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The Troubling Connection Between Antibiotics, Your Gut and Autoimmune Conditions

In recent years, antibiotic use in both human beings and animals has become a hot topic of discussion, and rightfully, an area of great concern, for those in the medical profession and laypeople alike.  Here we examine a small aspect of their impact on the global population, and whether there is any connection between autoimmune disease and human or animal antibiotic use.

Are there any studies about the effect on humans from antibiotic use in animal feed?

Yes, with increasing interest in this issue have come some studies examining the impact antibiotic use in animals and animal feed may have on the people who consume related products.

Other studies have focused on the problem in terms of antibiotic use in agricultural products or fish rearing, and their subsequent use in animal feed and the human diet.

Most research focuses on the issue of bacterial resistance as a consequence of such practices, but there is some information that applies to autoimmune disease, both directly or indirectly.

It seems clear from the literature that there are legitimate concerns regarding antibiotics in animal feed and the like, as well as concerns about problems related to not using them.  And the connection to bacterial resistance is fairly straightforward.

What isn’t as clear is the nature of the connection, if indeed there is one, between this type of indirect antibiotic consumption by people and the development or progression of autoimmune conditions.

How could our personal antibiotic use affect autoimmune disease onset?

It turns out that the issue of bacterial resistance as a result of overuse of antibiotics can be somewhat connected to possible autoimmune mechanisms.  As we’ve discussed in past articles, doctors are rapidly becoming convinced that there is a very real and important connection between the gut and the rest of the body, particularly with respect to the native bacteria that live in the intestines and make up the “gut flora” or “microbiota”.

Most of the research findings are dealing more specifically with the “gut-brain axis” and the neuropsychiatric ailments that may result from an imbalance of the flora.  However, there is increasing evidence to suggest that such an imbalance may have an impact on or even incite autoimmunity.

The idea behind this thinking is that when one is exposed to antibiotics, whether via animal/vegetable products or personal use, in addition to fighting off the intended infection, these medications also affect the bacterial flora of the gut.

Too much exposure can cause an imbalance in this delicate ecosystem, which can have very real consequences.  One is the emergence of opportunistic infections that were previously held in check by the normal flora.  But another concerns the more recent finding that such alterations in the gut flora and bacterial resistance may actually promote some autoimmune disease by stimulating T-helper cell production.

This contention is somewhat supported by other findings indicating a link between a floral imbalance and autoimmune disease.  A study examining infants, antibiotics and inflammatory bowel disease (IBD) found that children diagnosed with IBD were more likely to have been treated with antibiotics as babies.

And interestingly, one study found immunological effects in the offspring of pregnant mice treated with antibiotics.  In addition, a recent article in Science Daily has suggested another possible mechanistic link between autoimmunity and antibiotics, whereby certain antibiotics cause cells to produce new surface antigens that may then be mistakenly targeted for attack by the body’s immune system.

Still, there are also certain situations where antibiotics may be indicated for use in autoimmune disease, such as when infection is suspected as the inciting incident in the onset or flare of an autoimmune condition.  This obviously complicates the issue somewhat and clouds the picture as to the exact nature of the benefits and risks of personal antibiotic use.

What are ways to reduce the amount of antibiotics we are exposed to in our food?

There’s really nothing to say here that most people don’t already know.  But for starters, investigate your food your food and its sources, and read labels carefully.  The labels aren’t likely to reveal much, but it’s always smart to be informed about your food.  Look for keywords such as “antibiotic/hormone free” or similar, either on the packaging or in literature.

Of course there’s the option to eat mostly or only “organic” food, which if true to the label, should have been grown/raised without any use of hormones, pesticides, antibiotics, etc.  The problem is that there seems to be a broad definition of “organic”, and confusion about its meaning, and some companies may be exploiting this issue and misrepresenting their products as being purer than they are.

That’s why education is key.  Learn exactly what you’re looking for and what you don’t want in your foods, and then do some research until you find suitable products that fit your needs.

Questions for your doctor:

  • What are the most important foods or ingredients to avoid with respect to my disorder(s)?
  • Is personal antibiotic use of any concern regarding my autoimmune condition(s)?  Why or why not?
  • Are antibiotics ever useful in autoimmune treatment?  How and when?
  • What can I do, if anything, to counter or offset any ill effects that antibiotic use in animals may cause?  Should I take probiotics to normalize my gut flora?
  • Can you suggest a good source for more information on this topic?

About the Author
Dr. Rothbard is a professional medical writer and consultant based in New York City, specializing in medical education articles targeted at a variety of audiences, from children through clinicians.  After leaving medicine, he worked as a biology and medical science educator for several years, before deciding to pursue writing full-time.  He may be reached at

This blog post was originally published by, written by Dr. Rothbard, and first published on Jul 31, 2014.

This post contains the opinions of the author. Autoimmune Association is not a medical practice and does not provide medical advice, diagnosis, or treatment. It is your responsibility to seek diagnosis, treatment, and advice from qualified providers based on your condition and particular circumstances. Autoimmune Association does not endorse nor recommend any products, practices, treatment methods, tests, physicians, service providers, procedures, clinical trials, opinions or information available on this website. Your use of the website is subject to our Privacy Policy.


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