Tag Archives: microbiome

NY Resolution to Heal My Gut

Seven years after I got floxed, and 5.5 years since I wrote my recovery story, I am still doing well. I am working at a job that I enjoy, I am in a good relationship, I can hike, bike, swim, and otherwise move my body, I have my reading comprehension and intellect back, my energy level is decent, and my autonomic nervous system generally operates as it’s supposed to. I feel good, and I’m living a good life. As I’ve said many times before, I hope that my recovery gives you hope for your healing.

With it noted that I’m generally healed, and that I feel good in most areas of my life, I’m going to confess that…

My gut is a mess, and I am worried about it.

I have no idea whether my gut issues are from being floxed or not. GI tract problems weren’t part of my initial floxing–I didn’t have any gut issues until recently. But in the last year(ish), my gut has started to have… issues. Unfortunately, there is no way to describe GI issues without describing bowel movements, so here goes – I haven’t had a normal textured poo in ages. It has been at least a year. TMI? Sorry.

Poorly formed stools are definitely a sign of inflammation and other gut issues, and, despite the fact that I feel generally okay, I’m concerned about my gut health.

I want a gut that doesn’t hurt every day, that forms healthy-textured poos, and that I don’t worry about. I don’t want to be concerned that I’m developing IBS, or crohn’s disease, or that I have c-diff, or anything else. I’m guessing that I don’t have any of those things, and that I just have an inflamed gut, but I don’t want that either. I want a healthy, happy, healed gut that feels good and operates entirely normally. I don’t think that’s too much to ask for. I also think that my gut is my responsibility, and that no one other than me can do anything about MY gut health.

It’s December 28th as I write this, and the beginning of the new year seems as good a time as any to commit to healing my gut. Here are some of the things I plan to do to heal my gut in 2019 (public accountability is good, right?):

Clean up my diet

When I first got floxed I ate only meat and veggies. I was scared of most foods, and I ended up losing weight and feeling worn-down because I wasn’t ingesting enough calories. After I got over the fear of food, I added fruits and other good things to my diet, and ended up eating as outlined in The Floxie Food Guide. But, after a while of feeling better, I stopped restricting my diet entirely. I didn’t eat much processed food because I’ve never liked processed food, but I ate whatever I wanted. Perhaps my GI issues are the result of my “anything goes” diet (or maybe my GI issues stem from something else like mold in my house or fluoride in my city’s water or a parasite – it’s hard to tell). Anyhow, it’s time to restrict my diet again with the hope of calming the inflammation in my intestines.

Step 1: Give up gluten. My husband has been on a bread-baking kick lately, so this will take some willpower, but it has helped so many people, and it seems like a logical first step, so, I’m going to go gluten-free and see if that helps.

Step 2: Give up legumes. I like beans, but they make me feel like crap.

Step 3: Limit dairy. I love dairy too much to say that I’m going to give it up, but I’m going to try to be cognizant of how much I eat and how it makes me feel and limit it.

I want to be able to sustain these changes, so these are the only things I’m going to do at first. If they don’t work, I’ll move on to a more restricted protocol – probably something close to The Wahls Protocol because it has helped so many fellow “floxies.”

I’ve noticed that oatmeal makes me feel better generally, so I’m going to eat more oatmeal. I’ve also noticed that spicy food tends to make me feel worse, so I’m going to limit them even though many spices are supposed to be anti-inflammatory.

Cut the coffee and alcohol

This is a no-brainer, right? No explanation is necessary as to why these need to go in order for me to heal my gut. It’s hard though, so, here’s my public accountability.

Note that the coffee I drink is decaf. I haven’t been able to tolerate caffeinated coffee post-flox.

I really like both coffee and alcohol, and this is going to be tough. I’m only committing to cutting down on them, not to completely giving up either, but I can commit to cutting the coffee by 50% and the alcohol by 80%.

Eat probiotic foods

Sauerkraut and kimchi, here I come. Luckily, I like both.

Meditate, breathing exercises, eat mindfully, and otherwise stimulate the vagus nerve to heal the gut

Our guts are connected to our brains via the vagus nerve, and stimulating and toning the vagus nerve through meditating, breathing exercises, mindfulness, and other activities, can heal both the gut and the brain.

Here is an interesting post about how a guy healed his IBS through stimulating his vagus nerve through gargling: How I Cured My Irritable Bowel Syndrome.

As I was going through the early stages of my fluoroquinolone toxicity journey I was really good about meditating, doing breathing exercises, going to the chiropractor and/or acupuncturist, and doing other things that stimulated my vagus nerve. I think that these things helped me to heal. They were part of my healing journey, and I recommend them to others because they are healing for the body, mind, and spirit, and because they stimulate the vagus nerve and trigger the release of acetylcholine. Like watching my diet, conscientiously doing activities that stimulated my vagus nerve fell to the wayside as I healed. I felt good, so I didn’t need to do breathing exercises to feel better. But, I think that all the vagus nerve healing exercises were helpful for my gut when I was doing them, and that they’ll be helpful for my gut if I do them again.

Shoot, I wrote a book about healing the vagus nerve – I should make the time to practice what I preach.

Step 1: Meditate daily

Step 2: Swim weekly – it forces breathing exercises, and movement is good for the vagus nerve.

Step 3: Eat mindfully

Step 4: Gargle and/or hum daily


Those are my resolutions, and I hope that they result in a happier, healthier gut.

I’m open to suggestions for gut healing. Please feel free to comment below to let me know what has helped you to heal your gut. As you may gather from the post above, I am not willing to go on a super-restrictive diet unless/until all else fails, but I am willing to hear suggestions. I’m also open to trying supplements that heal the gut including aloe juice, collagen, bone broth, probiotic supplements, etc. If you have any recommendations based on personal experience with gut-healing supplements, please comment below.

Whenever someone asks in the forums about how to heal from fluoroquinolone toxicity, someone always answers, “heal your gut.” They’re right, of course–but it’s easier said than done. There are people in the “floxie” community who are much more better about having a “clean” diet than I am who still struggle with GI issues and other symptoms of fluoroquinolone toxicity. I’m hopeful that my modified “clean-ish” diet will help my gut to heal, and that the other things mentioned above help too. I want to acknowledge though, that “healing the gut” is not simple and that there isn’t a single answer for how to do it. I’m hopeful that the steps noted above will help me, and that I’ll have a healthier, happier gut in 2019 than I did in 2018.






