Celiac Disease and The Overuse of Antibiotics | Chris Kresser

Has Antibiotic Overuse Caused a Celiac Disease Epidemic?

by Chris Kresser

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Celiac disease is on the rise, and the population-wide overuse of antibiotics could play a key role in triggering disease onset.

There’s no denying that celiac disease (CD) is more prevalent now than ever. In the US, rates of CD have increased at least 5-fold over the past few decades, and prevalence in Finland has doubled. (1, 2, 3) The incidence of CD has also increased four-fold in the UK and three-fold in the Netherlands in the past 20 years, and the incidence of pediatric CD in Scotland has increased 6.4-fold. (4, 5, 6)

So naturally, everyone is wondering – why? We know that there’s a strong genetic component to celiac disease (and our ability to detect the disease has vastly improved), but the rising rates have occurred too quickly to be explained by a genetic shift in the population.

Besides, the genes that predispose an individual to CD are actually relatively common in the population, but only a very small percentage of those people actually develop the disease. In other words, genetics appear to be necessary – but not sufficient – for someone to develop CD.

Can the overuse of #antibiotics trigger celiac disease?

Antibiotics can cause intestinal dysbiosis and infection

Clearly, something has changed in the environment to trigger celiac disease in a higher proportion of genetically susceptible people. Multiple factors probably play a role, but evidence indicates that one big factor is the intestinal microbiota. And a major contributor to disordered intestinal microbiota is antibiotic overuse.

In my previous article on the effects of antibiotics, I reviewed several studies that demonstrate how drastically antibiotics can alter the gut microbiome. Just a single course of antibiotics can reduce the richness and diversity of the intestinal microbiota, and in many cases, people never completely regain the diversity they lost.

Even if a person doesn’t develop an overt, clinically-diagnosable infection such as C. difficile, imbalances in the types of bacteria that colonize the gut can still cause serious problems. But to understand how antibiotic-induced gut dysbiosis could trigger celiac disease in genetically-susceptible individuals, it helps to first understand some of the basic mechanisms behind celiac disease.

Celiac disease involves an immune reaction to both gliadin and tissue transglutaminase

The biological mechanisms behind celiac disease are complicated and still not fully understood, but the general idea is that gluten – a group of proteins found in wheat, rye, and barley – triggers an autoimmune response that results in severe damage to the epithelial lining of the intestine.

Gliadins and glutenins are the two main components of gluten, with gliadins being the primary trigger for celiac disease. These proteins are very difficult for the body to digest fully, but in most people, this isn’t a problem. However, in people with celiac disease, certain cells (known as “antigen-presenting cells”) get a hold of these large, undigested fragments of protein and present them to T-cells, triggering an immune response. (7, 8)

An enzyme called tissue transglutaminase (TG2) is also important in the development of CD. This is because antigen-presenting cells only bind certain types of proteins, and they don’t usually bind normal gliadin fragments. (9) On the other hand, TG2 readily binds gliadin, and actually modifies it to make the gliadin much more attractive to antigen-presenting cells. This vastly increases the likelihood of an immune response.

Once this happens, the body starts creating antibodies against gliadin. But because the gliadin is usually bound to TG2, the body also creates antibodies against TG2, its own enzyme. This attack of “self” is what earns CD the classification of “autoimmune.”

Intestinal dysbiosis and infection can lead to up-regulation of tissue transglutaminase

In healthy individuals, TG2 plays a role in tissue repair, as well as in other processes such as regulation of cell death; it’s not an enzyme that’s “supposed” to interact with gluten. (Interestingly, TG2 also plays a role in other diseases, such as Parkinson’s and Huntington’s, by modifying proteins that it isn’t supposed to modify.) (10)

Most TG2 appears to be either stored safely inside cells or inactive under normal conditions, and is only activated in the event of tissue injury, bacterial or viral infection, or another source of inflammation. (11, 12) This indicates that tissue damage or inflammation in the intestine (and subsequent TG2 up-regulation) might actually be necessary for the development of CD.

Without substantial TG2 activity, it’s unlikely that the antigen-presenting cells would bind and present enough gluten fragments to provoke a major immune response. But a bacterial or viral infection could create inflammation and tissue damage that would activate TG2, and thus trigger the cascade of events eventually leading to celiac disease.

Intestinal dysbiosis and infection can contribute to leaky gut

Another factor to consider is the location of tissue transglutaminase. Nearly all TG2 is found in the sub-epithelial region of the intestine, a place that gluten shouldn’t have access to. This means the intestinal barrier would need to be compromised in some way for gluten proteins to significantly interact with TG2. (13)

This fits with previous work done by researchers such as Alessio Fasano, who have hypothesized that a person cannot develop an autoimmune condition such as CD if they don’t have leaky gut. If the intestinal barrier is intact, the immune system will never “see” the antigens, so it won’t mount an immune response.

But one big risk factor for developing leaky gut is intestinal dysbiosis or infection. Bacterial components such as lipopolysaccharides can induce inflammation and increase intestinal permeability, which would allow gluten into the sub-epithelial region of the intestine where it could be modified by TG2 and trigger CD. (14)

Candida infection may trigger celiac disease through cross-reactivity

So far, we’ve been talking about dysbiosis in a general sense, but there’s evidence that specific microbes could trigger celiac disease as well. A recent study (hat tip to Questioning Answers for the find) found that an overabundance of the yeast Candida albicans could contribute to the development of CD, and unfortunately, antibiotic use is a big risk factor for developing a candida infection. (15)

Candida is a normal part of the intestinal microbiome of healthy individuals, but problems can arise when it overgrows relative to other inhabitants of the intestine. Remember how tissue transglutaminase (TG2) readily binds gliadin? Well, it turns out that candida expresses a protein named Hwp1 that also binds TG2, potentially leading to immune activation and cross-reactivity with gluten.

The study found that people without CD who had candida infections produced anti-gliadin antibodies, as well as the expected anti-Hwp1 antibodies. People with CD produced antibodies to both proteins as well. This means that in theory, a person who is genetically susceptible to CD but who doesn’t have the disease could develop the disease in response to a candida infection.

So, what does this mean for you?

As you can see, there are several ways in which antibiotic overuse and subsequent intestinal dysbiosis or infection could lead to the development of celiac disease. As I’ve said before, antibiotics can be lifesaving and are necessary in some situations, but that doesn’t mean they’re free of consequences.

It’s becoming more and more clear how vitally important it is to use antibiotics responsibly, whether that’s not using them at all, or properly rehabilitating the gut during and after a course when they’re deemed necessary.

Now I’d like to hear from you. If you have Celiac disease, do you have a history of antibiotic use prior to the expression of the disease? What do you think about this theory? Share your opinion in the comments below.


