Many of my SIBO patients ask me if probiotics are safe for folks who have SIBO. “Doc, I read that probiotics will make my SIBO worse- is that true?” Some sources even claim that probiotics “feed” SIBO. But does current evidence support this claim? Is it safe (or otherwise advisable) to take probiotics if you have SIBO? Read on to find out.

Right out the gate, I think it’s important for us to acknowledge that people with SIBO have been through a lot. Many of them have been misdiagnosed, poked, prodded, and scoped for many years prior to setting foot in my office, and they have little to no progress to show for it. I understand why they can be gun-shy or downright leery, even of so-called “experts.”

That being said, as a clinician I frequently find myself up against the totality of human knowledge that is the internet. And while it’s tempting to joke that they’ll give anyone a YouTube channel or a Website- they will- there are two sides to consider. On the one hand, I strive to use scientific evidence as the foundation for what I recommend. On the other hand, we must acknowledge that science isn’t done yet. Our knowledge (as individuals and as a collective) continues to evolve each day, and there are things that we will discover in the future… we just haven’t gotten there yet. This is all to say: a lack of scientific evidence does not automatically mean that something can’t happen or is false. That being said, I will base this article on the available scientific evidence as well as my clinical observations and experience.

Symptom Flare = SIBO Flare?

Much of the time, SIBO patients attribute poor probiotic tolerance to a worsening of their bacterial overgrowth. It’s easy to understand why you’d think that- “If I have too many bacteria in my intestine, then adding more bacteria must make the condition worse.” However, there are other possible reasons someone may respond poorly to a probiotic- many of which can exacerbate symptoms that are commonly associated with bacterial overgrowth (ex. bloating).

  • Too high of an initial dose– I often start probiotics slowly with my more compromised patients. Sometimes I tell patients that they’re going to start at a “wussy dose” if I think we need to go particularly slow.

  • Insufficient time to adjust to the probiotic– sometimes it takes a few days or a week to get used to a new probiotic- this seems to be particularly true if your gut ecosystem is really dysbiotic/imbalanced. This may be for a multitude of reasons like biofilm disruption or “die-off” reactions from direct pathogen killing.

  • Disruption of the ecosystem– as above, biofilm disruption and/or “die-off” reactions from direct pathogen killing are possible. The change may be from “bad” to “better,” but the time between can be rough going, depending on the terrain.

  • Immune system– probiotics interact with the immune cells in our gut and can influence them in a multitude of ways (many of which are likely not understood at this time). This has the potential to influence your immune system and inflammatory burden for the better or worse, depending on what your body needs.

  • Incorrect strains– not all strains of the same species do the same things or adhere to the human gut the same way. For example, there are many strains of Lactobacillus acidophilus. Ideally, your practitioner should have a good understanding of how to select particular probiotic strains depending on the job they’d like to accomplish. You wouldn’t want to use a probiotic that speeds up transit time in a patient with diarrhea, for example.

  • Other possible mechanisms that are poorly understood at this time:

    • Histamine, Oxalates, vitamins, amino acids, neurotransmitters, and other metabolic byproducts of the microbiota. The things the microbiota produce or degrade affect us in many different ways.

    • Methylation- See the above vitamin comment- some bacteria produce B vitamins. This then relates to:

    • Epigenetics- The Microbiota and it’s metabolism impacts how we use our own genes

A chiropractor I worked for in Phoenix once told me this in regards to ergonomics, and I think it’s fitting here to. We were talking about how a lot of people dislike new beds, pillows, or ergonomic set-ups for the first week or two, and they’ll often be more sore before they feel better. She told me the body doesn’t necessarily register good change or bad change- it only perceives change, and that the body may just need time to get used to the new setup. I think the same is true of the microbiota- you may be on the path from a worse, more dysbiotic state to a better one, but you often have to go through a lot to get there.

Current Evidence

A meta-analysis published in 2017 reviewed the research on probiotics and SIBO and concluded “the present findings indicated that probiotics supplementation could effectively decontaminate SIBO, decrease H2 concentration, and relieve abdominal pain…” Additionally, some probiotics are known to slow down motility, speed up motility, heal the gut barrier, or reduce methane, which can be incredibly therapeutic to individuals with SIBO.

Organic yogurt probiotics microbiome

What about D-Lactic Acidosis?

In June 2018 a study titled “Brain fogginess, gas and bloating: a link between SIBO, probiotics, and metabolic acidosis” made a big splash in the SIBO community. The premise of the article was that probiotic use was associated with brain fogginess, D-lactic acidosis, and SIBO, and discontinuation of probiotics improved brain fogginess. I don’t believe we can draw such conclusions from this study, however (full review here). Namely, my two biggest critiques of the study are:

  • The authors didn’t re-test for D-lactic acid or SIBO after the treatment period. It’s impossible to know if one or both were adequately treated without follow-up testing.

  • The study had too many variables to draw any real conclusions. Patients were given antibiotics to treat SIBO (which could have treated the brain fog in a D-lactate dependent or independent way (ex. LPS reduction)), individual dietary recommendations, and were advised to discontinue probiotics. Additionally, several patients were consuming large amounts of yogurt or kefir as their source of probiotics, and it is possible that they were in fact dairy intolerant rather than probiotic intolerant.


  • Current research does not support the idea that probiotics “feed” SIBO or generally make it worse.

  • There is good quality evidence that probiotics can enhance treatment of specific pathogens (ex. H pylori), treat SIBO, decrease the gases SIBO produces, heal intestinal permeability, improve (speed up or slow down) motility, and benefit the host immune system.

  • Probiotics are only as good as:

    • Your ability to match the appropriate strain to the individual patient- what are you trying to accomplish? What strains are capable of achieving this goal?

If you’re struggling with SIBO or the low FODMAP diet, I would love to help you. If you’d like to improve your gut and digestion in a holistic way please call my office in Chapel Hill, NC at 919-238-4094.

Wishing you zero bloating and fantastic poops,

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