Quinolones in our Environment

Why do some people have relapses of their fluoroquinolone toxicity symptoms? Why is fluoroquinolone toxicity an ongoing illness–a syndrome–and not a one-time event that ends once the drug is metabolized? Why do people seem sensitized after suffering from fluoroquinolone toxicity–with exposures to things that would be benign to healthy people throwing them into a relapse? Why does fluoroquinolone toxicity seem more like an autoimmune or neuroimmune disease than a drug allergy? What does fluoroquinolone toxicity have in common with autoimmune or neuro-immune diseases?

These are all perplexing questions about FQT/FQAD that currently we have no answers for. On the
website http://fluoroquinolonethyroid.com/ many ideas about possible mechanisms regarding some
of these questions are explored (here, here, and here). I found the most recent of these posts,
entitled Nature’s Quinolones: The 4Qs, to offer additional thought-provoking and insightful new
ideas to consider when thinking about questions like these.

This post is a summary of Nature’s Quinolones: The 4Qs, to share the information in it with the
Floxiehope.com audience. There is information in the original article that I won’t be covering in this
post, and I hope this summary inspires you to read more about the details in the original article. I
also hope that any researchers reading this will check out the original article, as it provides a more
comprehensive explanation, along with numerous references, that may be of use in your thought
processes about this topic.


There is a bacteria that is ubiquitous in our environment called Pseudomonas aeruginosa, or P. aeruginosaP. aeruginosa is everywhere, including, “soil and water, lakes, streams, rivers, other fresh water, potable water, and sources such as sinks, showers, and hot tubs.” People with healthy immune systems deal with P. aeruginosa without incident. However, P. aeruginosa is a pathogen associated with hospital-acquired infections in immune-compromised individuals, and perhaps it may also be possible that some people have immune systems that over-react to to the bacteria, or its byproducts.

Like many other bacteria and some fungi, P. aeruginosa “communicate” with each other via something called Quorum sensing (QS). The P. aeruginosa QS molecules are able to turn bacterial genes on and off, such as instructing the bacteria to form biofilms under certain circumstances. Just as people with normal immune systems interact with P. aeruginosa without incident, people with normal immune systems also interact with the P. aeruginosa QS molecules without incident.

However, one of the possible ideas explored in Nature’s Quinolones: The 4Qs is that people who have been “floxed” may not react to the P. aeruginosa QS molecules without incident. Rather, perhaps they may be sensitized to the P. aeruginosa QS molecules, and their immune-system attacks these molecules, causing a potential autoimmune/neuroimmune reaction.

Why might “floxies” have an immune-system over-reaction to P. aeruginosa QS molecules?

Because one group of QS molecules that P. aeruginosa QS makes are actually quinolones–“nature’s quinolones” (heterocyclic 4-quinolone/quinolines – abbreviated the “4Qs”). These 4Qs produced by P. aeruginosa share the basic 4-quinolone backbone of the commercially synthesized quinolone antibiotics. (More information about this can be found in Nature’s Quinolones: The 4Qs, as well as the articles linked-to in the post, including 4-Quinolones: Smart Phones of the Microbial World.)

I don’t know about you, but this BLEW MY MIND.

The production of natural quinolones may answer the question – why do people have ongoing reactions to fluoroquinolone antibiotics that last long after the drugs “should” be out of their system? Could it be because they are constantly being re-exposed to quinolones in our environment–through a common bacteria producing them to communicate with other bacteria? Could it be that Fluoroquinolone Toxicity is an ongoing syndrome because it is an immune reaction (and/or sensitization) to chemicals that are ubiquitous in our environment?

Again, these are just possible ideas the author of  Nature’s Quinolones: The 4Qs is exploring, but it MAKES SO MUCH SENSE.

QS Qinolones act as “signaling molecules for other bacteria. FQs also act as “signaling molecules” within us. In particular, they seem to target cytokines, which are heavily involved in the signaling and amplification system in our immune systems.” Pharmaceutical fluoroquinolones are given in a large enough doses that perhaps they may signal the immune system to over-react–especially to the presence of other quinolones. Nature’s Quinolones: The 4Qs describes some possible mechanisms through which fluoroquinolones may affect the immune system, providing numerous references in additional links in the article supporting this. Fluoroquinolones (and/or the 4Qs if production in larger amounts due to severe infection such as sepsis, for example) may also trigger epigenetic “switches” to be “flipped” in the immune system, causing a change that leads to a constant over-reaction to quinolone molecules.

The author of Nature’s Quinolones: The 4Qs ponders:

“I wonder if some of my existing natural antibodies were “switched on” in a major way, leading to global or specific hypersensitivities. And based on what I now know about FQs acting as ‘signaling molecules,’ I’m guessing that one or more of my cytokines or receptors were hit especially hard by what my body perceived as a whopping dose of quinolones.”

An over-active immune system that is hyper-sensitive to minute amounts of molecules that are harmless, and even unperceived, to people with normally functioning immune systems, is not unheard-of. Many people with ME/CFS believe they have autoimmune/neuroimmune reactions to tiny molecules of mold, and even minuscule amounts of mold appear to make them severely ill. Common allergies are also a result of an over-sensitized immune system:

“If this seems like an extreme leap to make, consider, for example, two very common allergies: hay fever and peanut allergies. There are microscopic particles of pollen and dust floating around in the air that most of us never see, feel, are aware of, or react to – unless you’re a person with hay fever allergies. There are microscopic proteins and aflatoxins in peanuts that most of us never see, feel, are aware of or react to – unless you’re a person with a peanut allergy. The first allergy typically leaves people with itchy and runny eyes and nose. The second allergy can result in anaphylaxis and even death. The point being, it doesn’t take much of these substances to make a person miserable or even kill them – if they’re hypersensitive.”

Might some people suffering from fluoroquinolone toxicity be sensitive to minute amounts of quinolones in the environment? Might some people who live in more humid and moist environments, for example, have increased exposure to quinolones by P. aeruginosa QS molecules? Additionally, might the fluoroquinolones have made epigenetic changes to the immune systems of those suffering from fluoroquinolone toxicity that make them have autoimmune/neuroimmune-like reactions to quinolones, including the 4Qs? Again, it makes all the sense in the world to me, but it needs to be examined by someone with the capacity to test these ideas.