Join the conversation

  1. I’ve always had Gi issues but they were non specific- reflux, gas,etc. I got Lyme disease, was misdiagnosed for 18 months- it progressed so far I was on Doxy for 4 months then off and on for another 1.5 years for Meibomian Gland dysfunction. My GI tract has never recovered from baseline. I have loose, pale stools, heavy, large multiple stools( 4-6 times per day) mouth sores, severe migraines, fatigue, dry eyes, severe anxiety from no-where. My muscles and joints ache. I also have endometriosis( surgically diagnosed). I have severe allergies now- the back of my throat has been chronically red for a few years; I have tingling in arms, tongue. So many weird issues- all of a sudden- since I took antibiotics for Lyme. Everyday I feel like I have the flu and it’s been 3 years since treatment. My celiac bx was negative, but wondering if I have gluten sensitivity. Have a brother with psoriasis , mother with chronic pain, GI problems, severe arthritis and chronic undiagnosed diarrhea; and sister/brother with gas, GI problems, diarrhea. I think we all have gluten sensitivity and chronic antibiotic use made mine much worse. I was born in the car and was started on antibiotics from the first day of my life. Also going thru menopause but don’t think these symptoms are typical of that.

  2. A few years ago I had strep throat 4 times within two months. Doctors kept prescribing stronger antibiotics each time. I found out one of my friends was a carrier. Now my body has built up antibiodies towards it today. Needless to say, this was a shock to my gut flora.

    Almost two years ago I developed a case of eczema on my left ring finger that I couldn’t cure. I saw dermatologists and allergists and they said it could only be environmental due to its localized placement. They kept prescribing steroids to treat the effect. I wanted to treat the cause so the problem would go away.

    I wanted to explore food allergies so I took gluten out of my diet for a few weeks and my finger cleared up. We went to a whisky tasting land the next day my hands and arms broke out in eczema. No gluten for the next week and it cleared up again. The next weekend we had pizza and that next day, same reaction.

    Since the antibiotic period, I’ve had candida on my face that I cannot get rid of. I’ve tried most of the -zoles medications and diflucan. No avail. It’s getting worse and I can’t finger out how to remedy it.

    Any and all help would be appreciated 🙂

  3. I too am celiac. You have a good informative post. You need to consider that you may have other food intolerances as well that can lead to inflammation and be causing more of your distress. It does not stop just with gluten. It is helpful to find a provider that tests for a host of immediate and delayed food sensitivities and also does work on your gastrointestinal tract (GI) or what the media and many call the gut. I was diagnosed with celiac when I started grad school and that changed the path of where I was headed and I pursued functional medicine. Look for a group that has medical professionals that do testing for food sensitivities and works with the GI tract. It does not end with celiac. It does help to find out what to avoid to reduce the inflammatory rudeness in your body.

  4. ps excuse my typos- was quickly writing under time pressure. Also to add- my son had multiple rounds of antibiotics for chronic sinus infections.. antibiotics he took as long 21 days to get rid of the persisted sinus infection that caused him to have a fever . In 2014 he had several rounds of antibiotics specifically.. which preceded the fever and stomach infection in April of 2015 which I suspect was the trigger . This timeline, is what your theory is as well.

  5. Hi. Your information seems spot on. My 17 year old son-just diagnosed with CD a week ago. After almost 20 months of misery. Random infections. Losing 30 pounds with zero explanation. Stomach pains. Bladder Spasms. Oral Thrush that persisted despite three rounds of treatment. ALL of this began after he was diagnosed with gastroenteritis in April 2015 . Soon after, Bladder spasms. Told the virus settled in his bladder. The 30 pounds of weight and summer of inexplicable stomach pain began. Sometimes nauseous, feeling full after eating a little bit, hurts too much to eat, stabbing pain, then just ashiness. etc. fatigued much more than usual. Then tested for mono, ultrasound of abdomen done, all normal. Shortly he had several allergic reactions to unknown substances. Patch testing revealed nothing abnormal. Pain in ankles and legs… shortly after, referred for exam by a pediatric ortho dr… He suspected auto immune disorder and sent him for blood work to look for RA. But it returned normal… Acne spiraled out of control — leading to more antibiotics.. prescribed prevacid for reflux..
    and daily Zyrtec to thwart allergy attack. still not normal… but managing ok… august of 2016 — more infections– first groin pain.. epididimitis was diagnosis.. bactrim for ten days.. then resume doxy antibiotic for acne… then he gets white coating on tongue and bumps in throat… diagnosis oral thrush normally seen in babies.. goes goes through three rounds of treatments.. ultimately taken off the doxy… and the thrush seemed to improve.. stomach pain worsens in upper abdomen.. sent for ultrasound, x ray of spleen area, blood work of mono.. has enlarged spleen but blood work good. My son is the one who saId he noticed if he did not eat bread or pasta he felt better.. that his father has a gluten intolerance he had been dealing with so my son decided to try to not eat bread or pasta.
    He still complaining of stomach not being right.. school intense.. is it stress???? Has ADD as well. We go to see an ADHD specialist in NY after Christmas to have brain mapping done to help with medication analysis… FIRST MOST GLARING ISSUE with this specialist.. HIS G I issues… Sent us back to Florida with orders to get gLUTEN TESTING DONE !!! Back home, got back to local drs… Son was immediately given an upper GI and all the blood work was taken in the IV the NY dr requested… JUST found out my son has Celiacs. 95 percent accurate full blown Celiacs.
    Biological father seems to have this as well. I am getting bloodwork tomorrow. It appears to me that all of his random health issues, seemed to begin after his stomach infection with a high fever in April of 2015 and he had to miss 6 days of his junior year because of this… and is on line his senior year now.. it was just too much . Thank you for your blog. I am in the process of finding out as much as I can. I feel so bad my son suffered so long during such formative and important years feeling so poorly. It leads to doubt, worry, depression, feeling like a hypochondriac and a failure. And it appears it mostly is due to Celiacs. We are praying that with a diligent gluten free diet his energy, spark, and health will return.

    • Have you ever tested for intestinal candidias? I have read a lot that antibiotic use create candida albicans growh. Unfortunately most doctors don’t believe on theory but a simple stool test can diagnose whether this is an issue or not. I am not sure why their ego gets hurt in getting this tested but please don’t ignore it and discuss about it with your doctor.

    • Don’t stop at just gluten- follow up checking for other “allergens/sensitivities”. Dairy(casein), peanuts, and soy can be very problematic too. It is crazy where they sneak soy into things!!

  6. HI, recommended to your site. I have CD, none of my reactions or immune responses happened until I had a C Section last year. Since then, my body seems to react to everything- gluten, dairy, sugars, you name it. I can’t help but claim this may be primarily caused by my c section and an infection. No doctor has been able to explain how this may have occurred, only that it is genetic. Do you think I may have an infection that caused CD

  7. My son, age 5, has Celiac. He only had one round of antibiotics in his first few days of life due to complications after birth. After that he was exclusively breastfedas and infant and continued to breast feed until 22 months. I don’t think the antibiotics where the main trigger of his disease but wonder if it was the traumatic birth experience. Otherwise he is a very healthy kid and it took us a long time to even notice his Celiac symptoms since is was so healthy. We found out due to iron deficient anemia despite being on an iron rich diet.

  8. I was on DAILY antibiotics for bladder reflux from 6mo of age until I was 10. I now (in my 30’s) have several autoimmune diseases one of which is Celiac. I often wondered if all of my autoimmune issues were related to prolonged antibiotic use. Still not sure if this is the csse, or if I will ever get an answer , but it’s definitely something to think about!

