How Antibiotics Affect Your Immune System and What to Do About It

Are you or your children caught in the cycle of non-stop sinus infections or ear infections or other sicknesses?  You know… you just get over something and then it seems like you have it again.  If your pharmacy and doctor’s office staff know you and your children’s names and birth dates without looking them up, then this is for you. 

There is a reason for that cycle, and unfortunately, the same antibiotics that are getting you well are making you sick.  In my previous post, 5 Supplements To Help You Avoid Getting Sick During the Cold and Flu Season, I explained that your immunity is very closely linked to your digestion.  Antibiotics are a bit like an atomic bomb.  They do not just select the bad bacteria and destroy that, rather they destroy everything in their path, including the friendly bacteria that lives in your digestive tract and that your digestive and immune systems need to function optimally.  The friendly bacteria living in your digestive tract help to fight off the bad bacteria, aid in digestion and nutrient absorption and keep yeast (such as candidiasis) in its proper balance. 

There is a solution that can help over time; probiotics.  I talked about this in my previous post, but let me expand.  Your doctor has probably told you to wait to take your probiotics until after your course of antibiotics is done.  That is because the antibiotics kill off the bacteria-based probiotics as you are taking them.  This is not true about yeast-based probiotics such as saccharomyces boulardii, however.  They can be taken in conjunction with antibiotics.  I would recommend that you take those during a course of antibiotics and switch to the bacteria-based probiotics once the antibiotics are done.  Once finished with a course of antibiotics, I would take at least 50 billion units (you may want to start with less and increase the amount slowly over a week or two).  This means you will probably be taking a probiotic several times daily.  Be sure to read on your supplement label and see what you are getting.  

These are foods that help the probiotics or friendly bacteria to flourish in your digestive tract.  They contain a kind of non-soluble fiber called oligosaccharides.  You may see that your probiotics have frucooligosaccharides or FOS added.  That is a prebiotic, and that is a good thing.  Many probiotic supplements include FOS or some other form of prebiotic, or you can buy them separately.  Food sources of prebiotics tend to be high fiber foods.  This is not a conclusive list, but some of the foods richest in prebiotics are flax, garlic, bananas, whole grains, such as oats, artichokes and dairy. 

Getting sick happens.  It is a normal part of life here on this earth.  However, when it becomes something that happens over and over again, you know that you need to do something different.  Whether or not you have been on antibiotics, probiotics are important.  If you have been on antibiotics, they are essential… and don’t forget to use the other top 5 supplements for a healthy immune system as well.


  1. Matt says

    Hi Bonnie,

    I read your comments and answers to the rest of the people above.

    I have had breathing problems since I was younger but as I have gotten older they have progressed. I am constantly getting sick and sinus infections. I notice that everytime I have taken antibiotics the next time I get sick it has gotten worse. In turn I believe that I am ruining my immune system and I refuse to take antibiotics anymore unless they are absolutely needed. My body I believe is over producing mucus to compensate for this.

    What probitics/prebiotics do you recommend I take? I know that most of your immune system sits in your gut and I need to restore all the good bacteria and in turn hopefully my immune sytem will return to how it once was. I have started to make changes to my overall diet and this tends to help. I am a 23 year old male and have already started to make diet changes and in overall good shape.

    Thank you!

    • says

      Hi Matt, I am sorry to hear about your health struggles. When I was in college, I had a very similar situation. I had asthma that was severe and chronic sinus infections, so I can relate to how miserable that is. The good news is that you can turn all of that around – I rarely even notice that I have asthma anymore, and I seldom get sinus infections any more.

      First of all, getting appropriate amounts of sleep (extra if you can) is essential.

      In terms of probiotics, I don’t necessarily have a brand recommendation, but I would suggest looking for a product that has in the billions of live active cultures. Also, adding fermented foods, such as yogurt (stick with plain) and sauerkraut, to your diet is helpful for gut health.

      Diet is such an important factor when it comes to immunity and overall health. Good for you for making diet changes! Trying to limit/remove processed food and sugar and add whole foods, especially fruits and vegetables, is so important. Also, sometimes eliminating dairy products can be beneficial for decreasing your mucous production. Try to drink plenty of water and herbal teas as that thins mucous and helps flush toxins out of your body.

      You may also try to take extra Vitamin D3, Vitamin C, and a sinus formula that contains quercetin, Bromelain and stinging nettles. Garlic is also a great benefit.

      I found acupuncture to be extremely helpful to get my body back on track. If you happen to know of a chiropractor, acupuncturist, naturopath, or other holistic doctor, I would seek their advice. And, remember, when you are healing your body from the inside out, it takes time – many times months, but it is so worth the hard work and time.

      I am not a healthcare professional, but am taking this from my experience, so please do your due diligence! I hope and pray you are soon feeling better.

