New discoveries just keep coming about the importance of the gut microbiome—that trillions-strong trove of microorganisms, including both “good” and “bad” bacteria, that live all along the gastrointestinal (GI) tract. We know that this healthy balance of bacteria not only keeps your digestion humming but also promotes overall good health.

However, certain popular medications, such as antibiotics, heartburn drugs known as proton pump ­inhibitors (PPIs) and oral nonsteroidal anti-inflammatory drugs (NSAIDs), have been called out for upsetting the gut microbiome’s delicate balance. Now, new research is making the list even longer.

Latest development: In a study ­presented at a recent United European Gastroenterology Week conference, researchers from the University Medical Center Groningen in Groningen, the Netherlands, detailed additional categories of drugs that can alter the balance of good and bad bacteria.

Disrupting this balance can not only lead to troublesome side effects, such as diarrhea but also increase the risk for other health problems, such as obesity, and set the stage for serious disorders, including inflammatory bowel disease, type 2 diabetes and heart disease. Some of the same drugs have also been found to promote antibiotic resistance.

What you need to know to protect your gut microbiome…

Drugs that change the gut microbiome

In addition to antibiotics, most
notably, tetracycline…PPIs, such
as esomeprazole (Nexium)…and
oral NSAIDs, including ibuprofen (Motrin), the following drugs have recently been found to alter the gut microbiome…

Metformin. This often is the first medication prescribed after a person is diagnosed with diabetes—or, in some cases, prediabetes. What the recent research revealed: Use of metformin was associated with higher levels of Escherichia coli (E. coli) in the gut. Some strains of E. coli normally live in the gut and help with digestion, but an imbalance can be harmful, potentially leading to such problems as diarrhea and urinary tract infections.

Important: When a drug is prescribed for a specific condition—in this case, managing blood sugar—researchers noted that it’s hard to tell if the gut microbiome changes are from the disease or the medication. If you’re taking metformin, be sure to note any new symptoms or if the drug isn’t working and contact your doctor immediately.

Alternatives to consider: A lifestyle plan focused on diet and exercise and, if medication is necessary, possibly a sulfonylurea drug, such as glyburide (Glynase)…or a heart-friendly diabetes drug  such as the GLP-1 agonist exenatide (Byetta), based on a person’s heart health.

Laxatives. These are big gut disruptors, associated with higher, potentially harmful numbers of two types of bacteria—Alistipes and Bacteroides.

Alternatives to consider: Natural fiber products such as psyllium and, even better, eating more fiber-rich foods, such as fruit (including pears, figs, prunes and apples), beans, peas and lentils. Add them gradually to avoid bloating and gas as your GI tract adjusts to the change. Also, be sure to drink a lot of water.

Oral steroids. People taking these drugs have high levels of the microbe Methanobrevibacter smithii, which has been associated with obesity, a known side effect of commonly used steroids such as prednisone, which is one of the steroids looked at in the study.

Alternatives to consider: There are few alternatives to oral steroids. Treatment could include IV infusions of anti-
inflammatory medications, but this carries risks, such as bleeding.

Selective serotonin reuptake inhibitors (SSRIs). Antidepressant medications, such as paroxetine (Zoloft) and fluoxetine (Prozac), led to increased numbers of the bacteria species ­Eubacterium ramulus, which lower the absorption of flavonoids, the powerful plant-based disease fighters.

Alternatives to consider: The SSRI duloxetine (Cymbalta)…a tricyclic antidepressant, such as imipramine (Tofranil)…or the herb St. John’s wort—all of which may be less likely to increase harmful bacteria.

Worth noting: Gut microbiome ­changes were greater in people taking multiple medications, such as PPIs, laxatives and antibiotics. Also, people with GI conditions, including an ­inflammatory bowel disease or irritable bowel syndrome, which directly affect gut bacteria, may experience even greater side effects from the medications that they take.

Important: When discussing with your doctor the risk/benefit of any drug you’re taking, consider whether you’re using the medication temporarily or need it long-term for a serious disease such as Parkinson’s disease or multiple sclerosis. Some medications are helpful, and there may not always be an effective alternative. Never stop taking a medication without consulting your doctor.

Diet: A powerful solution

Along with the findings on medications, the researchers reported on the effect of diet on the gut microbiome.

Using stool samples from healthy people and individuals with Crohn’s disease, ulcerative colitis or irritable bowel syndrome, the researchers found that foods commonly included in a Mediterranean-style diet (such as vegetables, fruit, legumes, fish and nuts) were associated with higher levels of friendly, anti-inflammatory bacteria. Also: The findings confirmed that low-fat, fermented dairy foods, such as yogurt and kefir, increase good bacteria.

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