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What To Do After You’ve Taken Antibiotics: Natural Steps to Regain Your Health

Robyn Openshaw - Jul 02, 2019 - This Post May Contain Affiliate Links

medication in blister packets

This post has been medically reviewed by Dr. Tim Jackson, DPT and functional medicine practitioner.

I’ve written a few times about alternatives to antibiotics and how I helped my daughter get well without them.

But antibiotics are still one of the most over-prescribed class of drugs--and one of the most debilitating, in terms of their long-term risks and side effects.

Antibiotics destroy ALL the bacteria in your digestive tract, even the good guys, which leaves you vulnerable to poor immune health and a whole variety of diseases and illnesses.

In this post:

Allie, a member of our GreenSmoothieGirl team, had a terrible experience after taking two rounds of strong antibiotics this past year.

She had a tooth abscess that a conventional dentist missed (twice, x-rays and all), and by the time she was officially diagnosed, the situation was serious.

Good and Bad Gut Bacteria

Antibiotics can not tell the difference between good and bad bacteria.

She took the antibiotic Clindamycin to get rid of the abscess, had her tooth extracted, then shortly after, was rushed to the hospital. She was diagnosed with Clostridium Difficile (C Diff), a severe colon infection resulting from antibiotics wiping out all of the “good” bacteria, allowing the bad ones to take over.

And guess what the cure for C Diff is? Stronger antibiotics. There went a lifetime of Allie’s body carefully cultivating healthy gut bacteria! It’s a vicious cycle.

Since abscesses and C Diff can both turn ugly (and deadly), she felt she didn’t have a choice in taking them. Once on Flagyl, the stronger antibiotics, she soon developed a painful, blistering rash all over her chest and torso: shingles!

It’s extremely likely that Allie developed both C Diff AND shingles as a result of losing all of her healthy gut flora, which weakened her entire immune system.

She was then prescribed anti-virals, while still taking the Flagyl, but she decided “enough was enough.”

Her body couldn’t handle any more immune suppressing, and since shingles wasn’t going to be deadly, she chose not to take more drugs.

This cluster of events, and the devastation of her good gut bacteria, began a horrible road for Allie. She developed Postural Orthostatic Tachycardia Syndrome, severe histamine intolerance, reactions to lights and chemicals, and extreme anxiety. (These may seem like very different symptoms, but they are all commonly linked to antibiotic use.)

She was in and out of the hospital for months without answers.

She took matters into her own hands. She decided to find a way to heal her body after all the damage the antibiotics did, and with extensive research, patience, and dedication to rebuilding her gut health with the steps below, she’s finally feeling much better.

If you’ve ever had to take antibiotics before, you know that healing your gut can take time. Years, even.

So it’s best to equip yourself with knowledge in order to have the best shot at repopulating your gut with the good probiotic organisms that are your defense against the microbes that cause illness we are all exposed to.

Here’s what Allie learned in her healing process after taking antibiotics:

Find a small-batch superior probiotic

This is vital, as the antibiotics have wiped out all of your bad bacteria in your body, along with the good bacteria. You’ll have to add it back in with probiotics, following your antibiotics course.

Ad for PZP

Probiotics are live, helpful bacterias and yeasts which are essential for digestion, immune health, and absorption of vitamins and minerals. There are many types of probiotic strains, and the more strains in your gut, the better.

In many studies, probiotics taken during and after antibiotic courses have reduced patient risk of developing complications like Allie experienced. L. casei, L. bulgaricus, and S. thermophilus are especially helpful strains.

Our GreenSmoothieGirl PreZyme Pro contains all three of these probiotic strains, along with 12 others, and many other excellent gut-healing ingredients. Taking this supplement alone will reintroduce 15 strains of the good bacteria back into your body!

Use digestive enzymes

Digestive enzymes should be your second line of defense for a gut that needs attention and healing, since they break down nutrients so your body can better absorb the food you eat.

Enzymes help your immune system function. White blood cells, which help fight off those viruses and bacteria, are full of enzymes.

In fact, if your body lacks digestive enzymes, undigested food can build up in your digestive system, which will activate your immune system unnecessarily. By taking enzymes, you’re ensuring your body can focus on rebuilding and restoring, rather than digesting.

Again, our PreZyme Pro is a wonderful place to start, since it includes prebiotics, 15 total strains of probiotics, and six enzymes all-in-one. This supplement is designed for total GI tract health, helping you absorb nutrients in every stage of your digestion.