  2. Joanne says

    Thank you, all, so much for taking time to write about your experiences with antibiotics. I’ve been blessed my 50 years with good health and rarely needing antibiotics. I recently developed a bacterial eye infection and was prescribed Cephalexin for 10 days. At the same time, I was taking probiotics to avoid a yeast infection and combat the consternation going on in my digestive system. My eye is doing much better, but on the last day of antibiotics (yesterday), I began developing what I think may be a viral throat infection (I do not have the classic strep throat symptoms). My throat is quite sore, I’m a bit sniffly, and I have a slight cough; no feved. It seems the antibiotics messed up my immune system! From what I’ve read here, a huge dose if probiotics is in order, in addition to the usual home remedies for coughs and colds.

    • says

      Hi Joanne, I know you posted this a week or so ago. I hope you are feeling much better by now.

      Yes, I would definitely recommend probiotics! Since antibiotics kill both good and bad bacteria, it can throw your body off kilter badly and definitely affect your immunity. Probiotics can help to rebuild the good bacteria.

      I have been blessed with a wonderful doctor, who said that after a dose of antibiotics it could take up to a month of supplementing with probiotics to rebuild intestinal flora. In fact, he recommends taking probiotics on a regular basis always.

      Obviously, you should always check with your own doc before taking anything. :-)

  3. crystal says

    i am concerned for my seven year old. she had taken two different courses of antibiotics to treat viral pneumonia within a month, in april 2014 and 7 days later a new one to treat a dog bite that needed stitches. now her body seems to overreact to everything from mosquito bites to toothaches to cat scratches. ive been concerned for a while about her immunities but am more worried than ever with her starting in a new school and her increased pain. she has low grade fevers for almost everything now. i was never told by all three of the doctors that prescribed her the medicines how to build back her immunities. if a three year old needs more than a billion units of probiotics a day, is it safe to assume my daughter needs between 5 or ten billion? please help, she currently running a fever and in pain and have no one to ask for ideas. thank you

    • Lisa says

      Hi Crystal, I posted on this article over 2 years ago, since then I have as good as completely healed my daughter. You need to get a book called Gut and Psychology Syndrome (GAPS) by Dr Natasha Campbell Mcbride. This book explains everything to do with the immune system, how to repair and more! It truly has changed my life and my more importantly my daughters life and health. It’s not easy and it takes a lot of dedication, but it is so worth it, I wish you all the best, you can turn this all around xxxx

  4. Whatever says

    The writer seems unaware that yeast-based probiotics can cause fatalities in those with compromised immune systems. She also seems unaware that FOS-based prebiotics cause indigestion in those with sensitivity to FODmaps.

  5. Lisa says

    I am so glad to have found this website.

    My daughter is now 3years and 4months old and up until 6 months ago, she was like any other average toddler, caught the odd cold, cough and bug, would be poorly for a few days or a week and then back to normal. Then she caught a particularly nasty virus that didn’t seem to want to shift. I finally gave in and took her to the doctors, they prescribed an inhaler and a course of anti-biotics called Cefalexin. I was unaware at the time of the damage that anti-biotics could do. We completed the course and just as she was beginning to get better, another cold hit. This cold put us in hospital, she had breathing difficulties and needed approximately 4-5 nebulisers and oxygen. She recovered within 12 hours and we were discharged. I can remember at the time thinking, where on earth did that come from but was so relieved to be home and able to get back to normal. Once we were home, she slowly got over the cold, but didn’t seem to be able to shake the cough, which also only appeared to happen at night or when she was running around. I knew this was classic symptons for asthma and I had a really hard time even thinking about her having asthma, especially as there was no history of it in my family or my husbands family. We also had no other typical conditions such as eczema which are related to asthma.

    3 weeks later, she was still coughing at night. Then I noticed that the cough would always happen about 30mins after having a glass of milk before going to bed, and continue for approximately 2 hours in her sleep. The following night, I didn’t give her any milk and just like that, the cough stopped.

    At the time I thought that she had developed some kind of intolerance to milk and/or dairy but couldn’t explain why. However, she did still seem to be able to eat cheese.

    Then she caught another cold and we ended up in hospital again. This time she needed more nebulisers and we were discharged approx 12 hours later.

    I couldn’t understand what was happening and how we were back at the hospital again. The doctors kept asking the same questions over and over again and making references to asthma. They discharged with a program of inhalers. I told them that she had appeared to develop some kind of intolerance to milk, but they never said anything about it.

    Again, she slowly got over the cold when we got home, but there still seemed to be this cough that would rear it’s ugly head at night and after she had been running around. It wasn’t until one night, after having 3 digestive biscuits and then also about 2 weeks later after having a bowl of wholewheat pasta, that I made the connection between her cough and wheat. The following morning I removed wheat from her diet and within a week the cough completely went, she was also finally able to run around without breaking into fits of coughing.

    I would like to add at this point, that the cough the milk and wheat caused also caused a build-up of access mucus in her body.

    I still couldn’t understand where these intolerances had come from and then she caught another cold.

    Basically, it has been one cold every 4 weeks (since the 1st course of anti-biotics) which has resulted in hospital admissions every time.