If fluoroquinolones change the genetic on/off switches in our immune systems, how do we flip those epigenetic “switches” again? That’s a very good question that I don’t know the answer to. Our environment is constantly affecting our genes though, and epigenetics is a burgeoning field of research. I’m hopeful that scientists will find targeted ways to flip gene switches. I’m also hopeful that, in the meantime, changes in your environment (eating healthy foods, reducing stress, supplements, etc.) may help you (the “floxie” reading this) to “switch” your immune system back to where you were pre-flox so that your body is not over-reacting to nature’s quinolones (if that’s occurring). I know that my body is not in a state of constant reactivity, and, as always, I hope that my recovery gives others hope for their recovery.




Fluoroquinolone Antibiotics and Oxalate Overload

According to the wikipedia entry for oxalobacter formigenes, “Quinolone, a broad-spectrum antibiotic, kills O. formigenes. If a person’s gastrointestinal (GI) tract lacks this bacterium, and therefore lacks the primary source for the oxalyl-CoA decarboxylase enzyme, then the GI tract cannot degrade dietary oxalates which on digestion get absorbed easily and after some vitamin B6-modulated partial metabolical degradation in the body, is excreted in the kidney, where it precipitates with calcium to form calcium oxalate kidney stones.”

Basically, this means that quinolones (and some other antibiotics) kill oxalobacter formigenes, a bacteria in the GI tract that is crucial for breaking down oxalates. When oxalates aren’t broken down properly in the GI tract, they move on to the kidneys where they form calcium oxalate kidney stones.

Kidney stones aren’t the only problems that oxalates cause though. Oxalates cause methylation problems that inhibit detoxification. According to Dr. Rostenberg’s article, OXALATES AND MTHFR: UNDERSTANDING THE GUT-KIDNEY AXIS:

oxalates create biochemical problems that make methylation issues worse. Since oxalate problems cause sulfate problems, the genes most effected will be the SULT and other phase II related pathways. The sulfate molecule is key in order for the liver to perform the daily task of detoxification. If sulfate levels drop, then the body cannot use the SULT pathway to detoxify. Instead it will be forced to use other Phase II pathways which can put greater demand on pathways that are also genetically slowed down. When we consider other slowed Phase II detoxification gene SNPs such as NAT2, ALDH, COMT, GSH, GSS, UGT, and SOUX we can begin to see that a lack of sulfate molecules can have a broad negative impact on all of our detoxification pathways.”

Dr. Rostenberg goes on to say:

As you will soon see, when oxalate levels are high, sulfate levels drop slowing down detoxification. Low sulfate levels put extra stress into the methylation cycle to provide the body with sulfate molecules. In individuals with an impaired methylation cycle this can provoke methylation issues such as high homocysteine, developmental disorders, gallbladder dysfunction, hormone imbalances, excess inflammation, poor growth and to name but a few. So with oxalate issues and the biochemical chaos it creates, a great deal of stress is placed on the methylation cycle.”

In OXALATES AND MTHFR: UNDERSTANDING THE GUT-KIDNEY AXIS Dr. Rostenberg asserts that a poorly functioning gallbladder is a cause of oxalate overload. While I agree that a well-functioning gallbladder and liver are necessary for all aspects of health, I wonder if the decimation of vital gut bacteria, like oxalobacter formigenes, by antibiotics like fluoroquinolones, is what starts oxalate toxicity damage.

Fluoroquinolone Destruction of Vital Gut Microbes

A floxie friend just noted that she got her microbiome mapped by ubiome and, “my Ubiome results tell me I have NO oxalobacter at all.” Additionally, her results showed that, “I also have NO bifidobacterium strains AT ALL.” (According to the wikipedia article for bifidobacterium, “Different species and/or strains of bifidobacteria may exert a range of beneficial health effects, including the regulation of intestinal microbial homeostasis, the inhibition of pathogens and harmful bacteria that colonize and/or infect the gut mucosa, the modulation of local and systemic immune responses, the repression of procarcinogenic enzymatic activities within the microbiota, the production of vitamins, and the bioconversion of a number of dietary compounds into bioactive molecules.”) Both oxalobacter and bifidobacerium are necessary for many aspects of health.

Might the root of fluoroquinolone toxicity, and possibly other chronic diseases of modernity, be the killing off vital microbes like oxalobacter and bifidobacerium?

Oxalate Overload

The depletion of oxalobacter formigenes, and other microbes, doesn’t just affect the gut. As Dr. Rostenberg noted above, oxalate problems (caused by not breaking down oxalates in the gut – caused, in part, by killing oxalobacter formigenes with antibiotics) lead to sulfate problems, which leads to methylation problems, which leads to detoxification problems, which leads to heavy metal overload and toxicity. Additionally, “Sulfate helps us seal our leaky gut and strengthen our body’s bones, ligaments and tendons; and it is required for Phase II detoxification of all kinds of nasty toxins, hormones and heavy metals. In fact, sulfate is so important for our health that it is the 4th most common nutrient in our blood stream!” (source) Sulfate is also necessary for proper hormonal function, “When sulfate levels are low, the body won’t just have disturbed liver function, it will also suffer with all kinds of hormone problems.” (source) As anyone who has experienced hormonal dysfunction will attest, hormonal disorders affect every aspect of health. In “Fluoroquinolone Antibiotics and Thyroid Problems: Is there a Connection?” it is noted that fluoroquinolones are endocrine disruptors that lead to disruption of thyroid function, and additional information about the effects of fluoroquinolones on the thyroid can be found on http://fluoroquinolonethyroid.com/.

The most thoroughly documented and accepted consequence of oxalate overload is kidney-stones. Kidney-stones are incredibly painful, and they can cause damage to the kidneys. In addition to kidney-stones, it is noted in The Role of Oxalates in Autism and Chronic Disorders that, “Even though oxalate crystals are most common in the kidney, they also can form in virtually any other tissue in the body, including the brain and the blood-brain barrier. Oxalate crystals resembling pieces of glass can form in the heart muscle. As the heart muscle contracts, these pieces of oxalate crystals actually tear into the tissue. If these crystals are deposited in skeletal muscle, normal movement and exercise can be very painful. I’m convinced this is also one of the factors responsible for fibromyalgia. Oxalates may also cause thyroid disease as they react in thyroid tissue.”