Eat prebiotic foods

Eating prebiotic foods is an easy way to stimulate growth of lactobacilli or bifidobacteria and other “good bacteria” in your gut and colon. They’re what probiotics “eat” to proliferate quickly.

Our PreZyme Pro contains the prebiotic Organic Yacon (FOS), which has been proven to have multiple benefits for your digestion and immune health.

You can also eat fibrous foods to get your prebiotic fill: greens, veggies, fruits, legumes, whole grains, nuts, and seeds.

Don’t take the nausea meds

Sometimes, antibiotics can make you nauseous. Allie’s antibiotics were so strong that her doctor prescribed the same anti-nausea meds used for chemotherapy patients. After considering the side-effects of this type of medication (dizziness, lightheadedness, fever, blurred vision, and more), she decided not to use it.

One good alternative is an acupressure wristband. It’s drug-free and proven in studies to work efficiently as a substitute for anti-nausea meds like Zofran.

Increase intake of gut-healing foods

Robyn Openshaw and a jar of fermented sauerkraut.

Robyn Openshaw and a jar of fermented sauerkraut.

Do you sense a theme here? Around 85% of your immune function is in your second brain (your gut), so you’ve got to focus on gut-healing foods.

Fermented foods increase your antibodies, which recognize foreign invaders, and also support your immune system with their beneficial bacteria.

Eat fermented foods like sauerkraut, make your own bone broth, drink aloe, and read my article on kefir (a cheap way to help your microbiome). I have an entire Rehab Your Gut With Food video in the 12 Steps to Whole Foods masterclass if you want to learn more.

Our Bone Broth Protein is another great option, giving you the nutrient benefits for your gut, joints, and muscle tone without having to simmer bones for days!

Boost your immune system

Your immune system is closely linked to your gut health. If you have a healthy gut flora, you have a stronger defense against viruses, bad bacteria, and other illnesses. In fact, you can think of your gut flora as your immune system warriors.

Because antibiotics wipe out your good gut bacteria, and therefore temporarily weaken your body’s defense system, there are some supplements you can take along with your antibiotics to give your body some additional immune system support.

I’ve written about 7 Natural Immune Boosters where I discuss my top favorites supplements for supporting the immune system, including Vitamin C and zinc.

We cannot produce our own Vitamin C, so we have to get it through plant foods, like strawberries or citrus, or by temporarily supplementing. Vitamin C works to support immune system cells, which destroy invaders like bad bacteria.

Zinc helps control inflammation and support T-cells, which are a type of white blood cell. T-cells are a vital part of the immune system, and important defenders against pathogens.

Another way to boost your immune system is to get enough rest and sleep, allowing your body time to regenerate.

Have a warm drink

Recover from Antibiotics with my Immune Fuel Hot LemonAid

Drinking hot tea with immune boosting ingredients is a natural alternative to antibiotics.

You’ll find ginger and lemon in my Immune Fuel Hot LemonAid recipe, which is easy to make and has immune boosting properties. I’ve seen this drink “knock down” a cold or flu countless times. After taking antibiotics, your body can use all the immune support it can get!

Fresh ginger has anti-inflammatory, antioxidant properties, and also has been found to activate your immune system’s T-cells. Ginger also has great digestive benefits, like stimulating saliva and gastric juices to help break down the food you’re eating.

Lemons are high in potassium and Vitamin C, which help support your body in fighting off invaders.

Keep a positive outlook

When you’re sick, it’s easy to feel upset and focus on the negative symptoms. Instead, do everything you can to stay positive.

Scientists have found that being optimistic actually helps strengthen the cells in your immune system, while being pessimistic depresses your immune system and makes it harder for your body to fight any "bad guys." While you can’t change the fact that you were sick and needed antibiotics, you can definitely control your attitude and keep it positive, especially now that you know it could help in your healing.

Create a gratitude journal and write in it every morning. Repeat positive affirmations to yourself, instead of dwelling on how crummy you feel. Write a mantra and post it all over your house or office where you can see it.

Try tapping

Another way to get yourself in the right mindset for healing is through Emotional Freedom Technique, or EFT, which is leveraging acupressure points, or the body’s energy meridians, without needing a professional. You tap on certain energetic points from the top of the body to the midpoint, while repeating positive or true mantras.

One example would be to say, “Even though I am feeling sick and I don’t have faith in my healing right now, I completely love and accept myself.” Then you would progress through the meridians, tapping with two fingers on your head, face, and collarbone, repeating mantras like, “I am safe. My body will heal itself. I release all stress and tension associated with this illness.”