  9. My fiancé has been taking antibiotics daily 250 mg a day morning and night since she was 11, for rheumatic fever, she is now 27, shortly after the birth of our child three years ago she developed signs of celiac disease or possibly chrohms, she’s been on a gluten free diet for almost three years now, and her symptoms are better except for one thing, she gets ulcers in her mouth, like 3-5 at a time, is this related to cd or her antibiotics?

  10. Chris,
    While working in the southern Philippines (age 38) I had an onset of severe diarrhea after eating some locally prepared food. After 7 days of GI distress I began a 30 day battery of antibiotics (US licensed physician treated and US supplied meds). The battery of antibiotics consisted of 10 days of amoxicillin (no improvement) followed by 10 days of ciprofloxacin (no improvement) followed by 10 days of flagyl and a simple diet of rice bananas and apples with improvements. The diarrhea along with abdominal distress bloating and brain fog would return upon gluten ingestion. After 3 x GI physicians diagnosis of celiac disease I finally accepted that my days of wheat barely and rye ingestion were over. Learning to manage my diet to avoid inadvertent gluten ingestion was another interesting journey…
    Hopes this helps,

  11. My son was born in 1969 and screamed from birth. He was 8 lb. and 22 in. long, so well developed. He was a difficult baby to carry,…kicked constantly in the womb, day and night, so much so that he caused me a hernia,!….(.I now think it was because of the Gluten I was eating). Finally, at 8 months of age, and equal number of doctors, I noticed puss on his nappy, and we were finally believed. The diagnosis was that he had caught a urinary infection in the hospital nursery at birth, and as a result they put him in hospital to check his kidneys etc. and feed him large doses of antibiotics. Not only that, but when we took him home, we were presented with a pint sized bottle of phenobarb and other sleep medications, (adult dose I was told), to quiet him down.
    We were told he was going to be ‘retarded’. From that time forward, ( I never gave him the meds.) but he was on antibiotics, he had dreadful nightmares and mood swings.
    By the time he was nine, the teachers at school told me that they couldn’t work him out. He was both brilliant and vague.
    I asked him why this was and his answer was that ‘after lunch, a ‘little man’ pulls a blind down and he can’t think.”
    He also developed dreadful tantrums where he would say that he wished he had a zip in his head to let the steam out!!
    At almost ten, a family member was researching in one of the Uni. Medical libraries and came across a book called…”Good Food, Gluten Free”. The book was delivered to my door with the words,…”read the Intro”. I did, and there, I saw an outline of my son. I was considered ‘mad’ by the doctors until I found my way to a doctor educated in Western and Chinese Medicine. At last, someone listened. I had already worked out a ‘natural food’ GF diet, which my son had been on for 8 weeks. They did ‘blind studies’ on him for 6 weeks, and then wanted him to return to a ‘normal diet’.
    The child refused saying that he didn’t want to be sick like that again. That little boy is now well in his forties,….married with three teenage daughters. He has university degrees and is definitely not ‘retarded’. He has never eaten gluten again.
    I then researched our family. My mother-in-law had had part of her bowel removed for colitis. Her mother died of dementia, and was known for her ‘bilious attacks’ and ‘rings’ on her tongue. I recognised this immediately as something my son had. Later my strapping 6ft.2in. husband began making regular night trips to the toilet, sometimes 2 or 3 times. WE put him on the GF diet and it all stopped.
    So now I was looking at my child, my husband, my mother-in-law and her mother!!! My daughter and I were not celiac, but she now has two boys who are. I think that makes about five generations! All these family members also carry MTHFR mutations. As for me,…I’m not celiac and I don’t carry MTHFR gene mutations, but I do have Hashimotos, vitiligo and various other ‘auto immune’ issues.
    My daughter has Grave’s disease.
    I’m taking the trouble to briefly write ‘our’ story, because I don’t think there are many who can prove the genetics for so many generations. With my son, I have NO doubt that his ‘treatment’ in hospital at 8 mths. of age, brought the problem to the fore much earlier than it otherwise would have become evident. As for previous generations, ..who knows. My son now suffers acid reflux, and sadly takes meds. for it that make me shudder. I’m very interested in the microbiome of the gut and can’t wait for more research on this. But I think we are just at the beginning, I DO know that ‘probiotics’ are NOT the answer. Specific varieties MIGHT be, but that’s going to take time to work out.
    Our whole family live on fresh organic food, and watch the water we drink, plastics and all manner of household products. Some of us do not eat grains at all. It helps us to stay on our feet! My husband is 74. He’s outside concreting in 35o heat!

    I hope that helps someone! Never give up, Auto immunity is a horrible thing, but it makes you ‘strong’ and disciplined in a
    sense. There’s some wonderful research going on at present, and we need to support it as much as we can.

    • I am 56 years old and is suffering now for 2 months from a problem that is unknown at present. I was in church and suffered a hot flash accross my stomach and arms. I went to my Dr. and was put on zoloft, after five days of taking the zoloft I started hearing voices, I thought I was dying. I quickly wake my husband and asked him to call 911, before 911 came the feeling subsided and I decided not to go because of financial concerns. The next night the same feeling came back and I decided to go to the emergency room. I was given drug test, had a Police officer pat me down but no test to find out what the problem was. I was then diagnosed with psychosis and sent home. The next week I had a very rapid heart palpitation went back to the ER for being scared and again nothing was done. I then decided to call someone that practices holistic medicine. I was told to stop eating food with gluten and I did. I am feeling a lot better and I am waiting to go to my Dr. to be diagnosed.

      • Did you ever take a fluoroquinolone drug… cipro, avelox, levaquin etc? These will also do it to ya.. long after you’ve taken the drug. Check out Fluoroquinolone toxicity group on FB. Good luck !

    • Do you think the high doses of antibiotics caused worse reactions to the gluten? Did he happen to get sores in his mouth like ulcerous?

  12. This is really interesting (as always). After 44 years of ‘perfect health’ with no digestive or other symptoms despite 20 years of developing country travel I returned from a trip to Nepal and started getting infrequent bouts of diarrhoea. Eventually I went to the GP who suspected Giardiasis and prescribed Metronidazole, the first course of anti biotics I’ve ever had. I rapidly went from bad to worse, lost 2 stone in weight and was vomiting daily. 6 months later was diagnosed with CD. My instinct has always been that the anti biotics not a gut infection triggered the condition. 6 years on I’m writing my MSc dissertation on FM approach to CD so some good came out of it!

    • Hi Nicky,
      The exact same thing happened to me. I was in Nepal last year and caught food poisoning. The doctor gave me antibiotics that I reacted badly too. After that, like you, I started having frequent episodes of diarrhea, which became worse, rash on my back, dizzy and nausea, etc. It took me a month to realise it was probably Celiac disease. I haven’t been diagnosed (as I really don’t want to eat bread for two weeks), but my symptoms and relapses are pretty clear.
      Is there anything new about your state or knowledge on what could have happened to us?

  13. Are you familiar with interstitial cystitis? It’s a chronic condition where one experiences symptoms of a bladder infection but no bacteria are found in the urine. Many acquire IC after having a bladder infection and taking antibiotics. Many have found that avoiding gluten resolves many symptoms. Perhaps there is a connection to this process. Millions of women are suffering from IC, some estimate as many as 3-7% of women in the US.