In THE DOWN SIDE TO HIGH OXALATES – PROBLEMS WITH SULFATE, B6, GUT, AND METHYLATION, Dr. Rostenberg goes over the connections between oxalates, sulfate depletion (by oxalates), and liver problems, hormonal problems, GI problems including leaky gut, cancer, and autism. Additionally, it’s linked to high homocysteine which is linked to blood clots, strokes, and heart attacks.

Fluoroquinolones and Oxalates

There are literally twenty plausible theories as to how fluoroquinolones cause fluoroquinolone toxicity—a multi-symptom, often chronic, illness that is similar to autoimmune diseases, mysterious diseases like fibromyalgia and CFS/ME, endocrine disruption diseases, and more. Though much of the research into fluoroquinolone toxicity has focused on what fluoroquinolones do to cells (especially mitochondria), as information about the importance of the microbiome emerges, it becomes plausible (and even likely) that the destruction of important microbes by fluoroquinolones is a large contributor to fluoroquinolone toxicity.

In Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues Dr. Martin J. Blaser hypothesizes that the extinction of critical microbes is behind many of the diseases of modernity, from autoimmune diseases to obesity. Dr. Blaser focuses primarily on h. pylori and its connection with both preventing inflammation and causing ulcers, but he acknowledges that many other microbes play important roles in human health and well-being. I wonder if oxalobacter formigenes and other microbial communities are just as interesting, contradictory, and important as h. pylori. I suspect so, and I also suspect that the basic hypothesis that missing microbes (from antibiotic use, glyphosate, and the Western diet) are causing the many diseases of modernity, is, indeed, true.

Fluoroquinolones obliterate the gut, and kill both helpful and harmful bacteria. In wiping out essential species of bacteria in our gut, are they starting the cycle of inflammation and chronic disease in genetically susceptible individuals? It certainly sounds like a reasonably hypothesis to me.

Can the gut be healed?

Can species of bacteria that have been depleted by fluoroquinolone antibiotics be replenished? Do probiotic supplements help? Can changing one’s diet help? What about fecal transplants?

Those are all million dollar questions that many researchers are working on answering. Unfortunately, I don’t know the answers to them. I am certainly hopeful that the gut can be healed, and I know from personal experience that healing after fluoroquinolone antibiotic toxicity can occur. Organizations like The Human Microbiome Project and Ubiome have many smart and capable scientists who are working to answer those questions, and more.

Until those questions can be more thoroughly answered, here are some helpful resources:

Resources for Healing

Trying Low Oxalates Facebook Group – https://www.facebook.com/groups/TryingLowOxalates/


Information about a low-oxalate diet can be found on Low Oxalate Info: Hope and Healing on the Low Oxalate Diet.

Dr. Rostenberg’s protocol for reducing oxalates can also be found here – http://www.beyondmthfr.com/high-oxalates/. Additional information from Dr. Rostenberg can be found through the Contact page on http://www.beyondmthfr.com/.

Additional information about MTHFR and other gene mutations, and how they affect health, can be found on https://mthfrsupport.com/.

If you would like to get your microbiome sequenced through Ubiome, here is a 10% off linkhttp://ubiome.refr.cc/VDDLNWP .

ubiome logo

Dr. Rostenberg’s videos on oxalates:



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Loss of Faith in the Healthcare System

After getting “floxed,” I lost a lot of faith in the medical system.

I used to think that the medical system, as a whole, was trustworthy. I knew that the system was imperfect, but I thought that most of the problems had to do with cost and insurance, and that drugs generally were well understood and regulated, and that they did more good than harm.

Getting hurt by a prescription drug, an antibiotic no less, shook my faith in the medical system. Researching fluoroquinolones and other drugs made me realize how little anyone knows about how drugs work, and why they sometimes don’t work, and I further lost faith in the system.

As I witnessed a prescription drug causing people to be chronically ill, I started to wonder if many of the chronic illnesses (autoimmune diseases, neurodegenerative diseases, mysterious diseases like ME/CFS and fibromyalgia, diabetes, etc.) were due to the cellular destruction inflicted by prescription drugs. Many prescription drugs, not just fluoroquinolones, wreak havoc on the microbiome, mitochondria, neurotransmitters, and more–and problems with those systems have been linked to many of the chronic diseases of modernity.

I saw that the only thing that the FDA is inclined to do about adverse drug reactions is to increase the size of the warning labels–as if anyone reads the warning labels and as if this is actually a solution. I noted that thousands of people are killed by prescription drugs each year, and I lost faith in the FDA’s ability to regulate the pharmaceutical industry.

The 21st Century Cures Act, a piece of legislation that is going through Congress right now, is a thinly-veiled give-away to the pharmaceutical industry that decreases drug regulation at a time when it needs to be increased. Congress is not only failing to recognize the problem of prescription drugs hurting and killing people, it is actively encouraging the pharmaceutical industry to do more of the same. I didn’t have a lot of faith in the U.S. Congress before I got “floxed,” but I have even less faith in them now. (If you want to read my take on the 21st Century Cures Act, I wrote about it in the post, “The 21st Century Cures Act” Is On Its Way – Here’s Why You Haven’t Heard About It that was published on Collective Evolution on 7/7/15.)

I wonder how many other people there are like me–who no longer trust the medical system after being hurt by it. I suspect that most (but certainly not all) people who get hurt by prescription drugs no longer view the system as a whole as trustworthy or credible.

Once a system loses credibility, many people opt out of it and seek alternatives. If the healthcare system loses credibility in the minds of most people, and most people opt out of it, it will, eventually, collapse. I have no idea when this will happen, or even if there are enough people who think like me that it will happen. We shall see.

Unfortunately, a lot of people are currently being hurt by adverse drug reactions, and more people will have to get hurt for a crash to happen. I don’t hope for a crash. I hope that the regulators (the FDA) start doing their jobs and that the pharmaceutical companies start upholding their credos and start having morals. I wish I saw that happening, but I don’t. Maybe we will reach a tipping point where it will happen–to be determined.