Tapping was especially useful for Allie in her healing process. Listen to my podcast episode for a more in-depth look at tapping. In the podcast shownotes, you’ll find a free 8-point EFT tapping chart you can download to get started.

Calm the nervous system

I talk a lot about raising your vibration through the foods you eat and the way you think. In fact, my podcast Your High Vibration Life is named after that very concept.

When you’re sick, you want to focus on habits that will take you to higher frequencies, such as health, joy, peace, and gratitude. One way to do that is to follow some guided meditations. This will be calming to your nervous system, which, in turn, will allow your body to focus on healing.

Another way to calm your nervous system is to make sure you’re getting enough highly absorbable nutrients and trace minerals, since your body needs them for its every function. By adding Ultimate Minerals drops to your water before bed and first thing in the morning, you’re supporting your neurological system when it needs it the most. Our formula allows nutrition to enter your cells, which lets your body begin recovering from the damage antibiotics can do. Ultimate Minerals are simply fulvic and humic acids from deep-Earth ancient plant deposits, which is the source of minerals for all plant life. (However, most plants, due to overfarmed soils and spraying, are depleted.)

Along with getting adequate rest and sleep, these above tips should help get your body back on track after taking antibiotics. Know that it can be a slow process. It can take months or even years to build your gut flora back up, since antibiotics kill virtually all flora in a matter of days, but building it up takes consistent effort over the course of a few months, at least. Be consistent with these rebuilding efforts, and have faith in your miraculous body that knows how to heal itself, with the right raw materials!

If you’ve taken antibiotics recently (or ever), then you definitely want to join my FREE video masterclass, 12 Steps to Whole Foods, happening now.

The Rehab Your Gut with Food video will be extremely helpful as you begin rebuilding your gut flora after taking antibiotics. Throughout the masterclass, you’ll be equipped with a great deal of knowledge, including how to eat healthy on a budget and how to use cultured foods for gut healing.

This course isn’t always available, but sign up here if it is, or get on the waitlist for the next time we open this very special class.

Watch the Rehab Your Gut video here!

Photograph of Robyn Openshaw, founder of Green Smoothie GirlRobyn Openshaw, MSW, is the bestselling author of The Green Smoothies Diet, 12 Steps to Whole Foods, and 2017’s #1 Amazon Bestseller and USA Today Bestseller, Vibe. Learn more about how to make the journey painless, from the nutrient-scarce Standard American Diet, to a whole-foods diet, in her free video masterclass 12 Steps to Whole Foods.

Disclosure: This post may contain affiliate links that help support the GSG mission without costing you extra. I recommend only companies and products that I use myself.


What To Do After You've Taken Antibiotics


  1. Chicoke, Anthony J. The Complete Book of Enzyme Therapy. Penguin, 1999.
  2. Hall, Danielle. "Ginger & the Immune System." LIVESTRONG.COM. Leaf Group, 10 July 2015. Web. 10 Apr. 2017.
  3. Kelesidis, Theodoros. “Efficacy and Safety of the Probiotic Saccharomyces Boulardii for the Prevention and Therapy of Gastrointestinal Disorders.” Therapeutic Advances in Gastroenterology 5.2 (2012): 111–125. PMC. Web. 3 Apr. 2017. S Boul study.
  4. Macfarlane, G. T., and J. H. Cummings. "Probiotics and Prebiotics: Can Regulating the Activities of Intestinal Bacteria Benefit Health?" Bmj 318.7189 (1999): 999-1003. Web.
  5. Pappas, Stephanie. "Optimism Boosts Immune System." Health. LiveScience, 25 Mar. 2010. Web. 10 Apr. 2017.
  6. Robertson, Chad. "The Link Between Vitamin C And Optimal Immunity." Life Extension, Nov. 2015. Web. 10 Apr. 2017.
  7. Sabater-Molina, M., E. Larque, F. Torrella, and S. Zamora. "Dietary Fructooligosaccharides and Potential Benefits on Health." Journal of Physiology and Biochemistry 65.3 (2009): 315-28. Web.
  8. White, Paul F., et al. "Comparative Efficacy of Acustimulation (ReliefBand®) versus Ondansetron (Zofran®) in Combination with Droperidol for Preventing Nausea and Vomiting." Anesthesiology. Lippincott Williams and Wilkins, 19 June 2015. Web. 03 Apr. 2017.
  9. “Zinc Helps Against Infection by Tapping Brakes in Immune Response.” Science Daily. Ohio State University, 7 Feb 2013. Wed. 09 Apr. 2017.

