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Natural Ways To Restore A Healthy Microbiome After Antibiotics

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Natural Ways To Restore A Healthy Microbiome After Antibiotics

Natural Ways To Restore A Healthy Microbiome After Antibiotics

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Why are we concerned about our intestinal flora?

Over the past decade, researchers have begun to pay more attention to the role of microorganisms living in the gut. Recent research has highlighted the importance of our intestinal microbiome and its role in regulating many aspects of our health including our mental health, metabolism, and immune function. As we begin to realize how essential this flora is to our health, it becomes apparent that there may be unintended consequences of antibiotics on our intestinal flora that could have long term effects.

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Effects of antibiotics

When we take antibiotics to fight a disease-causing bacteria, the friendly bacteria in our gut is also impacted. This is why doctors do not want to prescribe antibiotics for every minor cold; unnecessary use of antibiotics can lead to other health problems including indigestion, gassiness, weight gain, even depression. When antibiotics are needed to treat a disease, it is critical to take the entire dose recommended by the doctor, because skipping pills can lead to highly dangerous antibiotic-resistant diseases. In these situations, it is also necessary to take steps to restore a healthy microbiome following treatment.


Prebiotics are foods that stimulate the growth of healthy microorganisms in the intestine. These foods are generally high in fiber, complex carbohydrates, and complex starches that humans cannot digest, but are great foods for friendly flora. While you can purchase prebiotic supplements at most health food stores, many normal foods are good sources of prebiotic nutrients. Bananas, whole grains, beans, onions, garlic, and most green vegetables provide great substrate for a healthy micro biome.

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Probiotics are the microorganisms that go into a healthy intestinal flora. Following a course of antibiotics, a good probiotic supplement can help to restore the microbiome, but some of the best sources of probiotics are cultured and fermented foods.

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Yogurt is a classic source of probiotics, so are foods such as sauerkraut, kimchi, kombucha tea, tempeh, and kefir. Remember that not all foods are made equally, so check the label to make sure that your cultured and fermented foods have not been frozen or doctored with sugary flavoring that reduces the health benefits.

Avoid processed and artificial sugars

As you are probably starting to realize, your natural flora is greatly affected by the foods you eat. While good bacteria love complex carbohydrates, fiber, and starches, foods that are high in processed sugar are not a good source of nutrition for you or your microbiome. Processed sugars encourage the growth of bad bacteria in the gut; these bacteria can slow your metabolism, cause disease, and even increase your risk of cancer! Some research has demonstrated that artificial sweeteners like aspartame may be even worse for for your friendly flora and lead to an even greater risk of obesity. Limiting your overall sugar consumption and replacing processed and artificial sugar with natural sweeteners like raw honey, agave, and stevia, will encourage a healthier microbiome that translates into a healthier you!

What to do during antibiotic treatment

Eating prebiotic and probiotic foods while limiting processed sugar can improve your health at any point in your life, but these steps are particularly important during and following antibiotic treatment. Consuming probiotic foods while you are taking your medication will help maintain populations of healthy microorganisms in your gut, and insure that they will be restored more quickly following treatment. Eating prebiotic foods and avoiding processed or artificial sugar in the weeks after your antibiotic treatment will promote the growth of friendly intestinal flora and help prevent bad bacteria from taking over.


The best way to promote a healthy microbiome is to eat a good diet. Eating foods with naturally occurring microbes and taking a high quality probiotic supplement will populate your body with the friendly microbes; consuming high fiber foods that are free of processed ingredients insures that these beneficial microbes flourish in your gut.


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