The healthcare industry is immense, and it is much more complicated than the sub-prime housing market that crashed in 2007-2008. However, I see some similarities between the sub-prime housing market crash and my assertion that the healthcare industry is going to crash (at some point–maybe). Those similarities are described in the post, The Healthcare System Collapse: Lessons from the Housing Market Crash and “The Big Short” that was published on Hormones Matter yesterday – 2/4/16. (This post started as an intro to the Hormones Matter post, and it just morphed into its own post. Please read and share The Healthcare System Collapse: Lessons from the Housing Market Crash and “The Big Short” – Thanks!)

I foresee a crash in the medical system because I’ve lost faith in it. Maybe I’m wrong and other people will respond differently from how I have after getting hurt by the medical system. Maybe I really am “rare” and other people won’t get hurt by the medical system. Or, maybe drugs will get more and more dangerous because of lack of regulation, and more and more people will get hurt by pharmaceuticals and they will lose faith in the system just like I did, and the demise of the system as we know it will arrive. To be determined, and we shall see. Hopefully I’m just being too pessimistic and the FDA will start doing a better job at protecting people from dangerous drugs. I really do hope that occurs.

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Dr. Perlmutter Speaks About the Microbiome and Advocacy

Yesterday I went to a wonderful event at a Natural Grocers where Dr. David Perlmutter spoke about the importance of nourishing your microbiome with healthy foods.

According to his amazon.com bio, “David Perlmutter, MD, is a globally recognized leader in brain science. He is the recipient of the Linus Pauling Award, editor-in-chief of the global online and print peer-reviewed journal Brain and Gut, and author of the #1 New York Times bestseller Grain Brain, The Grain Brain Cookbook, Brain Maker, The Better Brain Book, Raise a Smarter Child by Kindergarten, and Power Up Your Brain. He lives and practices in Naples, Florida.”

Dr. Perlmutter understands the connections between microbiome health and brain health. He speaks out about the connections between microbiome destruction via over-use of antibiotics, and chronic illness. He has acknowledged fluoroquinolone toxicity on news-casts, and has made videos about fluoroquinolone-induced peripheral neuropathy.

His presentation was wonderful and if you get the opportunity to see him speak, I recommend that you do so.

I had the opportunity to thank Dr. Perlmutter for the work he’s done speaking out about fluoroquinolone toxicity.

I also had the opportunity to ask him, in the Q&A section in front of the whole audience, what can be done to encourage more doctors to understand that fluoroquinolone antibiotics are dangerous drugs that should not be used frivolously. He responded that speaking out was the way to bring about change, and that doctors and other people can be educated about the dangers of fluoroquinolones one person at a time.

Every time we share an article that connects microbiome destruction to chronic illness (several are linked to HERE), we encourage people to understand that microbiome health is critical for all areas of health, and that throwing a nuclear bomb into the gut with fluoroquinolones (information about the dangers of fluoroquinolones can be found HERE), can be devastating.

Dr. Perlmutter also spoke about how mitochondria are ancient bacteria, and every time we share information about how fluoroquinolones damage mitochondria, we are also increasing the chances of doctors and other people making the connections between mitochondria-damaging drugs and chronic illness.

The outreach advice I got from Dr. Perlmutter and Dr. Wahls (in Episode 14 of The Floxie Hope Podcast) was to keep screaming, keep telling people about fluoroquinolone toxicity, and one person at a time, minds will change.

For fluoroquinolone toxicity to be on the radar of someone as influential as Dr. Perlmutter is a HUGE step in the right direction for us. He reaches millions of people through his books, web site, journal, practice, and other contributions. If you get a chance to thank him for his fluoroquinolone toxicity awareness efforts, please do so. He is brilliant, thoughtful, interesting and a wonderful advocate. He has my respect and admiration.


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The Microbiome According to Michael Pollan

Cooked by Michael Pollan Microbiome

I recently read “Cooked: A Natural History of Transformation” by Michael Pollan.  You can buy it HERE and a portion of the proceeds will go to the QVF.  I recommend that you purchase it, not just because some money will go to the QVF, but because it is beautifully written, enjoyable, interesting, insightful and poignant.

On the surface, Cooked has very little, if anything, to do with fluoroquinolone antibiotic toxicity.  Cooked is about the transformation of raw ingredients into food when fire, water, air and earth are applied to those ingredients through the process we call cooking.  The section of Cooked that has to do with how things from the earth–bacteria, fungi, etc., are used to transform and “cook” food, is the section I am going to connect to fluoroquinolone antibiotic toxicity.

Fluoroquinolone antibiotics are like a nuclear bomb to the gut.  They obliterate the microbiome, killing both good and bad bacteria in the gut and throughout the body.  They lead to a massive amount of oxidative stress within the gut that further damages the balance of bacteria in the gut.  It is only because of lack of knowledge about the importance of the microbiome that Cipro/ciprofloxacin only has a 43 page warning label, not a 100 page warning label.  In Cooked, Michael Pollan goes over the importance of the microbiome.  He explains the microbiome better than I possibly could, so I’m going to highlight some of my favorite quotes from Cooked in this post.

“Could it be possible that the microbiota also affects mental function and mood, as some of the fermentos I met in Freesone claimed?  The idea no longer seems preposterous.  A recent study performed in Ireland found that introducing a certain probiotic species found in some fermented foods (Lactobacillus rhamnosus JB-1) to the diet of mice had a measureable effect on their stress levels and mood, altering the levels of certain neurotransmitters in the brain.  Precisely how the presence of a certain bacterium in the gut might affect mental function is unclear, yet the researchers found they could block the effect by severing the vagus nerve that links the gut to the brain.  Studies like this one make you wonder if it might someday be possible to cultivate, or garden, our microbiota, altering its makeup to improve our physical and possibly also our mental well-being.

Right now, of course, and for the last several decades at least, we have been assiduously doing exactly the opposite:  disordering the community of microbes in our bodies without even realizing it, much less  with any sense of what might be at stake.  Under the pressures of broad-spectrum antibiotics, a Pasteurian regime of ‘good sanitation,’ and a modern diet notably hostile to bacteria, the human microbiota has probably changed more in the last hundred years than in the previous ten thousand, when the shift to agriculture altered our diet and lifestyle.  We are only just beginning to recognize the implications of these changes for our health.”

A book that is on my reading list (but that I haven’t yet read) is “Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues” by Martin J. Blaser.  It’s supposed to be excellent.  It is about the diminishing diversity of our microbiota.

