Lisa Bloomquist

The Harmful Effects of Antibiotics on the Human Microbiome

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How many articles about the importance of the microbiome – and the relationship between microbiome health and chronic, devastating diseases – need to come out in order for the cognitive dissonance around antibiotic safety to stop?

People assume that all antibiotics are safe drugs, that they damage bacteria but leave people and animals unharmed.  People assume (soap commercials have conditioned us well) that bacteria are bad, that they are harmful and make us sick, and that human life is improved when they are killed.  Many also assume that all antibiotics are created equally and that the more powerful an antibiotic, the better.  Most people assume that there are no long-term consequences from taking antibiotics.

There is ample evidence that these assumptions are false, and that a microbiome that is disturbed by antibiotics makes people more anxious, intolerant of pain, and sick with a variety of diseases.

A disrupted microbiome has been connected with development of Parkinson’s Disease (PD), as shown in Gut microbiota are related to Parkinson’s Disease and clinical phenotype,” published in the journal Movement Disorder.  It was found that patients with PD had less Prevotellaceae (a type of gut microbe) than those in the control group, and that, “The relative abundance of Enterobacteriaceae was positively associated with the severity of postural instability and gait difficulty.”  It is also pointed out in the study that the reason for examining the relationship between PD and the gut microbiome is that:

“In the course of PD, the enteric nervous system (ENS) and parasympathetic nerves are amongst the structures most frequently and earliest affected by alpha-synuclein pathology. Accordingly, gastrointestinal dysfunction is an important non-motor symptom in PD and often present years before motor symptom onset. Recent research has shown that intestinal microbiota interact with the autonomic and central nervous system via diverse pathways including the ENS and vagal nerve.”

The microbiome profoundly affects neurotransmitters and thus mental health, as is shown in “The microbiome-gut-brain axis during early life regulates the hippocampal serotonergic system in a sex-dependent manner” published in Molecular Psychiatry, as well as “That Gut Feeling” published in the American Psychological Association magazine, Monitor on Psychology.  The article, “Altering your gut bacteria could ease anxiety and depression” on is also interesting and informative.  All of the articles point to the finding that, “that tweaking the balance between beneficial and disease-causing bacteria in an animal’s gut can alter its brain chemistry and lead it to become either more bold or more anxious” (quote from “That Gut Feeling”) and that temperament changes were induced by gut microbiome alterations. If you’re feeling anxious or depressed, you may want to look at your past antibiotic use.  Our guts and our brains communicate through a variety of signaling mechanisms including “the autonomic nervous system (ANS), the enteric nervous system (ENS), the neuroendocrine system, and the immune system” as well as the vagus nerve.

The connection between microbiome health and Alzheimer’s Disease is described in “Alzheimer’s disease and the microbiome” published in Frontiers in Cellular Neuroscience (and the referenced articles are interesting too).  In it, it is noted that, “GI tract-abundant gram-positive facultative anaerobic or microaerophilic Lactobacillus, and other Bifidobacterium species, are capable of metabolizing glutamate to produce gamma-amino butyric acid (GABA), the major inhibitory neurotransmitter in the CNS; dysfunctions in GABA-signaling are linked to anxiety, depression, defects in synaptogenesis, and cognitive impairment including Alzheimer’s Disease.”

Rheumatoid Arthritis is connected to microbiome health in the article on the NIH web site, “Gut Microbes Linked to Rheumatoid Arthritis,” in which it is noted that, “The immune system is influenced by the microbiome, a network of microorganisms that live in and on the human body. These microbes outnumber the body’s cells by 10 to 1. Trillions of microbes—both helpful and harmful—reside in the digestive tract. The gut microbiome has been linked to arthritis in animal studies.”

Inflammatory bowel diseases (IBD) Crohn’s disease and ulcerative colitis are connected to microbiome health in “Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment” published in Genome Biology. In the article, it is stated that, “The inflammatory bowel diseases (IBD) Crohn’s disease and ulcerative colitis result from alterations in intestinal microbes and the immune system.”

The microbiome has been shown to affect both Type 1 and Type 2 diabetes.  In “Intestinal microbiota and type 2 diabetes: From mechanism insights to therapeutic perspective” published in the World Journal of Gastrointerology the relationship to Type 2 diabetes is shown.  In “Type 1 diabetes: role of intestinal microbiome in humans and mice” published in the Annals of the New York Academy of Sciences the connection to Type 1 diabetes is shown.

More general information about the relationship between the microbiome and human health can be found on the National Institute of Health’s Human Microbiome Project web site.

Thousands of articles about the importance of the microbiome have come out.  Millions of dollars have been spent studying the microbiome and its relationship to human health.  Antibiotics indiscriminately destroy bacteria in the microbiome, and some even lead to oxidative stress in the microbiome. Yet misconceptions about antibiotic safety persist. Why is that?