  14. This is very interesting! In the study showing onset of celiac disease following candidal infection, this was a very specific, and somewhat rare subset of people with candidal infection, ie hospitalized patients with blood cultures positive for candida. It makes good theoretical sense that this might also apply to the much more common and less sick patients with intestinal candidal overgrowth- it would be great to see a study among this group of patients!

  15. As of 4 hours ago I was feeling like I was losing my 8 yr old son. For years the doctors told us he has asthma, although he never had an asthma attack. At 1st it was every few months he would catch a cold. It would progress to a high fever. The doctors would send us home saying it was a virus. in 2-3 days we were back at the doctors with deep non stop cough and 102-104 temperature. Sent home with antibiotics, then they added steroids.( Which we rejected) Over the past year -years and a half we have been at the doctor every month. We were repeatedly not a food allergy. Last month they said he had ADHD….my mommy instincts have been off radar for so long I thought I was losing it. Over the past few months he has had headaches, foot pain, and an upset stomach. 2 days age we are back at the doctors with headache, stomach ache, swollen foot, and a rash. The doctor, if you want to call him that, told me the rash had an unknown cause but was unimportant , and as a mother I should ignore the complaints of foot pain( even though you could plainly see the swelling) it was for attention. That was it I was watching my son suffer And I couldnt help. Today we took him to a new doctor. By the time we got there his lips looked so red and inflamed, feet swollen, and rash all over. The years of antibiotics wiped his system and he was now fighting his own body! His lower intestine is inflamed, his is rampant with yeast( another thing I questioned the other doctor about), his foot and joint pain is inflammation, and adhd is brain fog( basically inflamed). They said he is 6 months to a year away from celiac disease. He is on a non dairy non gluten diet, heavy duty probiotic, and oregano oil. All I have to say is The title doctor means nothing if you have that feeling , that something is wrong , bad energy feeling follow it. These “doctors” should have their licenses taken and be charged with something. As a mother I should have gone with my gut. Im just so thankful my son is going to be ok and that his years of suffering will soon be over. We have to use our voices and help each other!

  16. My younger brother use antibiotic for more than 1 year and doctor said he has celiac disease. He left wheat for last 1 year however there is no improvement and his anti ttg result still shows same result. Could you guys help …it seems he has some infection not sure candida or some other but not celiac disease…When we talk to doctor about this…they dont believe on our theory or this article…is there any test which can confirm candida yeast infection or any other thing?

    • Bharat, if it is celiac disease and an improvement is sought through diet, then he needs to cut out more than wheat, he needs to avoid all sources and every trace of gluten, including possibilities of cross contamination through surfaces, implements and so on. I did a similar thing, I mistakenly thought it was wheat and tried cutting that out for years. TO cut out gluten is really difficult and took me about 2 years to get fully sorted out, but this is what you have to do. Have a look at http://www.celiac.com/ or https://www.coeliac.org.uk/home/ for guidance. Good luck

  17. I’ve had a suspicion about this for a long time. But I’ve increasingly grown concerned about the effects of regular prednisone use. My daughter had “recurrent croup due to narrowed airway” and was prescribed a 3-day course of prednisone for each episode. We followed this religiously for 2 years (I’m estimating she had more than 100 doses) because she couldn’t breathe and my husband wasn’t taking any chances with homeopathy, etc. But I’ve been worried about the unknown side effects of the steroids on her system as a whole, especially since my 38-yr-old sister has recently been diagnosed with Celiac after constant antibiotic use to control acne.

  18. Hi Chris,
    I can absolutely relate to how use of antibiotics makes the gut more disposed to develop CD. Both my mom and my grandma got CD/gluten intolerance after using antibiotics.
    This was a really great article who highlighted and confirmed many of my previous thoughts about how CD might be developed, and who important good bacterias is for protecting us from CD.

  19. I agree with the possibility of a connection of antibiotic use and CD. I was diagnosed four years ago at age 58. I have taken antibiotics most of my adult life, for years at a time. Whenever I questioned my doctors about this long term use they just said “don’t worry we’ll keep an eye on you”. I’m not sure what that is suppose to mean since they only thing they did was write another prescription. Besides CD, I am allergic to soy and intolerant to dairy. I am continuing to react to other foods such as beans and tomatoes. Really getting tired of feeling bloated most of the time and hate that I may have contributed to my CD diagnosis by not listening to my “gut” about the excessive use of antibiotics. My new doctor is trying to say he thinks I may not have CD and wants me tested again even though I have told him I have been gluten free for four year, except for being “glutened” a few times by mistake. He said it doesn’t matter the intestinal damage will still be there. Does anyone know it this is true?

    • Please ask for candida infection test….it might not be celiac. If gluten level gets down after leaving gluten it may be celiac and if not chances are high that it might be candida overgrowth

  20. Thanks Chris for laying out the many avenues to food intolerance. Heavy duty antibiotics contributed all through my childhood.

    Avoiding all grains and starches as well as all sugar products has initiated an amazing outcome. Along with anti-inflammatory supplements I’ve gone down many sizes in clothing.

    I look forward to your guidance, especially in how to talk with the general public.

  21. Hi Chris,

    Very interesting. I have all the signs of CD though I haven’t gone through a formal diagnosis (though have discussed the issue with my doctor) and spent many years on antibiotics as teenager for acne. From the age of 12-19 I was on a constant course of minocycline or tetracycline and it was in my early 20s that I first developed IBS. I was checked out for all sorts of things (though not CD) and it is not until now (aged 40) that the penny dropped and I adopted a fully gluten (and grain) free diet despite being mostly wheat-free for years.

    That said, my sister and my partner, neither of whom received such antibiotic treatments, are both intolerant to wheat/gluten (as are several friends that I know of) so antibiotics are not the entire story where the development of intolerance never mind fully blown CD are concerned.

  22. Hi Chris,
    I found the article very interesting. There is no doubt about the relationship between antibiotic overuse and celiac disease. I agree with you about the increase in the incidence of celiac disease. I have been coming across a few number of people with this condition recently unlike before. Some have been placed on a long term course of antibiotics due to misdiagnosis which happened to have aggregated the situation. Some have been placed a very strict diet that almost left them with nothing to eat apart from drinking milk which triggers an allergic response.
    A few of the patients were misdiagnosed as having duodenal ulcers and one or two with gastric ulcers. Dairy milk and natural yoghurt were recommended hoping to have antibacterial and calming effect on the G. I. system.
    Personally, when dealing with patients with celiac disease, I recommend gluten free diet; I place them on a well researched Aloe Vera drinks, probiotic containing six strains of beneficial bacteria ( for two weeks), multi-minerals and anti-oxidant supplement containing beta carotene. Within 3 months, their condition is generally under control, no more leaky gut syndrome, they look better with amazing vibrant energy unlike before.

    • I wish Josephine had given us more information. I’ve had 7 rounds of antibiotics in the last 4 years and my digestion problems have greatly increased. I’m wondering what specific supplements she used. I’m going to my 6th gastro doctor next week and already know he will have no help.