Back to Cooked:

“The average child in the developed world has also received between ten and twenty courses of antibiotics before his or her eighteenth birthday, an assault on the microflora the implications of which researchers are just beginning to reckon.  Like the pesticides applied to a farm field, antibiotics ‘work,’ at least in the short term.  Yet as soon as you widen the lens from a narrow focus on the ‘enemy species,’ you see that such blunt weapons inflict collateral damage to the larger environment, including, in the case of pesticides, the microbial community of the soil.  Resistant bugs and various other health problems soon emerge; the soil’s ability to nourish plants and help them withstand disease is also compromised, because the toxins have reduced the community’s biodiversity and thereby compromised its resilience.  As in the soil, so in the gut.  The drive for control and order ends up leading to more disorder.”

“An interesting question is why the body would enlist bacteria in all these critical functions, rather than evolve its own systems to do this work.  One theory is that, because microbes can evolve so much more rapidly than the ‘higher animals,’ they can respond with much greater speed and agility to changes in the environment–to threats as well as opportunities.  Exquisitely reactive and fungible, bacteria can swap genes and pieces of DNA among themselves, picking them up and dropping them almost as if they were tools.  This capability is especially handy when a new toxin or food source appears in the environment.  The microbiota can swiftly find precisely the right gene needed to fight it–or eat it.”

“Taken together, the microflora may function as a kind of sensory organ, bringing the body the latest information from the environment, as well as the new tools needed to deal with it.  ‘The bacteria in your gut are continually reading the environment and responding,’ says Joel Kimmons, a nutrition scientist and epidemiologist at the Centers for Disease Control and Prevention in Atlanta.  ‘They’re a molecular mirror of the changing world.  And because they can evolve so quickly, they help our bodies respond to changes in our environment.”

Bacteria gene-swap at the drop of a hat.  Isn’t that fascinating?  It also makes the fact that fluoroquinolones disrupt the process of bacterial DNA and RNA replication quite consequential.  I wrote this post about antibiotics altering bacterial DNA back in 2013 – http://www.collective-evolution.com/2013/10/23/genetically-modifying-humans-via-antibiotics-something-you-need-to-know/.  The consequences of altering bacterial DNA are still being explored.

Another book of Michael Pollan’s, “The Omnivore’s Dilemma: A Natural History of Four Meals” goes over the hazards of applying the industrial model to biological systems–specifically, the folly of using the industrial model to produce food when food production should be a biological, not an industrial, process.  The same is true for medicine.  The medical system treats people as machines with inputs and outputs and predictable outcomes based on those measured inputs and outputs.  It doesn’t work though.  Humans are biological systems with feedback and feedforward loops, genetic differences and epigenetic differences, nature and nurture differences, and more–that make conceptualizing humans as machines with predictable outcomes foolish and wrong-headed.  When land and animals are used to make food in an industrial, rather than biological, model, unsustainability, externalities and consequences result.  When biological systems are respected for the complex systems that they are, sustainability comes naturally.  Likewise, when human complexity is ignored and stupid, foolish, one-size-fits-all, industrial medicine prevails, consequences occur in place of health.  It turns out that consequences look a whole lot like chronic illness.  Whoops.

Lisa’s one-sentence summary of Cooked and The Omnivore’s Dilemma is – Don’t eat processed food.  Read the books for a more thorough explanation.  They’re both excellent.


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The Importance of the Microbiome

The bacterial cells in our body outnumber the human cells ten to one.  Additionally, within each eukaryotic (human) cell in our body, there are many (hundreds in many cells) mitochondria – ancient bacteria that got absorbed into non-bacterial cells and formed eukaryotic cells.  Bacteria are an important, vital part of us.  Bacteria affect every aspect of human health, including immune system regulation, digestion, personality, etc.  Additionally, disturbances in the make-up of the microbiome has been connected with multiple chronic diseases, including Parkinson’s Disease, Alzheimer’s Disease, diabetes, autism, autoimmune diseases, etc.

Given the importance of the bacteria that work symbiotically with us, and that ARE US, it drives me a little nuts when people minimize the harm in damaging the microbiome with pharmaceuticals.  If a drug “just” damages bacteria, but doesn’t damage eukaryotic cells directly, it hurts the person who takes the drug, because the bacteria within that person are a vital part of him/her and an integral part of his/her health.

Dismantling the DNA of bacteria (and mitochondria), and inducing massive amounts of oxidative stress (the Fenton Reaction) with fluoroquinolones is particularly stupid.

The above is elaborated upon in the following post on Hormones Matter:


Thank you for reading it and for sharing it!


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Fluoroquinolone Induced Gene Upregulation and ROS

The article, “The Fluoroquinolone Levofloxacin Triggers the Transcriptional Activation of Iron Transport Genes That Contribute to Cell Death in Streptococcus pneumonia” is difficult.  It’s not light reading.  I wish it was.  I wish the articles that have information about how fluoroquinolones affect cells were easy to understand and to read.  I wish that we had easy, simple answers about how fluoroquinolones lead to the myriad of adverse events that are listed on the FDA warning labels for them.  I wish that more was known about how fluoroquinolones work.  I wish that a list of definitions wasn’t necessary at the beginning of this blog post.  But this stuff is hard, and a list of definitions is necessary, so, hereyago (some definitions paraphrased from the Wikipedia article because it’s easiest and I’m not a biochemist – for more info, go to the wiki page, or elsewhere):

Reactive Oxygen Species (ROS):  “Reactive oxygen species (ROS) are chemically reactive molecules containing oxygen. Examples include oxygen ions and peroxides. ROS are formed as a natural byproduct of the normal metabolism of oxygen and have important roles in cell signaling and homeostasis.  However, during times of environmental stress (e.g., UV or heat exposure), ROS levels can increase dramatically. This may result in significant damage to cell structures. Cumulatively, this is known as oxidative stress. ROS are also generated by exogenous sources such as ionizing radiation.”  ROS can be incredibly nasty.  They can lead to cellular damage, including DNA damage, and are related to every chronic disease there is.  They’re also related to ageing.  As damage from ROS (also called oxidative stress and free radicals) accumulates, ageing and the diseases of old age occur.  Interestingly though, ROS are not all bad.  They serve as signaling mechanisms within cells and play a large role in turning genes on and off (epigenetics).  They need to be in balance.  If they’re not in balance, a whole lot of things can go wrong.  They’re kind of like tequila.  A shot of tequila mixed with lime juice and other goodies, is excellent in a margarita.  But if you drink the whole bottle, and then mix it with some whiskey, it’s really bad and destructive.  The ways that ROS work within cells is not linear and difficult to study.  Not a whole lot is known about ROS or how they affect human health.  The article, “Exercise-Induced Oxidative Stress: Cellular Mechanisms and Impact on Muscle Force Production” has a really nice over-view of various ROS and their effects.  It’s easier to think of them as different  alcoholic drinks though.  Some are beer – pretty benign unless you have a ridiculous amount of them.  Others are potent – more like Everclear – and they can do a lot of damage to you quickly.

