Recently, my friend told me that antibiotics will weaken your immune system. Their reasoning is that:

Antibiotics remove the harmful bacteria from you, but they also remove the natural disease fighting bacteria, leaving your immune system crippled.

After some googling, I found that lots of people believe this. For example, these links from


Is there any scientific basis for this belief? I know that antibiotics can cause nausea and diarrhea, but can they cause a cold or a fever? Do they really harm your immune system?

  • Interesting. If this was true, you'd expect it to be easy to prove - many people take the antibiotic doxycycline for months or even years as an anti-malarial. You'd expect it to be easy to design a study comparing immune effects between doxy and non-antibiotic antimalarials over time. Commented Apr 20, 2016 at 23:07
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    There's a difference between an immediate effect and a long-lasting effect. For example, I took anti-biotics once, years ago, and ended up losing my appetite because it killed off my stomach bacteria. But people that take them regularly don't have that problem because their bacteria have built up an immunity. So it might only be a temporary weakening. Commented Apr 21, 2016 at 8:14
  • @PointlessSpike: your stomach hopefully doesn't harbor that many bacteria - it's the guts where you want to have them. (And, there exists also at least some medication where the tablet contains a non-antibiotic precursor which is later on metabolized into the antibiotic - much nicer for your gut flora while still delivering the antibiotic via blood stream without needing an infusion) Commented Apr 21, 2016 at 19:27
  • This sounds like a misunderstanding of the data to me. My understanding was that overuse of antibiotics led to the evolution of bacteria strains that are resistant to the antibiotics being used.
    – GordonM
    Commented Apr 22, 2016 at 12:04
  • There is probably a good reason why our own bodies don't produce antibiotics, in principle they would be easy to produce and could save our lives under certain circumstances. Yet the body has not evolved to do this. Commented Apr 23, 2016 at 21:09

3 Answers 3


How much antibiotics affect gut flora is open subject, there are studies showing there is long lasting negative effect. Eg. "Gut microbiota disturbance during antibiotic therapy: a multi-omic approach"

This matters, because gut bacteria does help immune system.

Part of an abstract of paper published in the European Review for Medical and Pharmacological Sciences:

The role of intestinal microbiota and the immune system.


Accumulating evidence indicates that intestinal microflora has protective, metabolic, trophic and immunological functions and is able to establish a "cross-talk" with the immune component of mucosal immunity, comprising cellular and soluble elements. When one or more steps in this fine interaction fail, autoimmune or auto-inflammatory diseases may occur. Furthermore, it results from the data that probiotics, used for the treatment of the diseases caused by the dysregulation of the immune system, can have a beneficial effect by different mechanisms.


Gut microbiota interacts with both innate and adaptive immune system, playing a pivotal role in maintenance and disruption of gut immune quiescence. A cross talk between the mucosal immune system and endogenous microflora favours a mutual growth, survival and inflammatory control of the intestinal ecosystem. Based on these evidences, probiotics can be used as an ecological therapy in the treatment of immune diseases.

  • And more than immunity too.
    – user11643
    Commented Apr 21, 2016 at 6:22

Antibiotics are designed to either kill or stop the growth of bacteria by targeting specific traits/functions of the bacteria (bacterial cells are prokaryotes) and not to target eukaryotic cells (human cells), which is rather easy due to the many differences between eukaryotes and prokaryotes. Some antibiotics target the cell wall of a bacteria (eukaryotes do not have a cell wall) or interfere with pivotal enzymes that allow them to survive and differentiate. Hence, antibiotics target prokaryotic cells and not eukaryotic cells, meaning that no, antibiotics do not weaken the immune system (this includes leukocytes (leukocytes, erythrocytes, etc. are all eukaryotes).

That said, antibiotics do not differentiate between harmful and non harmful bacteria, thus killing both indiscriminately. This means that the bacteria that were helping with normal bodily processes are killed, which may lead to problems.

The absence of functional/good bacteria in your e.g. gut and elsewhere also leaves you vulnerable to repopulation by unwanted/bad bacteria, which can be responsible for further issues.




