How Acid Reflux May Be Linked To Gut Dysbiosis

How Acid Reflux May Be Linked To Gut Dysbiosis

  • Gut Health

  • By Mathieu Millette, Ph. D., Mcb. A.

    Originally published in May 2018, updated in June 2024

    Gastroesophageal reflux (often referred to as just “reflux,” “GERD” or even “heartburn”), is defined as the backflow of food or stomach acid from the stomach up into the esophagus and is a condition many of us have likely experienced once or twice over the years. In fact, up to 25% of the general population is said to suffer gastrointestinal conditions resulting in heartburn at least one time per month.1 

    And while typical treatments include a wide assortment of over-the-counter acid-blocking drugs such as antacids and proton pump inhibitors (‘PPIs’), drugs of this nature have also been linked to negative side effects including gut dysbiosis as well as other more serious health conditions.2  Beyond that, frequent bouts of heartburn or acid reflux could be a signal that other health issues are occurring in the body, and even more specifically in the gut.


    The Acid Reflux - Gut Dysbiosis Connection

    Dysbiosis is a condition that occurs when there is an imbalance between good bacteria and bad bacteria in the gut. There are two ways acid reflux and gut dysbiosis are linked. The first is that heartburn or reflux actually might be a symptom of an unbalanced gut microbiome. In fact, this reflux could be your body trying to tell you that something bigger is happening within your body that needs to be addressed. The second link is that over-the-counter reflux medications, such as antacids and PPIs can actually cause gut microflora imbalance.


    1. Can acid reflux be caused by gut dysbiosis?

    Your frequent bouts of heartburn might be your body telling you that bigger things are happening, specifically in your gut. The catchall term ‘leaky gut’ is used when we have persistent symptoms of gas / bloatingconstipationdiarrhea, and even indigestion, heartburn or GERD and any of these symptoms are a sign of an imbalance of bacteria in the gut. It’s most common for acid reflux to be viewed of as an excess amount of stomach acid, but in fact, it’s usually the opposite - not enough acid to digest food is a major contributor to leaky gut.


    2. Can acid reflux medication cause gut dysbiosis?

    PPIs have been shown to have the potential to alter the normal microbiota of the gut. This change starts in the esophagus where the drugs modify esophageal bacteria and then continues into the stomach, small bowel and colon, altering the bacteria that is typically naturally present.2 PPIs change the diversity of bacteria in the gut and specifically, studies have shown that the differences between PPI users and non-users are consistently associated with changes that lead to a less healthy gut microbiome.3 Essentially, these drugs are wiping out good and bad bacteria in your body in their effort to remedy the absence of acid in the stomach.


    How to Support Your Gut & Reduce Reflux Symptoms

    The good news? Now that you know how reflux and gut dysbiosis are intricately connected, you can start to work on supporting your body through lifestyle, dietary and nutritional efforts that will help to bring balance back to your gut flora and mitigate the symptoms of acid reflux.


    1. Avoid trigger foods & drinks

    Some foods and drinks can exacerbate reflux symptoms. When dealing with a bad stretch of heartburn, consider eliminating carbonated beverages, alcohol, caffeine, coffee, acidic juices & sauces, and spicy foods.

    2. Increase probiotics

    It’s always good to incorporate probiotic-rich foods into your day but you should consider supporting a healthy microbiome with a daily probiotic supplement such as drinkable Bio-K+ or Bio-K+ capsules. While you can take a dose of Bio-K+ DailyCARE 12.5 Billion CFUs, if you’ve been taking PPI or antacid drugs or are frequently suffering from reflux symptoms, you might consider a higher dose with the Bio-K+ DailyCARE+ 25 Billion or our Bio-K+ ExtraCARE+ 30 Billion.

    3. Optimizing Your Stomach Acid

    It is often believed that too much stomach acid is the reason for acid reflux, having many people reaching for antacids to control it. However, it's not always the case of 'too much'; for a lot of people, it is a case of too little stomach acid that can be the cause of symptoms.

    Having enough stomach acid is essential for properly digesting your food and making sure levels of bad bacteria stay in check. In fact, it is believed that too little stomach acid might have links to SIBO. On the other hand, too much stomach acid isn't good either and can put you at risk for developing an ulcer. The tricky part about determining if your stomach acid is too low or too high is that symptoms often present in a similar fashion.

    Whatever side of the spectrum you are on, your symptoms of acid reflux are a sign that your digestive system is telling you something important. It's best to work with your healthcare practitioner to determine a plan that is right for you.  

    4. Rest & Digest

    In general, slowing down and being more mindful of eating can help with reflux. Try to avoid eating on-the-go or in a frantic and stressed state of mind. Additionally, stop eating 2-3 hours before bed to allow your body ample time to fully digest your last meal and prevent heartburn as a result of lying down.

    If you’ve ever experienced a bout of heartburn, you know exactly how uncomfortable it can be. And if you regularly suffer from this ailment, you know how frustrating it can be to chomp down on antacids regularly just for short-term relief. If you carefully consider your diet and your lifestyle, you’ll see that even minor changes can yield significant results. Focusing on foods that promote a healthy gut, supplementing with probiotics, and getting plenty of rest will all move you closer to a happy microbiome. 


    If you’re thinking about trying Bio-K+, head to our store locator. For more information on Bio-K+, probiotics and digestive health, contact usfind us on Facebook and Instagram or join our Gut Kommunity.


    This article is for information purposes only. Always check with your healthcare practitioner before starting or stopping a medication or supplement.



    1. Nutritional Interventions for Gastroesophageal Reflux, Irritable Bowel Syndrome, and Hypochlorhydria: A Case Report - PMC (

    2. The impact of proton pump inhibitors on the human gastrointestinal microbiome - PMC (


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    Mathieu Millette Mcb. A.
    About the author
    Graduated with honors from INRS-Armand-Frappier Institute, Dr Mathieu Millette is an authority on probiotics for the last 20 years.
    View all articles by Mathieu Millette
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