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Fluoroquinolones (Cipro, Levaquin, Avelox, Floxin, and their generic equivalents) wreak havoc on the gut. Of course they do–they’re powerful, broad-spectrum antibiotics that destroy all bacteria in their path. They indiscriminately kill both the good and bad bacteria in the gut–creating dysbiosis.

As more is learned about the importance of the gut microbiome (many people are now referring to it as an organ), it is being recognized that bacterial diversity is vital for many aspects of health. According to this guide to the microbiome, “a high diversity of GI organisms has been associated with states of relatively good health, while low diversity has been associated with states of disease or chronic dysfunction.” Many gut bacteria are linked with controlling inflammation and weight loss, including Butyrivibrio crossotusOdoribacterB. vulgatusBifidobacterium, and many others.

Unfortunately, because of antibiotic use (and over-use), deficiencies in the standard American diet (SAD), antibiotic pesticides like glyphosate, and other environmental factors, many important bacterial species are disappearing from our gut microbiomes.

In Missing Microbes: How the Overuse of Antibiotics is Fueling our Modern Plagues, Dr. Martin J. Blaser asserts that the extinction of our vital microbes is causally linked to many of the diseases of modernity–from obesity to autoimmune diseases. Missing Microbes is an excellent book, and I highly recommend it. One thing on display in Missing Microbes is ambivalence about antibiotics. We all know that antibiotics have saved millions of lives, and we know that antibiotic resistance is a serious problem. We are also beginning to learn that antibiotic use has consequences, including the diseases that are related to microbiome destruction which include many of the diseases of modernity like autoimmune diseases and autism. Perhaps a re-analysis of the costs and benefits of antibiotics is in order.

Many people with fluoroquinolone toxicity have high inflammatory markers, and fluoroquinolone toxicity often looks and feels like an autoimmune disease. Given the role of many bacteria in reducing (or increasing) inflammation, an examination of the roles of various microbes should be done for fluoroquinolone toxicity patients.

One way that you can test your own microbiome is through uBiomeuBiome is a biotechnology company based in San Francisco that gives individuals access to sequencing technology to sequence their microbiomes with a sampling kit and website. A floxie friend recently had her microbiome mapped through uBiome and discovered that she has no oxalobacter formigenes. Some of the potential consequences of not having oxalobacter formigenes are described in the post Fluoroquinolone Antibiotics and Oxalate Overload. If you are interested in testing your microbiome through uBiome, to see if you have any oxalobacter formigenes, HERE is a 10% off coupon for all uBiome tests:​​​​​​​


What role does oxalate accumulation play in fluoroquinolone toxicity? How does elimination of oxalobacter formigenes contribute to multi-symptom, chronic illness? How does gut health fit in with the many other theories about fluoroquinolone toxicity? (Many of which are described in the post, What is Fluoroquinolone Toxicity?) All of those are good questions that, unfortunately, are yet to be answered.

Some useful resources for learning more about oxalate overload are:

Trying Low Oxalates Facebook Group and

To learn about your oxalobacter formigenes, and other gut bacteria, status, I encourage each of you to test your microbiome with uBiome. Again, here’s a 10% off coupon:​​​​​​​