If you’ve ever suffered from acid reflux, you know how painful it can be. It feels like a raging fire is burning in your chest.
You feel awful when you’re standing or sitting, and even worse if you try to lie down. Your mouth fills with a bitter, acidic taste.
And you just want it to go away.
So you go for the most popular heartburn “solution” you can get without a prescription… an over-the-counter PPI (proton pump inhibitor) drug. And it works. Fast.
So you turn to a PPI every time you get indigestion, which starts happening more and more. And the drugs keep working, helping you feel better… but at a great cost to your overall health.
In fact, the more often you take a PPI, the more damage it does to your body… starting with your gut.
Quick Answer: Acid reflux, heartburn, and GERD are related but not identical: heartburn is the burning chest pain, acid reflux is the backflow of stomach acid that causes it, and GERD is chronic reflux. The most popular fix, over-the-counter PPIs (proton pump inhibitors), works fast, but it is meant only for short-term use. Long-term PPI use is linked in research to serious risks, including gut infections, nutrient deficiencies, and bone, kidney, and heart problems, largely by suppressing stomach acid and disrupting the gut microbiome. Supporting gut balance with spore-based probiotics, and traditional digestive bitters, can be a gentler way to address the indigestion that drives PPI overuse.
Are Reflux, Heartburn, and GERD the Same?
No, but they are closely related. Heartburn is the burning chest pain you feel, acid reflux is the backflow of stomach acid that causes it, and GERD is chronic acid reflux that happens more than twice a week.
People talk about acid reflux, heartburn, and GERD like they’re all the same. They’re not… but they’re close.
Heartburn describes the symptoms you feel, that burning pain in your chest.
Acid reflux happens when stomach acid flows the wrong way and moves up into your esophagus (the tube that connects your throat to your stomach). This causes heartburn.
GERD, or gastroesophageal reflux disease, refers to a long-term condition, where acid reflux happens more than two times a week.
| Term | What it means |
|---|---|
| Heartburn | The burning chest pain symptom |
| Acid reflux | Stomach acid flowing up into the esophagus, which causes heartburn |
| GERD | Long-term acid reflux that happens more than twice a week |
And if you’re suffering from any of the above, chances are you’ve tried PPIs to make it stop. And since they work so well for blocking acid, you likely felt relief. That’s why PPIs land in the top ten best-selling drugs in the world, racking up billions of dollars every year in sales.
Problem is… PPIs can do significant damage to your health.
Which Drugs Are PPIs?
You can find several different kinds of PPIs at the drugstore, including:
- esomeprazole, sold as Nexium
- lansoprazole, sold as Prevacid
- omeprazole, sold as Prilosec and Zegerid
How Do PPIs Damage Your Health?
PPIs are meant for short-term use (no more than 14 days, up to three times a year), but long-term use is linked to serious risks, from gut infections and nutrient deficiencies to bone, kidney, and heart problems, largely by suppressing stomach acid and disrupting the gut microbiome.
The real issue with PPIs and other acid blocking drugs has to do with time.
These drugs are meant to be used occasionally, for short periods of time: no longer than 14 days, up to 3 times a year.
But millions of people around the world use PPIs far more than that… for months, years, even decades.[1] And blocking stomach acid, especially over the long term, endangers your health much more than you’d think.
Here are 12 of scientifically proven ways that long-term use of PPIs could hurt you:
- Increase your risk of developing C. difficile, a potentially deadly bacterial infection, by up to 200%[2]
- Create conditions that lead to SIBO[3]
- Increase your risk of heart attack, stroke, and other major cardiac events[4]
- Weaken bones, increasing your risk of hip fractures by 35%[5]
- Triple your risk of iron deficiency[6], which can lead to anemia and other health issues
- Increase your risk of chronic kidney disease by up to 50%[7]
- Cause a dangerous electrolyte imbalance (called hypomagnesemia)[8] that can trigger convulsions, muscle weakness, and vomiting
- Increase your risk of pneumonia by 150%[9]
- Lead to severe vitamin B12 deficiency[10], which can leave you feeling weak and tired all the time
- Lead to inflammatory bowel disease (IBD), especially in children
- Increase your risk of bacterial infection, including Salmonella and Shigella, by up to 1,200%[11]
- Cause an imbalance in your gut bacteria, which can have dozens of severe health consequences[12]
How Do PPIs Affect Your Gut Microbiome?