  23. I have celiac disease (and sjogrens) and was on tetracycline for the first 2 years of my life. I was diagnosed with celiac when I was 51. I have a daughter who has celiac disease and was on antibiotics most of her childhood due to lung infections. My son and youngest daughter cannot tolerate gluten at all but are not celiac.
    I truly believe the antibiotics I had and a poor American diet is what made me prone to autoimmune disease. I am just sorry my kids are sick with autoimmune symptoms. It’s one thing to be chronically ill when you are older, but sad to have to deal with it as a young adult.

  24. Well… this is very interesting. I’ve known about the link between candida and gut issues for a long time but didn’t know it could cause celiac-like symptoms. This might explain a lot of things about my health.

  25. So glad this article was written. As a teen, I was put on antibiotics to help clear up my acne. I was on it a long time.
    I now have three beautiful children, all with Celiac Disease ages from 20-12. Each of a host of other minor related issues. Some have anxiety, some have dairy intolerance. I also had at least 3 miscarriages and one case of thrush between pregnancies. I am so convinced this is all connected. We eat 80% paleo and 80% organic and have seen wonderful improvements. I fear my gut is still in need of help yet keeps silent. I have extremely low b12, cholesterol, and more but generally feel well. I just wonder if there is more I should be doing

  26. Often times antibiotics are needed and a good plan for taking care of yourself afterwards is essential. Celiac testing is brutal because so many of us have figured out that gluten makes us sick. Many physicians test improperly. A very well know Celiac Center will not do the blood test if you have been gluten free unless your challenge is 10-12 weeks long. I see doctors write 4-6 weeks, this is wrong and may provide false negatives. Many people carry the gene, the blood and biopsy test is what you need. However, there is a new test coming out soon! It requires only eating gluten for 3 days and uses whole blood and is about 97% accurate! Believe it or not, the Ttg requires more skill and is open to error. So anyone reading this, there is a new possibility that is far more appealing.

    • @Laura. It would be good to hear more about this test. Do you know the name of it? If you say it uses whole blood, I guess you mean it uses the red blood cells, rather than plasma/serum. Cheers, Honora

  27. One question:

    Can anyone tell me for sure if one can have Celiac WITHOUT the genes.
    I have all symptoms from head to toe. Was test for Celiac but was negative. I the time of the test was eating Paleo because I cannot eat normal with problems everywhere.
    Tests for the genes came back negative as well.

    • What? For most people gluten isn’t a problem? There’s a hubris of evidence to link gluten to any other autoimmune disease aside from celiac disease and many other issues as well…I think that this two part article from Trevor Connor is one of the most well done http://thepaleodiet.com/wheat-opening-barrier-poor-gut-health/
      There’s enough to blame gluten for most people, not all the other way round, considering the level if sickness around

    • Becky – Tests for celiac disease are ONLY effective when you are eating gluten. If there has been no gluten in your system recently (for example, because you had been eating a paleo diet for some time prior), the tests would have been ineffective. The immune response has to be actively occurring for results from the blood and the small intestine to be accurate. To be properly tested, you will have to eat gluten for some time prior to the tests. Your GI physician should have known better, so you may wish to try a different one in the future. The issue may not be celiac, but improper testing won’t tell you that, one way or another.

  28. I was diagnosed with celiac 5 years ago after being misdiagnosed for 50+ years. I have not been on many antibiotics during my life. Found a celiac clinic recently headed by Shiela Crowe MD. She said there is recent evidence that the starch in gluten is more the problem than the gluten protein. Onion, shallots, leek and garlic are in the same category as wheat rye barley starch. You can eat the green part, but not the bulb or any of the white part. Going off of gluten brought my gut pain down about 60%, removing onion, garlic brought it down another 35%. Am currently using 1/4t (1 gram, will build up to 3 grams) of l-glutamine in water first thing in the am and wait 20 minute before eating. The l-glutamine is known for gut repair and it is making a real difference. I have weeks now with no pain at all.

    • This is a very interesting piece of data about the starch in gluten and the onion family plants. I just did Cyrex Labs Array 10, and came up with immune reactivity to the entire onion family. We were testing protien though, I believe. My gut pain is also improved eliminating them. I do know about FODMAPS. Is that what your doctor is refering to? I am curious about the science behind this recent evidence.

  29. Great article!! Thankfully I don’t have celiac disease, although I am sensitive to gluten, so I stick to a paleo based diet. Oh…for all the times I was prescribed antibiotics for no good reason – my gut flora was obliterated in my early 20s. Five years later I’m trying my best to build it back up, especially before I start having children!

  30. In 1993 I became very ill with the parasite Giardia. My Gastroenterologist said I had the worst case he’d ever seen. I took Flagyl antibiotics over and over and over. Just as I’d become better, the eggs would hatch and I’d have the terrible nausea and debilitation all over again. Finally I took lots of raw garlic and was able to halt the circle of parasitic regeneration.
    Fast forward to 2007. I began to experience severe intestinal cramping for no apparent reason. In and out of Emergency rooms. Taken by ambulance one night. Gastroenterologist said it was diverticulitis. Ordered Cipro. However, my Naturopath thought differently. I had the frozen poop test (Texas) and the results showed high intolerance to gluten.
    Fast forward to 2015. I have cut gluten out of my diet and hair products during the last 6 years. I get small amounts from eating out so I carry Glutenzyme for protection. Still get bouts of intestinal stress but with tea made from flax seeds, glutenzyme and a Xanax, the pain improves. The latest comfort comes from Ageless Hydro C and Ageless GI Recovery made by Ageless Nutrition. I take these supplements as drinks every morning. FAITHFULLY! If my Naturopath hadn’t discovered the gluten connection, my quality of life would have been dramatically altered.

  31. I remember my first round of antibiotics when I was 10 years old for a skin staph infection. I will never forget the diarrhea. But that was the only round as a child and I definitely had problems years before that—and nobody took antiobiotics in our family back in those days. Fast forward to raising my kids, and all of us had multiple, multiple rounds of antibiotics for whatever. But before even that, our daughter had problems as an infant with her first solid foods—horrible face skin rash, diaper rash, clingy baby—and of course in 1992, Celiac and gluten weren’t part of our national vocabulary. When the whole family of 4 tested in 2005 because we couldn’t ignore symptoms anymore, 3/4 are positive Celiac, our son is gluten sensitive with the SAME exact symptoms as everyone else. Going GF wasn’t enough and we ended up with such severe leaky gut, we had about 6 foods to eat and were still reacting. We have been GAPS, SCD and now Autoimmune Paleo and still battle histamine issues and super sensitivity to many foods that should be safe for regular Paleo. What the hell has happened??? What is in the environment causing illness like this?? I’m convinced it’s environmental/contagious due to the nature of how it has affected my whole family. The economy took away any ability to see a FMD to find out what the heck is still going on, so we treat with very clean living and the whole, fresh foods we can eat. Would love an answer though!

