Are your Probiotics Making you Feel Worse?

Are your Probiotics Making you Feel Worse?

Posted by Pernille Jensen on

I've heard it many times as a naturopath: "I have stomach problems, so I bought a broad spectrum probiotic, but they make me feel terrible." Or “I have been eating fermented foods for a while now and I feel like my brain fog has gotten worse” 

I love fermented foods such as Sauerkraut, yoghurt, kimchi, tempeh, and miso because they  are nutritious and have numerous health advantages, but in certain people they can aggravate gastrointestinal disorders and should be avoided until the underlying issues are resolved.

 AMPERNA® Probiotics Feeling Worse?

People are becoming more aware of the importance of gut health, so it's no surprise that they think a broad spectrum probiotic would be beneficial. Unfortunately, it's not that simple, and many people find that eating fermented foods and/or taking a broad spectrum probiotic can make them feel significantly worse, leading them to believe that probiotics aren't for them.

Why do Some People Have a Poor Reaction to Probiotics?

There are a variety of reasons why people react negatively to probiotics, but the two most common ones I've seen are:

  1. A bacterial overgrowth, such as small intestine overgrowth (SIBO). Symptoms of SIBO can include chronic bloating that gets worse during the day, nausea, feeling excessively full after a meal, and brain fog.
  2. Histamine intolerance is a condition in which the body produces too much histamine or is unable to break it down. When histamine levels are high, one or more of the following symptoms may occur: headaches, migraines, digestive issues, hives, nasal congestion or sinus issues.

Bacterial overgrowth and histamine intolerance can often go hand in hand, especially if the overgrown bacteria in the small intestines are histamine producing bacteria, in this case taking probiotics can be like adding fuel to the fire. 

AMPERNA® Probiotics Feeling Worse?

Choosing the Right Probiotics for Better Gut Health

Specific probiotics, such as Lactobacillus rhamnosus, Bifidobacterium infantis soil-based probiotics, such as Bacillus coagulans and Saccharomyces boulardii have shown promise as an adjunct in the treatment of SIBO and histamine intolerance, but many other probiotics will only make matters worse.

The probiotics that have shown to produce histamine are Lactobacillus casei, Lactobacillus reuteri, and Lactobacillus bulgaricus, Streptococcus thermophilus, Lactobacillus delbrueckii, Lactobacillus helveticus.

When you purchase a broad spectrum probiotic you may be buying one that contains a histamine producing strain, which will be counterproductive in helping you feel better and improve your gut problems.

Some of the histamine raising strains are found in most yoghurts, aged cheeses and fermented foods. Fermented foods such as sauerkraut, kimchi and miso are generally good for you and can help improve the health of your microbiome, however, if you suffer from SIBO and/or high histamine these foods and drinks can worsen your symptoms.

AMPERNA® Probiotics Feeling Worse?

Probiotics That Don’t Make You Feel Worse

Saccharomyces boulardii (SB) is one of the most researched probiotics and is a favourite of mine due to its stability (you won’t waste your money on this one as it will survive anything; your stomach acid and even antibiotics ) and the numerous benefits for so many conditions as well as boosting gut health in general.

Health benefits:

  • SB has the ability to restore a healthy microbiome in individuals. Maintaining or restoring your microbiome is the foundation of all health. If your microbiome is healthy your immune system, nervous system and hormones will all be healthier.
  • SB can have an antimicrobial effect (directly by exerting antimicrobial actions upon pathogens and indirectly by disrupting the activity of pathogenic species by reducing the PH of the gut.)
  • SB also enhances the immune system and its ability to detect and eliminate pathogens.
  • SB stimulate enterocyte, which are the cells of your gut lining helping to heal leaky gut and maintain a healthy gut lining integrity.
  • SB is anti-inflammatory and antibiotic and stomach acid resistant meaning you can take SB concomitant with antibiotics to minimise the damage the antibiotics are causing. In addition, SB will make it all the way to the colon where it will carry out its great work.