PPIs reduce the stomach acid that normally kills pathogens, which lets harmful bacteria grow and throws the gut microbiome out of balance (dysbiosis). Research suggests PPIs can alter the microbiome even more than antibiotics do.
Your gut microbiome contains trillions of bacteria, both helpful (probiotic) and harmful (pathogenic). In a healthy gut microbiome, you’ll find a wide variety of different types of probiotic bacteria that greatly outnumber pathogens. Those beneficial probiotic bacteria act as the centerpiece of your digestive, immune, and overall health.
When your gut microbiome is in good balance, probiotic bacteria:
- Help you absorb and use essential nutrients
- Promote natural energy production
- Support healthy inflammatory responses
- Defend against pathogens
- Keep your crucial systems and organs working properly
But if you add PPIs into the mix, they upset the delicate bacterial balance and create dysbiosis[13], a condition where pathogens outnumber probiotics. In fact, according to research, PPIs can alter your gut microbiome even more than antibiotics do![14]
One of the great things about your stomach acid is that it can kill off a lot of pathogens. When you keep your acid levels low via PPIs, you allow potential pathogens to grow and multiply.
To boot, studies show that PPIs can drastically change the makeup of the gut microbiome, as well as decrease the number of different types of bacteria found in the gut.[15] That can lead to a vast number of health problems far beyond your gut...
How Do Spore Probiotics Restore Gut Balance?
Spore probiotics arrive in the gut alive, help crowd out pathogens, and encourage a diverse population of beneficial bacteria, which supports the microbiome balance that long-term PPI use can disrupt.
Keeping your gut microbiome in healthy balance is one of the most beneficial things you can do for your body. And spore probiotics can help with that by:
- Arriving 100% alive in the gut
- Eliminating pathogens
- Encouraging many varieties of beneficial bacteria
As an added bonus, studies show that probiotics can help with the nausea, gas, burping, and indigestion that are often the chief reasons for PPI overuse. (totally not sure if it’s ok to include this line)
Can Digestive Bitters Help With Indigestion?
Digestive bitters are traditional plant extracts used to support healthy digestion. People have relied on them since ancient times to ease common complaints like indigestion, bloating, and reflux.
When any of these normal digestive processes doesn’t quite work, the results are noticeably uncomfortable. As ancient peoples didn’t have access to things like antacids, these natural digestive aids played a key role in promoting optimal digestion. That’s why traditional medicinal use of bitters goes all the way back to ancient times.[3] Because indigestion, nausea, bloating, diarrhea, constipation, abdominal discomfort, and reflux are all very common digestive consequences… and no one wants to experience them.
Frequently Asked Questions About Reflux and PPIs
Are heartburn, acid reflux, and GERD the same thing?
No. Heartburn is the burning chest pain, acid reflux is the stomach acid that backs up and causes it, and GERD is chronic acid reflux occurring more than twice a week.
Are PPIs safe for long-term use?
PPIs are designed for short-term use, no more than 14 days up to three times a year. Long-term use is linked in research to a range of health risks. Talk to your doctor before changing any prescribed medication.
How do PPIs affect the gut?
By suppressing the stomach acid that normally kills pathogens, PPIs can let harmful bacteria grow and push the gut microbiome out of balance. Some research suggests they alter the microbiome even more than antibiotics.
Can probiotics help with reflux or indigestion?
Studies suggest probiotics may help with the nausea, gas, burping, and indigestion that often drive PPI overuse, while supporting a balanced gut microbiome.
What are digestive bitters?
Digestive bitters are traditional plant-based extracts used since ancient times to support healthy digestion and ease common complaints like indigestion and bloating.
Support a Healthy Gut and Optimal Digestion with Just Thrive
A healthy gut microbiome counts on Just Thrive for daily support.
Just Thrive Probiotic contain four clinically studied strains of spore probiotics, including
- Bacillus subtilis HU58
- Bacillus indicus HU36
- Bacillus coagulans
- Bacillus clausii
These powerful probiotics work individually and together to help keep your gut microbiome in healthy balance.