Greg Spooner answered that question perfectly. He said:

“I think the reason for this is that the early antibiotics (like penicillin) were quite safe and they spared us from very serious infections that often lead to death. Our life expectancy jumped at this point, and they were rightly considered miracle drugs. But this was also their downfall, as they quickly became so overused that they lost their efficacy and killed off many people’s helpful biomes. When FQs (fluoroquinolones) came out, most docs probably thought they were just “better” antibiotics that were still effective. ‘All progress is precarious, and the solution of one problem brings us face to face with another problem.’ – Martin Luther King Jr”


Antibiotics, as a class of drugs, have saved millions of lives. That is undeniable. But their value in life-threatening situations does not negate their consequences. The increased risk of Parkinson’s, Alzheimer’s, depression, anxiety, inflammatory bowel diseases, diabetes and other diseases that result from microbiome disruption, should be weighed carefully and conscientiously against the risk of harm from the diseases that are treated with antibiotics. This analysis isn’t being done currently. Both patients and physicians will need to shift their thinking about antibiotic safety for a proper safety analysis to be conducted.  Unfortunately, the proper safety analysis involves comparing immediate and acute pain to potential future pain, and humans are horrible at doing that kind of analysis.

Also, as Greg pointed out, the value and safety of one antibiotic does not mean that all antibiotics are equally safe and valuable.  Though penicillin is not kind to the microbiome, it doesn’t cause multi-symptom, chronic illness like fluoroquinolones do.  Fluoroquinolones are broad-spectrum antibiotics that not only kill bacteria, they deplete mitochondrial DNA and induce a massive amount of oxidative stress, not only in the microbiome, but in the body generally.  Fluoroquinolones are related to the diseases mentioned above not only through the destruction of the microbiome inflicted by them, but also through the destruction of mitochondria and disruption of cellular mineral homeostasis.

It would be a good place to start for the dangers of fluoroquinolones to be considered before they are prescribed.  After all, fluoroquinolones have an extensive list of adverse effects (the Cipro warning label is 43 pages long) that include tendon ruptures and seizures, among hundreds of other adverse effects. There are thousands of patients screaming about how they have been hurt by fluoroquinolones, and demanding that they be used more prudently.

All antibiotics should be used with care and consideration of potential future consequences. Those antibiotics with the most severe adverse effects should be looked at most closely and immediately. Fluoroquinolones are not worth the harm that they cause in most cases. Restriction of the use of fluoroquinolones is a good place to start in thinking about antibiotics as dangerous, consequential drugs. They are, indeed, consequential, dangerous drugs.

The role that antibiotics and the microbiome play in the many chronic diseases of modernity is just starting to be recognized.  Though recognition has been slow to come about, there are thousands of articles about the importance of the microbiome. Perhaps it is time for us to consider more prudent use of antibiotics, especially the most potent and destructive ones (like fluoroquinolones).

Information about Fluoroquinolone Toxicity

Information about the author, and adverse reactions to fluoroquinolone antibiotics (Cipro/ciprofloxacin, Levaquin/levofloxacin, Avelox/moxifloxacin and Floxin/ofloxacin) can be found on Lisa Bloomquist’s site,

Participate in Research

Hormones MatterTM is conducting research on the side effects and adverse events associated with the fluoroquinolone antibiotics, Cipro, Levaquin, Avelox and others: The Fluoroquinolone Antibiotics Side Effects Study. The study is anonymous, takes 20-30 minutes to complete and is open to anyone who has used a fluoroquinolone antibiotic. Please complete the study and help us understand the scope of fluoroquinolone reactions.

Hormones MatterTM conducts other crowdsourced surveys on medication reactions. To take one of our other surveys, click here.

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Lisa Bloomquist was "Floxed" on her 32nd birthday by Cipro, a fluoroquinolone antibiotic. After 2 years of battling the mysterious health ailments that come with an adverse reaction to a fluoroquinolone, she has fought her way back to health. Lisa is now fighting for recognition of the harm that these drugs can cause and hoping to help those who are suffering from them through their fluoroquinolone induced illness to find recovery. Her web site, highlighting stories of hope and recovery, is After a while of studying how fluoroquinolones damage mitochondria, she noted that mitochondria were being systematically ignored when forming disease models. She started to bring attention to the role that mitochondria play in health and disease.


  1. Great article, should be in Time magazine ! You’ve got it. The Human Microbiome is already being called the most important medical discovery of the last century.
    Already, the following diseases have been reversed ; Chronic Fatigue, Depression, Rheumatoid Arthritis, IBS, Autism, MS, Chron’s, and C. Diff by microbiome transplants. It’s very impressive so far.

    Every Physician in the world needs to understand the Human Microbiome. Every person in the world needs to realize that antibiotics are not benign, and that there are consequences to the use of them.

  2. I was given Cipro. All doctors say it is polymyalgia Rhumatica not Cipro. I was given steriods and told they would calm my adrenals.
    The holistic folks say the opposite. I am shakey, dangerously anxious, have insomnia and am so depressed.

    Really afraid I will not get over this ??



    • Hi Janine,

      Many, but not all, people respond badly to steroids after exposure to fluoroquinolones.

      For the symptoms that you listed, I suggest that you look at this post and the links within it – I also recommend that you get your magnesium levels checked, and if they are low, supplement magnesium (under the care of a physician, of course).

      Meditation helped me immensely. Breathing exercises did too and I recommend that you do both.

      Try to be hopeful. What you’re going through is brutal, but it does get better. Hang in there.


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