What To Do When You Have To Take Antibiotics

What to do When You Have to Take Antibiotics...

A few months ago, in THIS post, I opened up about my diagnosis of giardia. I was diagnosed with this parasitic infection (along with a tapeworm…ewwww) in May of 2015. My first reaction was complete disgust, followed by complete relief. I had been to so many doctors for so many years who just couldn’t understand my symptoms. My GI symptoms never fully lined up with my ulcerative colitis diagnosis and it had been such a mysterious struggle to keep my ulcerative colitis in check. Finally, I had something that made sense, that was actually relatively common, and that could be cured! All I had to do was one short round of antibiotics and I would be better, right?

Well… that is not exactly how it has played out.

Here is brief timeline Samantha V. Giardia:

June: 1 week course of tinidazole (limited spectrum antibiotic/antiparasitic) and albenza (anti parasitic/tapeworm medicine)

RESULT: no change in giardia infection, tapeworm gone

July: 1 week course of Flagyl (antbiotic/antiparasitic/straight-up poison) I was not at all prepared for this medication so I did nothing to help support my gut outside of just following my normal diet. I was super sick and began having an ulcerative colitis flare within a week of taking the medications.

RESULT: giardia infection dropped 4 points from a 6++ to a 2+ but was still present

August-November: I followed a natural protocol involving taking diatomaceous earth, Raintree A-P, and bidens pilosa daily for 2 months.

RESULT: No Change in Infection

November: another 1 week course of flagyl. This time I actually prepared, which is what I will talk about in this post, and avoided a flare but the medicine stage was still terrible.

RESULT: Infection dropped from a 2 to a 1 (Right about now I was losing my mind)

February 2016: 1 final week of flagyl along with a simultaneous month long natural protocol of the Amazon A-P, GSE, Goldenseal, and Berberine.

RESULT: Still Pending

So as you can clearly see, there has been nothing simple or easy about this process. You may be surprised to see that I have been on as many rounds of antibiotics as I have been and you should be surprised. Antibiotics are a huge trigger for my ulcerative colitis and avoiding them, when at all possible, was one of the biggest lifestyle changes contributing to my initial healing. However, I strongly believe that eradicating this parasite is a big piece of my healing puzzle so I decided that for me personally, the risk was worth it in the long run. That being said, this experience with the antibiotics has been a huge lesson for me because I learned that there really is a better way to go about taking them than to just pop pills first and ask questions later.

Hurting beneficial gut flora is inevitable when taking antibiotics but there is a lot you can do to help support your gut and body during the process that will improve your healing process post-antibiotics and minimize the likelihood of an autoimmune flare. Here is the routine I created that has helped me:

  1. Fermented Foods: Even though you are intentionally killing a lot of the bacteria in your body by taking an antibiotic, you should still be consuming as many probiotics as you can during the process because their presence (however brief) helps to protect you from bad bacteria and yeast taking over in the mean time.
  2. Probiotic Supplements: There is some debate over probiotics and autoimmune disease in the natural health community but I know for me and my fellow IBD sufferers they are a must, and they are definitely a must during a round of antibiotics. Probiotics can act as immune modulators while they are in your system so even though they are not colonizing in your gut they are helping minimize inflammation and reduce negative immune responses in the gut. During antibiotic treatment variety of bacterial strains is key so I take both a traditional probiotic and a soil based probiotic.
  3. Prebiotics: Are you sensing a trend? The good bacteria in your body need all the help they can get right now and that means food! This continues to be true in the weeks following antibiotic treatment while you work to re-colonize the gut. To achieve this I eat lots of veggies both cooked and raw and add a small amount of inulin fiber to my tea in the morning.
  4. Gelatin: I talk a lot about the importance of gelatin on this blog so I won’t go into tons of detail but for a very very very oversimplified mental picture think of gelatin as a glue that helps protect the lining of the gut from getting leaky! Gelatin is a big part of a gut healing diet.
  5. Water: Drinking plenty of water helps to gently detoxify the body and support your overall health
  6. Gentle Exercise: walks outside, yoga, dancing any form of enjoyable moderate exercise is important for your mood, overall health, stimulating the lymphatic system which helps to detoxify the body and lowering inflammation.
  7. Epsom Salt Baths: I talk nightly Epsom salt baths as a way to gently detox from the medicine and reduce inflammation. For some added detox add in baking soda to the baths as well. The bath needs to last 20-40 minutes for adequate detoxing.
  8. Sleep: getting adequate sleep is more important now than ever to help avoid a flare.
  9. Diet: Obviously I recommend following the autoimmune protocol diet to heal the gut, but while on antibiotics I also recommend steering away from ALL added sugar including honey, maple syrup, and the sugar in bacon along with avoiding caffeine and alcohol. Avoiding sugar decreases the likelihood of a future yeast or bad bacteria problem, avoiding caffeine helps to limit the stress on your adrenals and thyroid and avoiding alcohol helps preserve the integrity of the gut.

What To Do When You Have To Take AntibioticsHere is My General Daily Routine While taking and Recovering from an Antibiotic:

Breakfast: Breakfast Hash with Raw Sauerkraut plus Ginger tea with Grass fed gelatin and inulin fiber. Plus soil based probiotics, water and a little bit of bone broth.

Lunch: Salad with salmon and avocado plus a half a cup of water kefir and some bone broth

Exercise for 30 minutes, drink water

Dinner: any manner of veggies and meat with bone broth

Bedtime: Epsom salt bath, traditional probiotic, another cup of ginger tea with gelatin

(this schedule does not include the supplements that are part of me regular healing routine)

Obviously there is no way to guarantee how your body will react to a certain situation or medication. I was lucky enough to have been able to avoid antibiotics completely for two years while I began my initial AIP journey, but I have seen a huge difference in proactively working to protect my gut while on antibiotics rather than waiting to rebuild until after I was finished. I hope that this helps you as well.


Jesse St. Jean

Jesse St. Jean

I am many things: a wife, a daughter, a sister, a nutritional therapist, a dog-mom… and I’m an autoimmune warrior.


  • Great post! I’ve been searching out ways to protect my body during an antibiotic course. This post is very detailed and thorough. Thank you for sharing your experience.

  • Great information! I also found out I have a parasite. It’s called endolimax nana I strongly believe that it’s the reason for my IBS. I’m nursing my son so I can’t take anything strong right now but I’m starting DE soon. I’ve been eating AIP for about a week now. Hopefully I can kill it. Definitely not a fun time. I’ve been suffering for a long time and went to 2 Gi doctors of course they didn’t find it. I went to a functional practioner and did the extensive stool test and found it!! I was excited and grossed out at the same time. Cheers to healing!

Comments are closed.

Nutritional therapist Jesse

Hi, I'm Jesse

I empower women autoimmune warriors to reclaim their health by teaching each woman how to make the right food choices to heal her body while confidently owning her journey so she can live a vibrant life with chronic illness.


Copyright and Affiliate Disclosure:

* All recipes, photographs and articles on this site, unless otherwise noted, are my original creations and may not be copied or republished in any form.
The statements made here have not been approved by the Food and Drug Administration. These statements are not intended to diagnose, treat or cure or prevent any disease. You assume full responsibility for how you choose to use this information.
* Amazon Disclosure: “Jesse of AIP Sisterhood is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to [AIP Sisterhood (amazon.com, amazonsupply.com, or myhabit.com)].”

Recent Posts