Bacillus coagulans (BC) spore probiotics are another favourite of mine. Spore-based probiotics are soil-based bacteria that are present in dirt and vegetation and are created from spores. They are adaptable and universal in nature, and I believe that with all of the sanitising we are now doing and the lack of contact with healthy soil, these probiotics are crucial for our gut health and provide much-needed support from modern living.

AMPERNA® Probiotics Feeling Worse?

Health benefits

  • BC Produces L-lactic acid which has shown to be tolerable for people with gut issues and has a more potent immune activity than the D-lactic acid produced by some probiotics.
  • CB may help to stave off viral respiratory tract infections, such as the common cold and the flu,
  • May help relieve stomach pain and bloating related to IBS
  • BC enhances the microbiome and supports the integrity of the gut lining

Both SB and BC are great options for use in people with gut issues such as SIBO and histamine intolerance.

Most of us can benefit from eating or taking probiotics, but we need to make sure the type of probiotics are the right ones. SB and BC are general in nature and can be used in most conditions, which is why after many years of research these are the probiotics we have chosen to include in our proprietary blend Biotics-Max® synbiotic pre and probiotic blend FEED.


By Bundle of FEED and REPAIR




Barc MC, Charrin-Sarnel C, Rochet V, Bourlioux F, Sandré C, Boureau H, et al. Molecular analysis of the digestive microbiota in a gnotobiotic mouse model during antibiotic treatment: Influence of Saccharomyces boulardii. Anaerobe. 2008 Oct;14(4):229-33. doi: 10.1016/j.anaerobe.2008.04.003.

McFarland LV. Use of probiotics to correct dysbiosis of normal microbiota following disease or disruptive events: a systematic review. BMJ Open. 2014:25;4(8). doi: 10.1136/bmjopen-2014-005047.

Joshi A, Suja S, Jashbhai P. Identification of Lactobacillus rhamnosus GG bacteriocin gene determinants expressed in vivo in murine gut. World J Food Dairy Sci. 2014:9(1):70-8.

Patel R, DuPont HL. New approaches for bacteriotherapy: prebiotics, new-generation probiotics, and synbiotics. Clin Infect Dis. 2015 May 15;60 Suppl 2:S108-21.

Travers M-A, Florent I, Kohl L, grellier P. Probiotics for the control of parasites: an overview. J Parasitol Res. 2011 Sep 28:610769. doi:

Dinleyici EC, Eren M, Dogan N, Reyhanioglu S, Yargic ZA, Vandenplas Y. Clinical efficacy of Saccharomyces boulardii or metronidazole in symptomatic children with Blastocystis hominis infection. Parasitol Res. 2011 Mar;108(3):541-5. doi: 10.1007/s00436-010-2095-4.

Goldin BR, Gorbach SL, Saxelin M, Barakat S, Gualtieri L, Salminen S. Survival of Lactobacillus species (strain GG) in human gastrointestinal tract. Dig Dis Sci. 1992 Jan;37(1):121-8. PMID: 1728516.

Mira Baron, MD. Original Research: A Patented Strain of Bacillus coagulans Increased Immune Response to Viral Challenge. Postgraduate Medicine 2009 Vol 121(2): 114-118

Michielan A, D’Incà R. Intestinal permeability in inflammatory bowel disease: pathogenesis, clinical evaluation, and therapy of leaky gut. Mediators Inflamm. 2015;2015:628157.

Stier H, Bischoff SC. Influence of saccharomyces boulardii CNCM I-745 on the gut-associated immune system. Clin Exp Gastroenterol. 2016;9:269-279. doi:10.2147/CEG.S111003

Tiago FCP, Martins FS, Souza ELS, et al. Adhesion to the yeast cell surface as a mechanism for trapping pathogenic bacteria by Saccharomyces probiotics. J Med Microbiol. 2012;61(PART 9):1194-1207. doi:10.1099/jmm.0.042283-0

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