Antibiotics are known to upset the harmonious balance of the microbiome—the trillions of bacteria in your gastrointestinal (GI) tract that are critically important to maintaining your overall health. As antibiotics eradicate harmful bacteria, they may inadvertently target the good-for-you ones, too, that keep this balance in check.

Shocking new finding: One out of four non-antibiotic drugs also inhibits the growth of at least one strain of healthy gut bacteria, according to a new study in Nature.

Among the medications known to disrupt your friendly microbiome flora…

• Acid-reducing medications. Proton pump inhibitors (PPIs) such as omeprazole (Prilosec OTC) and esomeprazole (Nexium) treat heartburn, ulcers and reflux by reducing acid production in the stomach. That ultimately lessens the amount of acid that reaches your gut.

But your gut microbiome wants an acidic environment, which helps healthy bacteria, such as Lactobacillus and Bifidobacterium, thrive and keeps harmful ones at bay. So while changing the gut’s pH to a more basic, less acidic level may improve symptoms, it allows dangerous bacteria to proliferate.

Recent finding: A review of studies that included about 300,000 patients found a 65% increase in the incidence of Clostridium difficile (C. difficile)–associated diarrhea among PPI patients. C. difficile releases toxins that damage the intestinal wall, causing pain, diarrhea and fever. Unwanted Streptococcus and Staphylococcus bacteria and Escherichia coli (E. coli) also tend to be more prevalent in the gut microbiome of PPI users.

Note: H2 receptor antagonists, known as H2 blockers, such as ranitidine (Zantac) or cimetidine (Tagamet), exert similar effects on the microbiome, though their impact is less potent than that of PPIs.

Try instead: As many as 70% of PPI patients may be taking them unnecessarily. Ideally, you want to take the smallest dose of these drugs for the shortest duration possible. Talk to your doctor about possibly tapering off by switching to a 20-mg dose of a mild PPI, such as omeprazole…then to an H2 blocker for a week or two…then slowly stopping altogether. Lifestyle modifications, including weight loss, smoking cessation and dietary tweaks to curb acid reflux, often are a first line of defense for indigestion.

Algae-based heartburn medicines such as Gaviscon may ease stomach upset by coating the stomach lining and, in turn, have less impact on the microbiome. Most people take two to four tablets after meals and at bedtime, up to four times daily.

Bifidobacterium has been shown to inhibit or prevent C. difficile infections, so consider a Bifidobacterium-containing probiotic, such as MegaFlora for Over 50 ($41.90 for 60 capsules, Mega when taking a PPI.

If you use both a PPI and a probiotic, take them separately to avoid canceling out the effects of each one. Most people take the PPI first and wait several hours before taking the probiotic. Talk to your physician to determine the best timing based on the PPI you’re taking.

• Nonsteroidal anti-inflammatory drugs (NSAIDs). NSAIDs, such as over-the-counter ibuprofen (Advil, Motrin) and naproxen (Aleve) and prescription celecoxib (Celebrex) and meloxicam (Mobic), relieve pain by blocking the formation of inflammatory compounds called prostaglandins. But there actually are several types of prostaglandins in the body, including one that protects the lining of the GI tract. Chronic NSAID use can erode this lining, causing leaky gut syndrome. That’s when dangerous bacteria “leak” into the bloodstream where they don’t belong and can wreak havoc by triggering inflammation, allergies, autoimmune disease and more damage to the microbiome.

Even worse: As the lining erodes, stomach bleeding and ulcers can occur. Patients end up using an acid-blocking medication to get relief, further compromising the microbiome.

Recent findings: NSAIDs also change the composition and diversity of gut microbes. In a study published in Clinical Microbiology and Infection, taking celecoxib or ibuprofen was linked with a surplus of Enterobacteriaceae bacteria, which can lead to serious infections in older adults.

Other research shows that when NSAIDs alter the microbiome, how the drug itself is broken down is impacted and its effectiveness is diminished. So when you must use an NSAID, take the lowest dose for the shortest duration possible.

Try instead: Yoga and physical therapy may ease pain and help you avoid NSAIDs altogether. Acupuncture stimulates the production of endogenous opioids, your body’s own natural pain relievers and may ease back, neck and shoulder osteoarthritis and headache pain.

A combination of feverfew, an anti-inflammatory plant in the daisy family, and ginger was shown to eliminate or significantly reduce migraine pain in 63% of participants within two hours, according to a study in Headache. Run-of-the-mill headaches should respond, too. (Try: GelStat Migraine.) Drinking 10.5 ounces of anti-inflammatory tart cherry juice can ease muscle soreness after a workout.

According to a study in Phytotherapy Research, rheumatoid arthritis patients who took 500-mg supplements of curcumin, a natural anti-inflammatory compound found in turmeric, experienced more pain relief after eight weeks than those taking an NSAID. Note: Avoid curcumin if you have ulcers or gallstones or take an anticoagulant.

• Iron supplements. Do you take an iron supplement or a multivitamin with iron? Many older adults begin taking these on their own to avoid anemia. If you have colon cancer or a GI disorder such as ulcerative colitis or Crohn’s, you may have been prescribed iron pills to counter the iron deficiency that often accompanies these conditions.

The problem: Less than 20% of the iron in most supplements is absorbed, mostly in the small intestine. The rest makes its way to the colon where nasty bacteria, including Salmonella, Shigella and E. coli, depend on it to survive and proliferate. So once that unabsorbed iron reaches the colon, it fuels bad bugs.

Try instead: Most healthy people can get enough iron through diet. In fact, women typically experience an increase in iron stores postmenopause, as they’re no longer losing iron through menstruation. A simple blood test can determine whether you need supplements.

If so, try a brand containing ferrous sulfate, which is better absorbed than other forms. (Try: Nature Made Iron.) That said, ferrous sulfate is notoriously constipating, so up your daily fiber intake to 30 g, drink plenty of water and get regular exercise to keep things moving.

After a few months, you may be able to switch to less constipating ferrous gluconate (it has less elemental iron by weight than ferrous sulfate, making it a step-down choice).

Tip: Look for the words “Slow Fe” on the bottle. This means the iron is released at a slower rate, which can be less constipating.

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