True health lies in the ability to live a balanced lifestyle. Here at Emily Eats, we’ll do our best to educate and inspire you to be at your best. Our holistic approach is complemented by scientific research because we believe a balanced lifestyle is the way to go.

True health lies in the ability to live a balanced lifestyle. Here at Emily 's Formula, I'll do my best to educate and inspire you to be at your best. My holistic approach is complemented by scientific research meaning you can be confident in my advice. 

How to restore your gut after taking antibiotics

How to restore your gut after taking antibiotics

So the other week disaster struck, something I have successfully managed to avoid for an impressive number of years (not to toot my own horn or anything....)

 Antibiotics. I am pretty sure I could hear my gut bacteria crying as I swallowed the pills. I know… overly dramatic, but it is no denying the negative effects of antibiotics on your gut micro-biome. While it is important to avoid antibiotic use, there is a time and a place and many cases when it is absolutely necessary.

In case you are wondering what I am talking about, antibiotics kill bacteria. The problem being that they don’t discriminate, so not only do they kill the bad bacteria, they wipe out all the good stuff too. A healthy gut microbiome is crucial to good health so it is important you work to restore the healthy population as quickly as you can.

So what can you do to repopulate the good bacteria that antibiotics have destroyed?

Plenty of antioxidants and rest

If you are taking antibiotics you are obviously sick, so rest is crucial as it is. However during a time of illness there will be a lot of oxidative stress as your body kills off all that bad bacteria. This means loading up on vitamin C, Vitamin E and other antioxidants is vital. Berries are antioxidant superstars so ensure to get those in. If your appetite is lacking, then berry powders in water or in a smoothie can be a great alternative to solid food.

Fermented foods

While antibiotics impact gut flora, the main problem is recovering the diversity. One of the best ways to expose yourself to more diverse bacteria is by consuming a whole range of fermented foods. While it is recommended that you consume fermented food every day anyway, during antibiotic use this becomes especially important! Eating a good variety of wild fermented foods (sauerkraut, kimchi, kefir, Kombucha, fermented vegetables etc.) will ensure that your gut microbiome will not get too out of whack. Kombucha is a good option if you are off solid food but just be mindful of the sugar content in some brands as it can quickly add up.


If you have taken a course of antibiotics, unfortunately fermented food on its own is not going to cut it. Your best bet to ensure your gut microbiome returns to normal is to take a good quality probiotic. A good protocol which I use myself and recommend to others is to take the probiotic halfway between your antibiotic doses (e.g. a morning and night antibiotic protocol would mean taking the probiotic at lunch time) for the duration of the antibiotics plus twice again (so 1 week antibiotics= 3 weeks of probiotics).


Prebiotics are very effective at promoting the growth of beneficial bacteria in the gut and thus are an important part of any regimen to rebuild a healthy microbiome. During and after antibiotic use, focus on getting plenty of fibre from sources such as starchy tubers, squash and fruits. Unripe bananas are a great source and can be nice on the stomach during times of illness.  

Bone Broth

During times of antibiotic use, the gut lining and digestive function can be impacted too. To soothe your digestive system, bone broth can be a great idea. Not only can it make you feel better when you are ill, it is rich gelatine so will promote gut healing. A report published in the Journal of Clinical Gastroenterology found that gelatine effectively supports intestinal health and integrity. 

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