I'll be up front and say I have a very strong bias against organizations such as that. If Dante's version of the afterlife is correct, there is a very special place for those people when they die.

That said, there's a grain of truth in what they wrote.

But first, Alexander Fleming realized the true risks of using antibiotics in his 1945 Nobel Prize acceptance speech:

But I would like to sound one note of warning. Penicillin is to all intents and purposes non-poisonous so there is no need to worry about giving an overdose and poisoning the patient. There may be a danger, though, in underdosage. It is not difficult to make microbes resistant to penicillin in the laboratory by exposing them to concentrations not sufficient to kill them, and the same thing has occasionally happened in the body.

I'll look at the first claim later. The second claim is becoming reality. There are a number of extremely dangerous bacteria that are now immune to most, if not all, antibiotics. The World Health Organization, along with many other organizations, is worried that Fleming's concern has become a severe problem. We may well be entering the post-antibiotic age. In the end, everything we do to defeat the immense powers of evolution are best short-lived solutions.

The problem is that we haven't discovered any new classes of antibiotics for thirty years. Thirty calendar years in terms of a dog's life is a long time. In terms of a bacteria's life, it's a long, long time. We may well be entering an age where a paperclip cut can kill. Those "natural" sites do not recognize that. Paperclip cuts could kill are 70 years ago, but not now. Those days will appear again.

Let's look at that first claim. While antibiotics are generally much more effective against gram positive than gram negative bacteria, using antibiotics on a massive scale kills almost kill all bacteria. Our gut bacteria are mostly gram negative.

Recent discoveries show that our immune system apparently depends,at least in part, on the presence of a healthy gut bacteria. Fleming's statement that "penicillin is to all intents and purposes non-poisonous so there is no need to worry about giving an overdose and poisoning the patient" is not correct.

However, it's important to remember Isaac Asimov's distinction between "wrong" and "not even wrong". The naturalists who reject antibiotics (and immunizations, which the linked articles reject) are "not even wrong." They are, IMNHO, worse than not even wrong. They are evil.

  • I was very close to deleting this as a non-answer. Almost all of it doesn't answer the question. The one sentence that does ("Recent discoveries show that our immune system apparently depends,at least in part, on the presence of a healthy gut bacteria.") is unreferenced.
    – Oddthinking
    Commented Apr 21, 2016 at 1:34
  • Here's the problem, @Oddthinking: There is a good amount of evidence that a healthy set of gut bacteria is very important to our overall health. However, the "natural" world has cherry-picked this literature to show that antibiotics are inherently bad. We do not want to go back to the world of 1928 when a paperclip cut could and did kill people. Commented Apr 21, 2016 at 5:51
  • @Oddthinking -- In one of your own very highly rated answers (skeptics.stackexchange.com/questions/30337/…), you yourself have inadvertently have shown that antibiotics are (or at least were) incredibly beneficial. Antibiotics were the key reason for the incredible drop in mortality in childbirth. Please delete my account at this part of the SE network. Commented Apr 21, 2016 at 7:12
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    @DavidHammen - If you're still around to read this, Oddthinking's issue with your answer isn't that he disagrees with your conclusion. It's that skeptics.SE requires answers based on documented evidence and you have not provided references to that documentation. As a result, your answer reads more like personal speculation which, even if it is 100% correct, does not qualify as a good answer on this SE site. Add citations to back up your statements, maybe tighten up the answer a bit to focus more closely on the claim in the question, and I don't think anyone will have a problem with it. Commented Apr 21, 2016 at 7:59
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    You seem to have concluded that I am against antibiotics. Nothing could be further from the truth. If this is the reason for wanting to delete your account, I hope you will re-consider. My concerns are about relevance: The question asks whether antibiotics weakens the immune system by killing gut flora. Your answer addresses your opinions about some organisations, the risks of antibiotic resistance, and the nature of "wrongness". However, it does not show - via references based on empirical evidence - whether antibiotics kill gut flora and whether that is a problem from the immune system.
    – Oddthinking
    Commented Apr 21, 2016 at 14:43

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