    • I have severe allergies to antibiotics having taken so many as a child. Cypro is the only antibiotic other then Sulfa. I started having sensitivity to store bought wheat bread several years ago. I developed a cough in the winter that went away in the summer. Then the cough did not go away in the summer. I had trouble breathing mildly. Went to an allergist and my oxygen was way low. He gave me epinephrine, and a breathing treatment along with a prescription for Symbicort and Montelukast. A month later my doctor recommended a Flu shot. Within a short time I was sensitive to everything. I could not eat but a few foods. My stomach would swell after eating most food and thereafter I would have a sever asthma attack. I had only been coughing up to that point before I used all these drugs. I could eat most things except for wheat bread. Because I could not breathe after eating most foods I lost 30 pounds in four months. Coughing and chocking almost constantly became the norm. I stopped Symbicort cold turkey, which I found out was not to be done. My adrenal glands had shut down and I could not breathe. I ended up in the hospital where they put me on 160 mg of prednisone twice a day for three days. As I tried to wean down from this high dosage of Prednisone, I realized again I could not breath without it. I have spent more then two years trying to wean from prednisone and Symbicort. I have resorted to making a yeast free bread with no wheat. And am only eating organic food now. Eventually I held my weight. I believe I have developed silent acid reflux, which causes me to choke up mucus now after I eat most foods. I have found that allevira juice is helpful for relieving this symptom. These medications are not safe. They only give you short term relief then give you suppressed adrenal glands. Your adrenal glands control many of your bodily functions. Once you become dependent on steroids, such as prednisone and symbicort, the chance of death is very possible. Prednisone kills.

      • Michael, you said we are being sprayed by Chemtrails?

        First off, how does that affect celiacs and if it’s real how do we protect ourselves from these “chem trails”

        • Raquel,I believe chemtrails are real and must therefore be taken in consideration when discussing digestive health. I believe chelation and detoxing is the best way to protect yourself.

  32. Celiac disease is not a disease.

    It is an intoxication, or poisoning. In the same way as poisoning by cyanide. Or by carbon monoxide.

    Stop ingesting the poison (gluten, in this case) and the symptoms go away.

    • If everyone’s gut lining is compromised by gluten, then it might be viewed as a poison as you say.

      However in celiac, only some 8-12% of celiacs have gut lining fully restored longer term by stopping gluten. Celiac is identified by tissue transglutaminase 2 antibodies (tTG2 Ab) that can remain to some degree for the rest of the person’s lifetime, a setup for some degree of chronic leaky gut and related low-grade systemic inflammation. I speculate that endothelial degradation from celiac can extend in many cases to a susceptibility to endothelial degradation in other parts of the body. It’s also documented that pancreatic digestive enzymes can be compromised in old celiacs, resulting in a cascade of detox, congestive, inflammatory, and degenerative problems — I speculate there is a connection to the tTG2 Ab.

    • I agree that this is a response to a poison and I think the increased incidence has to do with the genetic modification of our food, including gluten and other foods.

  33. I go with Dr McBrides theory that the cause may well be mothers who have been on the pill for years and therefore have no good bacteria left in them, birthing babies who then START life with no good bacteria in them either. Mothers who have hysterectomies also give birth to babies who have a sterile gut. I think this is cause for my son, who was diagnosed at age 18, now 27, and had only 5 courses of anti biotics all his life by using natural alternatives. UK

    • Just checking in, Pippa. At what stage did the women who had the babies have their hysterectomies? It must have been just after they gave birth. So did the babies’ gut bacteria get wiped out from the mothers’ antibiotic-laden breast milk?

  34. Very informative article. I too have many of the symptoms as many of the commenters. Also, I’ve had a lot of antibiotics and I’ve always thought they had something to do with my becoming disabled.

    The thing that I can find no information for, is that I’m transgender. Going on testosterone made me much worse. It was like pouring gasoline on a fire. I can’t find a doctor who believes me. I see so many transgender people who are sick like me, I have to believe that there is a connection between leaky gut and HRT, not that HRT causes leaky gut, but that it keeps us from healing. I don’t want hormones, but my insurance company makes it a requirement to qualify for sex reassignment surgery. I’m risking my life if I go back on hormones, but I’m risking it if I don’t. I’m trapped….

  35. I am a 57 year old male with CD. I am more than 50% Italian as well as Scottish. I have read that those two nationalities are the highest for CD. I had undiagnosed dermatitis herpetaformis as a young child. I was not plagued by infections and do not recall being ill much except for DH. I did not take antibiotics much as child. I self diagnosed CD at around 43 years of age that was later confirmed by a gastroenterologist.

  36. All my life, I’ve had skin issues, bronchial asthma, yeast infections & sinusitis! Therefore, antibiotics have always been in the mix, at all levels. At age 50, my health turned crazy; not responding to ANYTHING MEDICAL! That’s when I was advised to take ALL SUGARS out of my diet; that most likely, I had an overgrowth of Candida!
    I followed this process, trying to get my skin to clear up; but something was drastically wrong with my anti-inflammatory system. It was working at all; I was in serious trouble!
    Months later, I saw am allergist, who ran test. The blood test showed that I was “boarder-line” Celiac! I then started removing gluten from my diet! I still have flare-ups; but I’m trying desperately to heal the lining of my stomach! My skin is the main area to which, the swelling, itching, redness, pain; is evident. My face is the other area affected, when something I’ve eaten or a product I’ve used, is not compatible to gluten free living.

  37. I have had CD all my life but never knew it because doctors kept treating me for what they saw or guessed and not look for the root of the problem. ie growing pains, nervous stomach, allergic to something, etc. (yes I had allergy test, negative, CD is not an allergy) only after I retired, had time and the internet, started my own research. at that time large blisters with intense itching. I told the dermatologist and doctor what I had from internet info. they said had something different. I compared photos, tested each medicine and vitamins and herbs, I was on twice. photos of my skin before starting something, photos after 2 weeks on each thing. made my own medical journal. took my findings to my new doctor. she looked at the photos and my research then ordered a CD test. positive plus gastritis. my hives and itching let up about 60% only. several years earlier I had test that showed leaky gut. from my research I realized I have IBS. on internet I read if you have CD, IBS, and leaky gut, you are no doubt histamine intolerant. back to internet, researched histamine. found some foods enhance histamine and some foods block histamine. after I stopped all histamine enhancing foods the rest of my hives, rash, itching cleared up. I have found most medicines contain gluten or hi histamine in them. I cannot take any medications or pain deadeners orally as the binders or fillers cause my reactions. the steroids doctor had me on caused 60 pound weight gain, stopping them taking on the paleo plus diet, dropped those 60 pounds. I found several vitamins and herbs have one or the other in them as well. almost 80 years old and just now getting a handle on my health. sad isn’t it. by the way the CD has caused calcium loss from my bones. I also have spinal stenosis, peripheral neuropathy, effects of years of CD. on cane, canes, wheel chair, power chair, at times depending on the severity of the low back and knee problems at the time. I am hoping my story will benefit others out there. Walter Wermuth.

    • Vitamin C is a natural anti-histamine. Ever since I began hi dosing of Vitamin C, my “hay fever” has been stifled.
      Also, there is an anti-inflammatory enzyme that reacts in the body like NSAIDs without any of the side effects. It is called Wobenzym. Available most health food stores or online. It cured my snoring, sleep apnea, chronic nosebleeds, my daughters’ carpal tunnel, wife’s sciatica.