Fenton Reaction:  “Iron(II) is oxidized by hydrogen peroxide to iron(III), forming a hydroxyl radical and a hydroxide ion in the process. Iron(III) is then reduced back to iron(II) by another molecule of hydrogen peroxide, forming a hydroperoxyl radical and a proton. The net effect is a disproportionation of hydrogen peroxide to create two different oxygen-radical species, with water (H+ + OH–) as a byproduct.”  Basically, iron can “donate or accept free electrons via intracellular reactions and help in creating free radicals.”  Free radicals are ROS.  Some of the nastiest ROS are created in the Fenton Reaction – hydroxyl radicals and hydroperoxyl radicals.  (“Exercise-Induced Oxidative Stress: Cellular Mechanisms and Impact on Muscle Force Production” has good info on both of those.)

Type II topoisomerases, gyrase and topoisomerase IV:  “Type II topoisomerases maintain DNA topology and solve the topological problems associated with DNA replication, transcription, and recombination (20). Gyrase introduces negative supercoils into DNA (21), whereas topo IV relaxes DNA and participates in chromosome partitioning (22). Chromosomal topology in Escherichia coli is maintained homeostatically by the opposing activities of topoisomerases that relax DNA (topo I and topo IV) and by gyrase.” (from “The Fluoroquinolone Levofloxacin Triggers the Transcriptional Activation of Iron Transport Genes That Contribute to Cell Death in Streptococcus pneumonia”)


You got all that?  Even the definitions are difficult.  Now onto some highlights of the article, “The Fluoroquinolone Levofloxacin Triggers the Transcriptional Activation of Iron Transport Genes That Contribute to Cell Death in Streptococcus pneumonia.”

Basically, the researchers found that levofloxacin upregulated genes that are involved in iron uptake and triggered the Fenton reaction in certain bacteria.  The increase in reactive oxygen species that ensued contributed to the lethality of the levofloxacin.

There are a few interesting things that should be noted about this.  First, levofloxacin can upregulate genes.  How consequential is this?  Can eukaryotic genes be upregulated, or can only bacterial genes be upregulated?  What about mitochondrial genes?  What does upregulation of bacterial, mitochondrial and even eukaryotic nuclear genes do to the person who has taken levofloxacin?

Some interesting research is being conducted about the relationship between the microbiome and genetic, heritable traits.  This National Geographic article, “The Most Heritable Gut Bacterium is… Wait, What is That?” notes some of the relationships that are being explored.  Our genes can affect our microbiome, our microbiome can affect our genes, can the genes of our microbiome affect…. US?  Where does the microbiome stop and where do we begin?  Those are all questions that have not yet been answered.  Unfortunately, fluoroquinolones, like levofloxacin, are thoroughly messing up our microbiomes and even causing the upregulation/expression of certain genes.

The second thing of note from the article is that the upregulated genes caused the activation of the Fenton reaction in the bacterial cells.  Again, how does this affect our microbiome?  How does it affect US?  Hydroxyl radicals and superoxide anions are nasty ROS that damage everything in their wake.  What happens to the health of the microbiome, and the host (the person) when their gut is suddenly full of toxic ROS?  Leaky gut syndrome?  Autoimmune reactions?  The multi-symptom, chronic illness that is fluoroquinolone toxicity syndrome?

There is quite a bit of evidence that fluoroquinolones do to mitochondria what they do to bacteria – disrupt the process of DNA replication and reproduction and lead to destruction and cell death.  I think that mitochondrial destruction has a lot to do with fluoroquinolone toxicity.  However, I don’t think that the role of disruption of our microbiome and destruction of our gut bacteria should be overlooked.  The signaling that goes on within our microbiome, and between “us” and our microbiome, is critically important and poorly understood.  Triggering bacterial DNA destruction and death, upregulation of genes and the Fenton reaction – which leads to production of highly destructive ROS, is a very, very, very bad idea – even if it just stays within the microbiome.

The conclusion of “The Fluoroquinolone Levofloxacin Triggers the Transcriptional Activation of Iron Transport Genes That Contribute to Cell Death in Streptococcus pneumonia” is that:

“In conclusion, we have shown for the first time that fatDCEB transcription is regulated by the supercoiling level. The primary effect of the interaction of LVX-topo IV is the upregulation of the operon by local increase in DNA supercoiling. This upregulation would increase the intracellular level of iron, which activates the Fenton reaction, increasing the concentration of hydroxyl radicals. These effects were observed before the inhibition of protein synthesis mediated by LVX. All these effects, together with the DNA damage caused by the inhibition of topo IV, would account for LVX lethality. The possibility to increase FQs’ efficacy by elevating the levels of intracellular ferrous iron remains open.”

Because, apparently, seeing the big picture of the symbiotic relationship between the microbiome and the rest of the organism (the person), isn’t the goal.  The goal is to kill bacteria.  It’s ridiculously short sighted.  Sigh.

Because we’re in Floxieville, there has to be a paradox.  Supplementing iron helped me more than just about anything else.  Iron is one of the few supplements that made me feel markedly better immediately after taking it.  Other Floxies have reported that their ferritin levels are low post-flox.  The role of the Fenton reaction in fluoroquinolone toxicity would lead one to think that iron should be the last thing that a Floxie might need or want.  It helped me though.  I had more energy and even my tendons felt better when I started supplementing iron.  I don’t know if this has something to do with the kind of iron in my supplement/body – FE3 or FE2 – or if the iron had been converted to other chemical compounds and I needed to replace it, or what.  I do know that, as I said in the beginning of this post, this stuff is hard.

