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Medicines and How It Affects the Gut

The gut microbiome is home to tens of trillions of microbes, including at least 1000 different species of bacteria. The microbiome’s population is influenced by several factors, including the use of antibiotics.


It’s truly amazing that we have effective, life-saving medicines like antibiotics for so many bacterial infections which previously have been untreatable. It’s been long enough that we now begin to see the effects of widespread use of antibiotics, and they are not a pretty picture.


Antibiotics can adversely affect the gut microbiome. However, research has found that many common drugs can have a significant impact on the gut including those that treat:

  • Digestive problems
  • High blood pressure
  • Diabetes
  • Bacterial infection
  • Depression

These common drugs can disrupt the delicate balance of the gut’s microbiome. Like antibiotics, they have a similar effect on the gut bacteria, which helps digest foods and maintain the immune system.


Medications whether the prescription and over-the-counter, while usually safe and effective, have harmful effects on our body. They can help treat diseases, manage symptoms of chronic health conditions, but they bring side effects.


Common drug to have the biggest impact on the gut’s microbiome


  • Antibiotics- fights bacterial infections
  • Metformin- used in treating type 2 diabetes
  • Proton pump inhibitor (PPIs): It’s commonly used in treating acid reflux, dyspepsia, and in reducing stomach acid. The microbiome of PPI users has an abundance of upper GI tract bacteria and increased fatty acid production. The use of this medicine can significantly decrease the overall diversity of the gut microbiome.
  • Laxative- used in treating and preventing constipation
  • Antipsychotic- These medications can help relieve the symptoms of depression, anxiety, other mental issues. But it appears to interact heavily with the gut microbiome. It reduces the overall number of good bacteria in the gut and shifts the profile of the gut to the type of bacteria that facilitates weight gain.
  • NSAID- It’s an anti-inflammatory medication prescribed for a wide range of conditions. The use of steroids is associated with high levels of methanogenic bacteria among obese people. It can cause damages to the gut lining, allowing bacteria to seep through the holes.


Metformin users, on the other hand, have a higher level of E. coli bacteria. IBS patients who use SSRI have an abundance of the potentially harmful bacteria Eubacterium ramulus. Patients who use statins can affect the balance of the gut in a way that alters the metabolism of cholesterol.


The good news: The role of probiotics in the gut microbiome


While all the information is definitely a downside, here’s the good news- you can help restore the balance of the gut microbiome with probiotics. Probiotics are live beneficial cultures found in foods, drinks, and even supplements. Below are health benefits linked to probiotics:

  • Probiotics help restore the balance of friendly bacteria in the gut.
  • Reduce the symptoms of certain digestive disorders, so you won’t have to take common drugs in treating digestive issues anymore.
  • Probiotics help boost the immune system and inhibit the growth of harmful bacteria.
  • It can keep your heart healthy by lowering bad cholesterol and blood pressure.
  • Helps improve some mental health conditions

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