Those of us in the functional nutrition and medicine world view antibiotics as the plague…but in certain scenarios, they are actually appropriate. If you come down with a severe infection that needs attention now antibiotics can be life-saving. And more and more research is showing the efficacy of using Rifaximin for SIBO treatment (with the right probiotic regimen, too, of course — see below).

The main problem with antibiotics is they not only can wipe out the bad bacteria, they can also wipe out your good bacteria that your gut absolutely needs in order to digest food and to crowd out future infections. Another issue with antibiotics, which most of my clients understand well, is they don’t always work because of biofilms. I’ll save the longer description of these for another day, but essentially a biofilm is a protective layer that things like bacteria, viruses, and parasites create to protect themselves from antibiotics and immune cells, effectively deflecting them away so they can survive. 


This can render antibiotics completely useless…and redirect them at your good bacteria. That’s even worse news for your poor lil’ microbiome!

As with anything, it’s all about finding a balance and making the right decision at the moment for your health. In acute, serious cases, antibiotics can save your life. But in many more cases, it’s an over-prescribed medication that does more harm than good.

So, if you do have to take antibiotics for something, how can you protect your gut to be sure it doesn’t also wipe out all of your beneficial bacteria?

Last week I traveled to San Diego, California for a Functional Diagnostic Nutrition (FDN) conference (one of the many schools I went to) and learned about a new antibiotic protocol from my favorite probiotic company, Microbiome Labs (the makers of Megasporebiotic!)

They gave me permission to publish their antibiotic protocol so everyone can have it. Below is the protocol:

Probiotic-Antibiotic Protocol

Step 1: Take (1) Restorflora and (1) HU58 with Breakfast
Step 2: Take (2) Megaspore Biotic with Lunch
Step 3: Take (1) Restorflora and (1) HU58 with dinner


Take this protocol during and then 21-30 days after completing the antibiotic protocol to protect your gut.

Order Probiotics

 (You’ll need to create an account, so use the patient direct code thrivebyfood when signing up.)

The combination of these three potent probiotics provides your gut with a powerful boost of the “good guys”. This can protect your microbiome from wipeout and rebuild it from any damage.



If You Have a History of Chronic Gut Infections…

…chances are antibiotics alone aren’t going to address the issue. To get to the root of it, you need to understand WHY your system is prone to infections (is it poor immunity, leaky gut, low stomach acid?) and from there, you need to build a good foundation to strengthen your system. This can significantly reduce the chances of recurring infections and GI issues. This is exactly what we cover (plus tonssss more) in my signature program, Love Your Gut. You’ll learn the in’s and out’s of gut health, how gut dysfunction occurs, and how to rebalance your system to keep it strong for life. This foundational program has helped people ranging from severe autoimmunity and IBD to those who just want to be more proactive about their digestion and do all the right things find answers and a practical set of habits they can implement daily to have a healthy gut AND healthy body.

Space is limited in this program because you get 1:1 time with me so only a limited number can join at a time. Learn more and enroll below!


Join the Love Your Gut program here >


Taking Antibiotics? How to Use Probiotics to Protect Your Beneficial Bacteria & Microbiome






Kristin Thomas is a health coach and Functional Diagnostic Nutrition Practitioner specialized in helping women with hormone, digestion, and autoimmune health concerns. Having gone through these health challenges herself, she now helps clients find their own path to complete wellness through practical and natural diet and lifestyle changes.





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