Try Just Thrive Probiotic today… You and your gut will be happy you did.
Sources
- Hálfdánarson ÓÖ, Pottegård A, Björnsson ES, et al. Proton-pump inhibitors among adults: a nationwide drug-utilization study. Therap Adv Gastroenterol. 2018;11:1756284818777943. Published 2018 May 30. doi:10.1177/1756284818777943
- Trifan A, Stanciu C, Girleanu I, et al. Proton pump inhibitors therapy and risk of Clostridium difficile infection: Systematic review and meta-analysis. World J Gastroenterol. 2017;23(35):6500-6515. doi:10.3748/wjg.v23.i35.6500
- Cleveland Clinic. Long-term use of PPIs has consequences for gut microbiome. Published September 18, 2018. Accessed April 3, 2025. https://consultqd.clevelandclinic.org/long-term-use-of-ppis-has-consequences-for-gut-microbiome
- Li S, Liu F, Chen C, et al. Real-World Relationship Between Proton Pump Inhibitors and Cerebro-Cardiovascular Outcomes Independent of Clopidogrel. Int Heart J. 2019;60(4):910-918. doi:10.1536/ihj.18-584
- Fusaro M, D'Arrigo G, Pitino A, et al. Increased Risk of Bone Fractures in Hemodialysis Patients Treated with Proton Pump Inhibitors in Real World: Results from the Dialysis Outcomes and Practice Patterns Study (DOPPS). J Bone Miner Res. 2019;34(12):2238-2245. doi:10.1002/jbmr.3842
- Tran-Duy A, Connell NJ, Vanmolkot FH, et al. Use of proton pump inhibitors and risk of iron deficiency: a population-based case-control study. J Intern Med. 2019;285(2):205-214. doi:10.1111/joim.12826
- Lazarus B, Chen Y, Wilson FP, et al. Proton Pump Inhibitor Use and the Risk of Chronic Kidney Disease. JAMA Intern Med. 2016;176(2):238-246. doi:10.1001/jamainternmed.2015.7193
- Park CH, Kim EH, Roh YH, Kim HY, Lee SK. The association between the use of proton pump inhibitors and the risk of hypomagnesemia: a systematic review and meta-analysis. PLoS One. 2014;9(11):e112558. Published 2014 Nov 13. doi:10.1371/journal.pone.0112558
- Lambert AA, Lam JO, Paik JJ, Ugarte-Gil C, Drummond MB, Crowell TA. Risk of community-acquired pneumonia with outpatient proton-pump inhibitor therapy: a systematic review and meta-analysis. PLoS One. 2015;10(6):e0128004. Published 2015 Jun 4. doi:10.1371/journal.pone.0128004
- Lam JR, Schneider JL, Zhao W, Corley DA. Proton pump inhibitor and histamine 2 receptor antagonist use and vitamin B12 deficiency. JAMA. 2013;310(22):2435-2442. doi:10.1001/jama.2013.280490
- Bavishi C, Dupont HL. Systematic review: the use of proton pump inhibitors and increased susceptibility to enteric infection. Aliment Pharmacol Ther. 2011;34(11-12):1269-1281. doi:10.1111/j.1365-2036.2011.04874.x
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Bruno G, Zaccari P, Rocco G, et al. Proton pump inhibitors and dysbiosis: Current knowledge and aspects to be clarified. World J Gastroenterol. 2019;25(22):2706-2719. doi:10.3748/wjg.v25.i22.2706
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Takagi T, Naito Y, Inoue R, et al. The influence of long-term use of proton pump inhibitors on the gut microbiota: an age-sex-matched case-control study. J Clin Biochem Nutr. 2018;62(1):100-105. doi:10.3164/jcbn.17-78
- Imhann F, Bonder MJ, Vich Vila A, et al. Proton pump inhibitors affect the gut microbiome. Gut. 2016;65(5):740-748. doi:10.1136/gutjnl-2015-310376
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Macke L, Schulz C, Koletzko L, Malfertheiner P. Systematic review: the effects of proton pump inhibitors on the microbiome of the digestive tract, evidence from next-generation sequencing studies. Aliment Pharmacol Ther. 2020;51(5):505-526. doi:10.1111/apt.15604