  38. I eat mostly Paleo. I take one Prescript Assist per day. I take 400mg mag glycine the per day. I am now taking basic digestive enzymes. My gut feels much better. Much less gas. But my stool still floats!

  39. This seems to be right on point with me and my medical history, but, for me, the screaming question is–how do I improve the situation?

  40. Hi Chris,
    It seems we’ve all taken so many antibiotics- I’m the only one in my family with Celiac though. I’m wondering if it has to do with the fact that I was on heavy-duty antibiotics for being “exposed” to TB when I was younger. I had a positive skin test, then was on those antibiotics(NIH I think it was called?) for 6 months to a year.
    I’m diligently following the Specific Carbohydrate Diet to heal my leaky gut at this point- hopefully once and for all. Any thoughts on that?

  41. I am wondering how overwhelm/trauma fits into the picture. Fear has “its seat” in the gut.
    I am under the impression that many people have unhealthy (getting/staying “stuck”) autonomic nervous system regulation patterns. All of them have gut problems in one way or another. I am more inclined to think that ANS dysregulation contributes to an unhealthy gut which weakens the immune system which leads to illeneses that “require” antibiotics/ stress triggers the expression of genes.

  42. This is a very interesting article. I have a family history of gluten intolerance and CD.
    I may have always had the problem but un-diagnosed. A few years ago I had DVT (deep vein thrombosis) which was treated with a series of injections. It was after this that I realized that I could no longer eat wheat based foods.
    Perhaps a coincidence Perhaps not.

  43. I have wondered more than once if the near constant antibiotics in the first years of my life for ear infections altered something in me, or rather exposed a weakness already present in my system,
    More recently I have had to take antibiotics for intestinal bugs acquired while traveling.

    In the past year I have been diagnosed with lymphoma and celiac disease. Which came first? Who knows, but the bulk of my cancer is centered around my gut, in my mesentery and the paraaortic area, which I highly doubt is coincidental.

    My celiac was silent, incidentally, until very recently. I thought the cancer was causing my discomfort, but now I am not sure who the real culprit is.
    I am leery of antibiotics these days, but am keenly aware that my system is much more delicate and susceptible than before. Forging ahead and just doing my best.

  44. Thank you so much for this article! I have thought for some time that there must be a link between celiac and antibiotics! My daughter has been on antibiotics so many times for chronic ear infections that she is immune to several antibiotics. She has also had chronic stomach pains and headaches for several years. Last year, at age 12, she was diagnosed with celiac. She has now been GF for almost 1 whole year now (except for a few times she accidentally ingested gluten) and feels good most days. She still does get stomach aches occasionally but we are thankful they are rare these days!

  45. People who get this problem usually don’t have a clue about what’s happening initially. It’s only after their gut is ruined by the recommended antibiotic regimen, that our own personal research finds the real problem; because these conventional GI doctors have No Idea how to treat anything without using abx. I put this on the doctor, not the patient.
    Live and Learn, hopefully.

  46. Our story is not Celiac related but “antibiotic overuse” caught my attention as my son has been on daily prophylactic antibiotics since the age of 8, he is now 12. He has PANDAS (Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections) occurs when strep triggers a misdirected immune response that results in inflammation on a child’s brain. In turn, the child quickly begins to exhibit life changing symptoms such as OCD, anxiety, tics, personality changes, decline in math and handwriting abilities, sensory sensitivities, restrictive eating, and more. The treatment is simply daily prophylactic antibiotics along with a gluten free diet and pre/probiotics that will continue until sometime after puberty. We don’t have a choice, without antibiotics he can’t function. But we wonder what long term effects this treatment may have. Today he is very happy and healthy, and at this point, no signs of Celiac.

  47. I had celiac symptoms my entire life, but wasn’t diagnosed until age 42, when I finally figured it out for myself and insisted on the biopsy. For whatever reason my doctors never tested me, whether they were unaware of celiac, or just didn’t think of it; despite years and years of stomach and digestive issues, diagnoses of “migraine stomach”, and later IBS, migraine diagnosis at age one, severe menstrual symptoms starting at age 10, eventual infertility diagnosed at age 21, etc etc etc…all classic symptoms and effects of celiac! I don’t know if I had a lot of antibiotics when I was a kid, likely, but since my symptoms started so early, even before I can remember, I don’t know if there is a connection. Perhaps my mother took a lot when she was pregnant? Which is also likely. Or perhaps I just got the short end of the stick with the gene lotto.

  48. What can I take instead of antibiotics for a recurring staph infection? I think it’s gone systemic, but I don’t want to take antibiotics unless it gets way worse.

    Right now I have a couple of new lesions pop up every week as soon as the older ones are on the wane. This has been going on for about 45 days.

    So far I’m taking probiotics, washing entire body with Hibiclens (chlorhexidine gluconate) daily, eating lots of gelatin and bone broth. What else should I be doing?

    • Allimax Pro 450 mg. you can find it on amazon. It’s not cheap, but it works! I used it to get rid of my chronic, late stage Lyme disease.

    • Good luck on getting a mainstream GI doctor to do that. Mine gleefully said that since I don’t have C-diff, I don’t need a fecal transplant. It seemed like he was actually pleased with himself to deliver this news. Meanwhile, I discovered the mega-probiotic VSL#3, which inundates your gut with a combo of 8 probiotics, leaving no space for the bad guys to live in their “takeover volume”. I recommend it as an interim measure until the right “help” is found. It has helped me a lot, but I don’t have the slightest idea how long this will keep working.

    • I have a friend who has had MRSA ..presenting itself as reoccurring lesions…as she worked in a medical facility they made her cover all lesions with band aides ..a doctor told her the minute she sees one lesion try putting bacitracin ointment in her nose…and this does stop the lesions in their tracts..she was so grateful for this suggestion ..made her life much easier…Hope this is helpful and does work for you..

      • Thanks Pat, I’ve read about staph living in the nose and seen where some docs prescribe killing it there. I do sometimes get a sore in my nose too, which I guess is the staph also. I recently had one recur and did use Neosporin on it and it went away pretty quickly. Maybe I should put it in my nose more often. Thanks for the tip.

    • I already went through what you went through, with MRSA, which is what I’m gambling you are dealing with. Doctors were utterly worthless, ignorant and sneering with “helping” with any of this. So, I decided to come at this from every direction full force. Firstly, I picked up Stephen Buhner’s book Herbal Antibiotics and read all the pertinent parts and bought the herbals I thought were what I needed. Then I bought every natural product ever listed for antibiotic properties. I ended up really liking Meleleuca Q. (which I found at Young Living, but whatever, wherever you buy it I think it will help) and used that on any “spots” that would crop up. The herbals seemed to help and I took those long-term, for about a 6-8 months. I also took/take iodine, vitamin A, D3, vitamin C, a good multi, garlic, oregano, yada, yada, yada. I took a few bleach baths (which you can Google) and think that that helped initially, and also bought Hibicleanse (sp) but ultimately quit with baths and threw the Hibicleanse away as I decided that that would ultimately do nothing but perpetuate the problem. I had also been extremely stressed- physically, mentally, emotionally- before all this happened so I attempted to rectifiy that as much as I could. Ultimately I knew it was that my “microbiome” was extremely compromise so I went out and bought every, single probiotic supplement at our local Swanson’s. If it said to take 1, I took 15 (as I wrote somewhere else). And I did that with each of them several times a day. I never have any ill-effects from doing this and I truly believe that this is what pushed me over the hump to better health again. My thought process was to overwhelm the staph bacteria with the bacteria that promote life and health in the human body. We never will get rid of staph and probably shouldn’t- I have read that certain kinds promote health in humans also- but we need to get into balance again. My bought with MRSA was my red-flag to slow down and take note of life, my life and being healthy. I hope this helps, I know how frustrating and terrible this can be. Sorry, for any grammar mistakes, etc, I haven’t had my two cups of coffee yet for the morning!