Posted in: 12 Steps To Whole Food, Holistic Care, Immunity, Natural Remedies

15 thoughts on “What To Do After You’ve Taken Antibiotics: Natural Steps to Regain Your Health”

Leave a Comment
  1. Sue Anne mortimer says:

    Very informative. Thank you. I must print it so I can study it

  2. Angela says:

    Poor Allie! While I try to keep my kids healthy and avoid antibiotics, my adult children HAVE had them – and one has developed POTs, and most of my kids have autoimmune disorderS. Do you have any suggestions for dealing with POTs? Most doctors have never even heard of it. 🙁

    1. Nikki says:

      I’m sure sorry your family is dealing with this issue! The research on the link between gut health and autoimmune disorders is growing all the time. The list of tips in the post are what Allie does to deal with her POTs; you may find something there that helps your family.

  3. Jim says:

    Does anybody remember the series on the thyroid and the disease Hashimotos? It lasted like a week or longer and I am trying to find it because my wife was diagnosed with this disease…Any help would be appreciated…Thanks

    1. Robyn says:

      Jim, it’s not avail right now but I am nagging my friends the Wentzes who created it, so message me in a month to see if it’s available yet.

    2. Debbie Farmer says:

      Jim that documentary was The Thyroid Secret .
      It is by Izabella Wentz
      I bought the DVD’S for my daughter.
      She said that finally someone understood how she felt.
      I bought Isabelle’s book, Root Cause.
      It tells what blood work to get done that the Drs do not usually do.
      We found an open Dr and he put her on desiccated Thyroid, not Synthroid, and she started feeling better immediately.

  4. Joan says:

    Not all supplements are created equal. Do you have a reliable source where I can get zinc? Thanks!!!

    1. Nikki says:

      GSG doesn’t endorse any particular zinc supplement. The best source of bioavailable zinc is real food (pumpkin seeds, spinach, and soaked or sprouted legumes are good choices), but if you or your health care practitioner believe you should supplement, look for a quality chelated version of zinc, like zinc citrate or zinc gluconate.

  5. Susan says:

    All good, but if I have a UTI and am sick with an infection, what do I do?

    1. Nikki says:

      You should always check with your medical practitioner, but you may want to try some of the immune-boosting and probiotic supplements and foods mentioned in the post while you’re on a course of antibiotics, to support the good flora and your immune system.

  6. Ann says:

    I just stumbled upon this while researching issues/what to do after taking antibiotics. I have had about 4/5 (can’t even remember now) prescribed antibiotics since February. I didn’t finish every single one. The last round which was back in mid April landed me in the ER. I felt as if I was going into labor. I had intestinal spasms. Since then I feel like I have acid reflux. The reason for the antibiotics is for a large tooth infection that resulted in a tooth extraction. Problem now is I still have pain around the gums and was told by an ENT specialist I may need to go back on antibiotics. I’m beyond scared and nervous. He will have to discuss problem with oral surgeon and we will go from there. I’m hoping the information provided can provide me with some relief. I never knew prior to all of this that antibiotics could really take its toll on you, I wish I had been better prepared.

  7. Jacqui O’Connell says:

    My ten month old grand daughter has been prescribed antibiotics for bronchitis (and in the past for other respiratory illness) I worry so much about the affects on her gut. What can I do to help?

  8. Dawn says:

    I had the same experience as Allie a couple years ago. A tooth infection, several courses of broad spectrum antibiotics, including Clindamycin, then a C. Diff infection, more rounds of antibiotics, etc. I had finally had enough and wanted to find a natural way to heal. I did thorough research and was so thankful to find Michelle Moore, a microbiologist that developed a C. Diff. protocol that finally cured me. Her products that she sells on her site will work for other infections besides C. Diff. so I encourage anyone that would like to avoid antibiotics and their debilitating side effects to head over to her sites
    She uses natural herbal antibiotics that are powerful and do not cause collateral damage to good bacteria. These truly were a life saver for me.

  9. Simone says:

    I was wondering if there was anything available for those on low dose antibiotics due to structural issues with a bladder that doesn’t drain completely, leading to chronic and painful UTIs.

  10. Joyce noland says:

    Allie’s symptoms are very similar to what I experienced after Clindamycin .would you be able to tell me how long it took to heal the rash and also did the histamine intolerance eventually go away.?

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