    I finally went to see a Homeopath who gave me the missing part of the puzzle. I knew she couldn’t eat/drink milk/wheat, but I didn’t know why and I didn’t know why she was catching every cold/illness there was and ending up in hospital every month. The homeopath explained what the anti-biotics could have done to my daughters gut which also explained why she suddenly couldn’t tolerate milk/wheat. She also explained about how this could have effected her immune system and why we had got caught in a viscous cycle of colds and hospital admissions.

    I have now started her on acidophilus and a prebiotic rich diet, but I still haven’t managed to make any headway. We literally came out of hospital again this weekend due to more breathing difficulties and a chest infection. The doctors have given me even more anti-biotics, steroids and inhalers, but will not listen to me at when I question them about the balance in her gut being the cause of all these issues, which was originally compromised from the 1st course of anti-biotics she was given.

    I note from you article above that you recommend to take 50 billion units (adult) and I am currently only giving my daughter acidophilus, 1 billion a day, she weighs 15kgs. Do you think this is enough?

    I am also going to make an appointment with a Naturopath following your advice to the comment above, but would be interested in any info you could give me to help me on my journey to get my daughter well again.

    Thank you again for you website!

    • says

      Lisa, I am so sorry to hear about your situation. I can feel your frustration and concern for your little one, especially when hospital stays and breathing difficulties are involved. I think you are on the right track with taking her to a naturopathic doctor who can review her history very thoroughly and work with you step by step. He/she will have a handle on figuring out the source of your daughter’s issues and work with you to get her body back into balance. It is not easy at all to track down the source of things like a chronic cough, so good for you for figuring out that dairy and wheat play a part. I think you are very much on the right track with trying to rebuild her intestinal flora by a pre and probiotic rich diet. You said that you are also supplementing her with 1 billion units of acidophilus. I do think it would be beneficial to give her more probiotics throughout the day and, also, to add in some of the other strains that you may find in healthy digestive systems. There are child-specific formulas out there that you could look at using. In terms of her overall immunity, I have been using Vitamin D3 with my kids (upon my doctor’s recommendation), and I feel like it has really helped to limit the amount of colds and flus that we have had. A maintenance amount is 2000 units/day. I would double-check these things with your naturopath and see if he/she recommends varying the amounts I gave you. A couple of other things to consider: digestive enzymes may be helpful to your daughter to begin to process food normally again. Also, keeping her away from the wheat and dairy for a time and letting her body have a break from them may be just what she needs. I have known people who’s bodies became sensitive to various foods and after a time period of complete elimination they were able to introduce them again with no negative reaction. It may take an extended period of 3-12 months, though.

      • Lisa says

         HI Bonnie,

        I just wanted to do a follow up as the progress we have had with our daughter has been amazing! I started to give her a pre & probiotic supplement specifically tailored for children by Optibac and the difference it made in her was just astonishing. She went from being very lethargic all the time to bounds of energy, sleeping properly and finally being able to get over her colds with no further complications and no visits to the hospital. I have also began to introduce dairy and wheat back into her diet with no negative effects.

        It still amazes me that a simple course of anti-biotics can do so much damage and that I didn’t manage to find one doctor here in the UK to acknowledge this. Getting my duaghters health and food sensitivities back on track has all been down to hours upon hours of trawling the internet and piecing together information.

        Not to mention, what if I hadn’t made the connection between her cough when she ate dairy/wheat??? She would still be coughing all through the night and day and the doctors would have still be giving me more and more steroids to give her with more talk of asthma….it really is quite frightening and I worry for any other parents out there going through the same thing.

        I hope they find this website and my story to help them xxx

        • says

          Thank you for your follow up!  I am so relieved and glad to hear that your daughter is doing better!  What a great momma you are to follow your instincts and figure out how to get her health back on track naturally.  I too hope that other people can be helped through your experience and mommahealth.

  6. john says

    10 years ago my immune systeme was almost completely destroyed by antibiotics…
    I became and am still allergic to 90% of foods,pollan,dust,ect…if anybody can help,please please,e-mail me at I am in great need of help..thank you!

    • says

      Hi Joseph,

      I am terribly sorry to hear your story about how antibiotics have affected your immune system. I can only imagine how difficult it is to function around those kind of health issues. I do think that it is possible to “rebuild” your immune system with some time and work.

      The first thing I would recommend that you talk to your doctor about taking probiotics and digestive enzymes to help the flora in your digestive tract. Since immunity begins here, this is often the root of allergy issues. Are you seeing an allergy specialist? I would recommend that you talk to them about the types of probiotics and enzymes that would be best for you, because if you are allergic to the source from which they are derived, they may also trigger some allergy symptoms. Because of the severity of your allergies, you need to consult with someone who is trained to help you get your body chemistry back into sync like a naturopath, an accupuncturist, or some other holistic practitioner who can sit down with you, examine your history and the intricacies of your allergies and work with you step by step to eliminate the trigger foods from your diet and rebuild your immune system. With time, you probably will even be able to reintroduce some of those foods back in to your diet, but your body needs a break from them.

      If you are in the Chicago area, please let me know and I can offer a couple of recommendations.

      I truly wish you the best of luck with this.


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