system. The Key to digestion is activating the vagus nerve.
  3. Herbal Prokinetics like the ones in Motility Pro. The word means promoting (pro) and move (kinetic), so it’s about promoting movement. Pro kinetic herbal supplements help amplify and coordinate the gastrointestinal muscular contractions to facilitate the movement of the contents within your digestive tract. Prokinetics can work on the upper GI tract where they can be especially helpful for burping, nausea, and acid reflux. Prokinetics can be helpful for lower digestive system where constipation, gas and bloating, feeling full all the time are the main symptoms.

Digestive Conditions Associated with Poor Vagal Nerve Function

Now that you know how the vagus nerve helps stimulate and regulate the organs of the digestive tract, it’s easy to see how poor vagal nerve function can be connected to the following conditions:

  • Heartburn, acid reflux or GERD
  • IBS – chronic constipation & diarrhea
  • Inflammatory bowel disease such as ulcerative colitis
  • SIBO (Small Intestine Bacterial Overgrowth)

I wrote an article that discusses several ways of Improving Vagus nerve function and some of the  Vagus nerve Exercises that have been shown to improve GI motility, I also find it helpful to perform the Ileocecal Valve release technique. 

Reason #4  Prebiotics

The Fourth  reason, you feel worse when you take probiotics is that your probiotics contain prebiotics or 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 in the initial stages of 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 may all be contributing to your bacterial overgrowth. 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.

Reason # 5 Brush Border Enzyme

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. The brush border glycohydrolases are responsible for the degradation of di- and oligosaccharides into monosaccharides, and are thus crucial for the energy-intake of humans and other mammals. Without these enzymes doing their job- sugars and starches sit in the small intestines, ferment, and cause SIBO.

This is why Brush border digestive enzymes are so important for Patients who have SIBO and especially those who have SIBO and are losing weight.  Vital-Zymes Complete supports healthy digestion of all major nutrient types (proteins, fats, carbohydrates). Perfect for those with occasional food sensitivities or indigestion, and delivers a full complement of high activity enzymes.

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



Vital-Zymes™ Complete

  • Contains highly purified enzymes to meet the needs of food-sensitive individuals
  • Contains no porcine or other animal-derived enzymes
  • Avoids fruit-derived enzymes (bromelain, papain, and kiwi) for improved tolerance by sensitive individuals
  • Active across a broad range of pH conditions (pH of 2 to 10) for benefit throughout the entire intestinal tract
  • Supplies a broad spectrum of disaccharidases (lactase, maltase, sucrase/invertase, pullulanase, and isomaltase) to assist in cleaving of sugars that may be fermented by organisms that shift the balance of microbiota†
  • Assists protein breakdown, but avoids excessive amounts of proteases that may irritate GI tissues
  • Dipeptidyl peptidase IV (DPP-IV) activity supports optimal cleaving of casein and gluten and their exorphin peptides (casomorphin and gluteomorphin)
  • Supplies Serratia peptidase enzyme to support sensitive GI tissues from irritation and lysozyme for its unique lysing action on bacterial and yeast cell walls and broad immune support




Best Way to Take Probiotics When You Have 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.

Points To Remember About Today’s Article

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- this 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.

We Know How Frustrating It is to Self Treat SIBO. If Are Tired of Trying to Figure it Out on You Own and Ready For Expert Help- 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
  • Still have questions? contact us 
  • Want to Get Tested for SIBO but your doctor won’t test you? Order a test and consult here


People Who Viewed and Watched Today Video Also Watched

  1. 10 warning signs you have SIBO & When To Get Tested
  2. Breath Kind Of testing for SIBO 
  3. Eradicate SIBO by incorporating Biofilm Disruptors
  4. SIBO and Prokinetics- The Missing Piece In Treating SIBO 
  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
  11. What You Need To Know Before Getting Tested For SIBO
  12. 5 Food Additives You Should Avoid, If You Have SIBO
  13. Ileocecal Valve Release- Self Massage-How, When And Where To Massage Your Ileocecal Valve
  14. Why The Ileocecal Valve Holds The Key to IBS and SIBO- What It Is and Why It’s Important 
  15. Vicious cycle of Nutritional Deficiencies Associated With Low FODMAP and SIBO Diet
  16. SIBO/IBS And The Connection To Thyroid Disease
  17. Why Antibiotics May Not Be The Best Approach for SIBO
  18. Medications That Cause IBS, SIBO and Leaky Gut
  19. Studies Now Connect Fibromyalgia and Chronic Pain to Bacterial Overgrowth (SIBO)

When To Get tested for SIBO-10 Most Common Signs of SIBO (Small Intestinal Bacterial Overgrowth) 1


  • Vantrappen G, Janssens J, Hellemans J, et al. The interdigestive motor complex of normal subjects and patients with bacterial overgrowth of the small intestine. J Clin Invest. 1977;59:1158–1166.
  • Stotzer PO, Bjornsson ES, Abrahamsson H. Interdigestive and postprandial motility in small-intestinal bacterial overgrowth. Scand J Gastroenterol. 1996;31:875–880.
  • Husebye E, Skar V, Hoverstad T, et al. Abnormal intestinal motor patterns explain enteric colonization with gram-negative bacilli in late radiation enteropathy. Gastroenterology. 1995;109:1078–1089.
  • Pimentel M. A New IBS Solution. Sherman Oaks, Calif.: Health Point Press; 2006.
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