The Fluoroquinolone Levofloxacin Triggers the Transcriptional Activation of Iron Transport Genes That Contribute to Cell Death in Streptococcus pneumonia provides a good description of how fluoroquinolones work:

“The killing effect of FQs has been related to the resolution of reaction intermediates of DNA-FQ-topoisomerase complexes, which generates irreparable double-stranded DNA breaks (31). This could occur in E. coli by two pathways, one dependent on protein synthesis and the other independent of it. It has been shown that hydroxyl radical action contributes to FQ-mediated cell death occurring via a protein-dependent pathway (32). This result agrees with a recent proposal suggesting that, following gyrase poisoning, hydroxyl radical formation utilizing internal iron and the Fenton reaction (33) is generated and contributes to cell killing by FQs (34) as well as by other bactericidal antibiotics (35, 36). In this mechanism, proposed for Enterobacteriaceae (35, 37), the primary drug interactions stimulate oxidation of NADH via the electron transport chain that is dependent on the tricarboxylic acid cycle. Hyperactivation of the electron transport chain stimulates superoxide formation. Superoxide destabilizes the iron-sulfur clusters of enzymes, making Fe2+ available for oxidation by the Fenton reaction. The Fenton reaction leads to the formation of hydroxyl radicals that would damage DNA, proteins, and lipids (38), which results in cell death. Instead of a generalized oxidative damage, a recent study supports that the main action of hydroxyl radicals is the oxidation of guanine (to 8-oxo-guanine) of the nucleotide pool. The incomplete repair of closely spaced 8-oxo-deoxyguanosine lesions caused lethal double-strand DNA breaks, which would underlie much of the cell death caused by beta-lactams and FQs (39). However, recent investigations have questioned the role of hydroxyl radicals and intracellular iron levels in antibiotic-mediated lethality using antibiotic concentrations either similar to (40) or higher than (41) those used previously. The disparate results obtained using diverse antibiotic concentrations and times of treatment emphasize the complexity of the lethal stress response (42).”

Similar destruction happens in mitochondria.  As I mentioned though, even if it didn’t happen in mitochondria, and only happened in bacteria, that destruction and those reactions are horrible things to do to a person’s microbiome.  It is, after all, part of us.

All of the people at the FDA who think that it’s okay not to strictly regulate drugs that disrupt the process of DNA replication and reproduction, and lead to the upregulation of genes and induction of the Fenton reaction, which leads to high levels of highly reactive ROS, should be fired.  I’ve learned enough biochem in the last 3 years to know that induction of the Fenton reaction in any part of the body is a really bad idea.  The scientists at the FDA should be able to figure this out.


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Antibiotics After Fluoroquinolone Toxicity

People often ask about what they should do to treat infections post-flox.  Here are my tips.

First, please INSIST on getting your infection cultured and confirmed before you take any antibiotics.  As anyone who has had an adverse reaction to an antibiotic can tell you, antibiotics are not benign drugs.  They have side-effects (HERE is the 43 PAGE warning label for Cipro/Ciprofloxacin).  Some of those side-effects are life-altering and/or life-threatening.  You don’t want to put any drugs into your body unless you absolutely need them.  A culture should be done to confirm that an infection is present before you take an antibiotic – no matter what.

Because antibiotics have been shown to wreak havoc on the microbiome and bactericidal antibiotics damage mitochondria – and because both microbiome disruptions and mitochondrial dysfunctions are linked with every chronic disease there is – I highly recommend looking into some non-pharmaceutical options first.  Garlic has been shown to have antibiotic qualities and to be more effective against biofilms than many antibiotics.  For urinary tract infections, D-mannose has effectively helped thousands of people get rid of their infection.  Some other non-pharmaceutical remedies for urinary tract infections can be found HERECoconut oil has been shown to have anti-bacterial qualities and it may be good for treating skin and GI infections.  Colloidal silver not only has anti-bacterial qualities on its own, it also has been shown to increase the effectiveness of pharmaceutical antibiotics when used in conjunction with them.  Andrographis is an herb that has antibiotic qualities.

If non-pharmaceutical options aren’t working and you need an antibiotic to get rid of your confirmed infection, here are the antibiotics that I recommend along with reasons as to why I recommend them (or not).

  1. Most Floxies seem to do well with doxycycline and other tetracyclines. Tetracyclines are bacteriostatic antibiotics that, “stops bacteria from multiplying but does not kill them.” (source)
  2. Several Floxies have taken Z-pack’s without incident
  3. Amoxicillin seems to be about as benign as antibiotics get. So, it’s not harmless, but it’s well tolerated generally.
  4. Penicillin seems to be well tolerated – unless you’re allergic to it.
  5. Cephalosporins seem to be well tolerated

There are probably some other antibiotics that are fine for Floxies, I just haven’t heard about them.  Please feel free to leave a comment below if there is an effective and relatively safe one that I’m missing.

Here are the antibiotics that I recommend avoiding because they have side-effects that are similar to those of fluoroquinolones, and because many Floxies react badly to them –

  1. Macrobid / Nitrofurantoin
  2. Flagyl / Metronidazole
  3. Bactrim / Trimethoprim / Sulfamethoxazole
  4. Augmentin


Fluoroquinolones – Cipro/Ciprofloxacin, Levaquin/Levofloxacin, Avelox/Moxifloxacin, Floxin/Ofloxacin and a few others – should be avoided entirely unless you are dying and make the decision that getting “floxed” is preferred to death.  Every warning label for every fluoroquinolone says that people who have an existing hypersensitivity to a fluoroquinolone should not take them again.  “Ciprofloxacin is contraindicated in persons with a history of hypersensitivity to ciprofloxacin, any member of the quinolone class of antimicrobial agents, or any of the product components.” (Warning Label)

Before you take an antibiotic, or any pharmaceutical for that matter, I highly recommend that you look up the review for that drug on http://www.askapatient.com/ and look it up on http://www.peoplespharmacy.com/.  Also, look up the drug’s warning label.  Be informed.  Make an informed decision.

Here is a list of antibiotics – http://en.wikipedia.org/wiki/List_of_antibiotics  I didn’t get close to going through all of them.  But I hope that this post gives you some guidance when/if you are faced with an infection.

I’m not a doctor, so please take this advice for what it’s worth.  Doctors should be consulted when you have an infection.  The internet should be consulted too though, because doctors aren’t capable of knowing everything and informed consent is really important.


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