How to keep your microbiome healthy when on antibiotics

Author: Dr. Michelle Durkin on 14 December 2021

Antibiotics may be the biggest reason for why our microbiome becomes unhealthy and yet they may also be necessary to treat an infection. So what is a patient to do?

Here are 5 tips to keep your microbiome healthy when prescribed an antibiotic:

1. Take a probiotic during the entire course of your antibiotics + up to a month afterward

This goes against the previous recommendation to wait until your antibiotic is finished to take a probiotic. The old thinking was that the antibiotic would just kill off the probiotics and nullify their effect. However updated research by Dr. Nigel Plummer from the UK shows probiotics have an added benefit when taken duringantibiotics.

Here are results from a clinical trial:

  • antibiotic without probiotics – significant growth of undesirable bacteria in the gut; undesirable bacteria present at day 7 and persisted at day 28
  • probiotics after antibiotics – significant growth of undesirable bacteria present at day 7 but gone on day 28
  • probiotics along with antibiotics – no undesirable bacteria at day 7 or 28

2. Use a high dose probiotic instead of a maintenance dose for up to one month

Using a probiotic that has a 100 billion CFU count will protect the microbiome more robustly than one that only has a 5 billion CFU count. 

When is comes to the CFU count you want one high enough to match the strength of the antibiotic otherwise the antibiotic will win the battle. 

Think of the antibiotic on one side of a teeter-toter and the probiotic on the other side. You need them to be about the same weight to keep it balanced. 

My current go-to supplements are Ultra Flora BiomePro by Metagenics (keep in fridge) OR OrthoBiotic 100 by Orthomolecular Products (shelf-stable). Both are available at the office or through Fullscript

3. Take your probiotic at the opposite time of day as your antibiotic

This helps reduce the amount of contact time the antibiotic and the probiotic have in the digestive tract together. This will ensure you get the highest dose of your probiotic possible to the intestines. 

Sometimes this is not logistically possible, eg. your prescription is to take your antibiotic three times a day. Just do the best you can.

Bottom line - it's better to get the probiotic in versus worry about the timing. 

4. Consuming yogurt to obtain your probiotics is like digging a hole with a spoon 

Whenever I hear the recommendation to just eat yogurt to get your probiotics I cringe. But then I don't like to waste time. I like to work efficiently. 

Could yogurt be beneficial to your microbiome? Possibly. If you are getting organic, sugar-free and you are not dairy or lactose intolerant. And if you have time to spare. 

Bottom line - I think of yogurt as a food source of probiotics that will help maintain your already healthy microbiome. I do not think of it as a therapeutic prescription. 

Some other fermented foods that will help maintain a healthy microbiome that are not dairy-based include:

  • Fermented vegetables (e.g., sauerkraut, kimchi, unpasteurized pickles)
  • Fermented soy products (e.g., miso, tempeh, natto)
  • Fermented beverages (e.g., kombucha, kvass, water kefir)

5. If you are getting gi symptoms on antibiotics even when taking a high dose probiotic you might have a leaky gut

For some patients a high dose probiotic is just not enough because they already have an underlying condition that needs treatment. The most common one is leaky gut syndrome, but others include SIBO, hypochlorhydria, and histamine intolerance. 

If this is the case an individualized protocol developed by your naturopathic doctor is appropriate. 

In the meantime an anti-inflammatory for the mucus membrane of the gi tract can help with symptoms. One of my favourites is DGL (a special type of licorice root). I use one called DGL chewable by Bioclinic Naturals. 

6. If you are chronically being prescribed antibiotics you need to start looking for the root cause

If you are being prescribed antibiotics more than once a year you are likely not treating the root cause, you are only treating the symptoms. 

Some common recurring infections that I have investigated the underlying cause for patients include: urinary tract, sinus, chest/bronchial, ear, tonsils, and dental. 

Now they no longer need recurring antibiotics and their microbiome is thanking them for it!

Now I would love to hear from you! Leave a comment below and I'll be back next week with my last edition of Doctor as Teacher Tuesday!

2 Replies to “How to keep your microbiome healthy when on antibiotics”

Barbara Cooney

Thank you for this. So informative.

Dr Michelle Durkin ND

You’re welcome Barbara!

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