      • Thanks for your input Jane. I’ve been using tea tree oil on cold sores, at the first sign, and it really works – along with about 3000mg of l-lysine. I always get a cold sore when even a little bit of stress is upon me. I did try it on these staph bumps/cysts during the painful growing stage but it didn’t help. I’m going to try taking a garlic/allicin pill next since it seems to be systemic. I also tried a mixture of manuka honey and activated charcoal but you can imagine how messy that was, LOL.

    • Laurel, I struggled with this 8 years ago as a 22 year old healthy person, I had MRSA colonization in nares and after three months of Bactrim and twelve infections, the solution recommended by an infectious disease doctor was Mupirocin ointment in nose (prescription required, not the regular Neosporin ointment) twice a day and soak in bath with 1/4 cup of Clorox bleach, sounds crazy but it worked and I didn’t need to keep treating recurrent infection with systemic antibiotics, never had another infection and get swabbed in my nose every year to make sure I am still MRSA negative. Now just trying to repair damage done by three months of needless antibiotics!

    • At the risk of sounding gross what about the following for a natural solution.
      We all know children who pick their noses and eat the snot. As a society we stop this behaviour, but what if the children are unconsciously following a natural behaviour and challenging their immune system on a regular basis.
      Following on from this would adults benefit from eating their own MRSA laden snot and naturally stimulating their own immunity to Staph bacteria?

    • re: Anyone have the “guts” to try FMT (Fecal Microbiota Transplant) for celiac?

      Anyone contemplating FMT needs to consider first trying a probiotic enema. Perlmutter describes a protocol in his new Brain Maker book. The point of PBE is to enhance [re]colonisation, which oral probiotics often don’t do reliably.

      The big challenges with FMT are the donor and doctors. Consensus MDs are utterly incompetent at nutrition, metabolism and generally ignorant on gut biome. They are consequently dangerous. They’ve already managed to transplant obesity via FMT.

      • A company called Open Biome that is non-profit and costs are reasonable seems like a good alternative but you actually have to be participating in a clinical trial to get a hold of the “stuff”. Doctors do move very slowly (glacially in fact) when changing medical practice but many are now so frustrated with the non-performance of pharmaceuticals, I feel a rebellion very soon.

        • re: … you actually have to be participating in a clinical trial to get a hold of the “stuff”.

          That brings up a 3rd challenge with FMT. In the U.S., it’s presently only FDA-approved for C.Diff. For anything else, like post-CD gut remediation, you either get into trial or leave the country.

          PBE can be done at home, without having to ask the FDA if any of their Big Pharma cronies object.

    • The problem with fecal transplants is that, for most problems, it is needed repeatedly. With C. Diff it seems that once is enough, but not so much with others.

      • re: The problem with fecal transplants is that, for most problems, it is needed repeatedly.

        It seems like one could reduce the risk of needing repeat treatments by identifying and eliminating all gut biome antagonists. I wonder if FMT clinicians are clued into all this.

        This would obviously include prescription antibiotics, but also ABs in oral care and topical products – these latter, alas are both numerous and not always obvious.

        Many food-like substances are also gut antagonists. I would mark all of the artificial sweeteners as suspects. I consider the gluten-bearing grains to be antagonists, and probably the other grains with iffy lectins. A full-time glycemic diet is also likely a problem.

        Pesticide uptake in crops is another obvious problem. Crops with Bt genetics, of course, ARE pesticides. Organic non-GMO is helpful here.

        Finally, the daily diet needs to include prebiotic fiber to maintain the population of desired bugs.

    • I havent used antibiotics for the past two years even though ive had the cold and flu. lol this is not medical advice but truly i spoke to the bacteria…i asked ‘why destroy me when we can live together forever, just tell me whats your flavor:-)’ im sure they responded to my em fied. I also told em to deal with the virus! and poof flu only lasted 3 days-i was raised on antibiotics btw. Seriously i think stress and ill mental health are the only health problems that exist.

  49. Chris, Thank you for this article. I went to an infectious disease doctor last winter to see if I could pin point where my issues with autoimmunity, candida, gluten intolerance and food sensitivities began. The information he provided was helpful but not conclusive regarding the starting point. I remember having signs of candida as a child. I am wondering if my mother did not pass a candida infection on to me and younger my sister, who also has an autoimmune condition. Is that possible? My mother had intestinal issues and autoimmunity. Outside of me having pneumonia at age 7, that would be the only antibiotics I can think of having taken until I was a teenager when I took long term courses of it for cystic acne, which I now know was caused by a reaction to gluten and other food sensitivities. So the damage was done by the time I was in junior high. Any thoughts?

  50. Hello,
    I grew up in the 1950’s and had pneumonia at ages 4 and 8. By age 10 I was chubby while my siblings were slender. I could not stay away from wheat based junk food. I was told I needed to exercise self control and tried to do that for the next 50 years.
    Four years ago I began to read on the Internet about the problems with wheat–especially today’s hybridized franken-wheat–GMO’s, pesticides, etc. I stopped eating wheat and the cravings disappeared three days later and never returned except when I cheated. Over the next few months I lost 20 pounds then plateaued. It was suggested to me that those sensitive to wheat are often sensitive to dairy, so I stopped the dairy. My last 10 pounds fell off over the next several months, and minor sinus conjestion, morning backache and finger stiffness stopped. I lost all desire for chocolate.
    I am convinced antibiotics in childhood caused my gut problems with wheat and dairy. BTW, I tried eating Einkorn wheat and the cravings came right back. No digestion problems, ever.
    Dr. Chris, do the wheat and dairy proteins enter the blood and attach to opiate receptors in the brain?
    Today, through many trials and experimentation, I can now enjoy Goat dairy (raw when I can get it) and real sourdough bread once in a while as long as it’s processed at least 18 hours. Thanks for all the information and help you provide. XOXO

  51. As a young kid I had many food allergies and hayfever which prompted coughing, sore throat and bronchits frequently. My mother gave me arithromycin and decadron (steroid) like candy. At 18 I developed ITP (an autoimmune disease) which is now in remission after a splenectomy. Fast forwarding through my life of frequent infections (use of antibiotics) , brain fog, heart palpitations, fatigue after eating (not knowing about gluten) I was diagnosed with celiac disease at 44 years old and have been gluten free since. I’m now 49. Since celiac diagnosis, I have active EBV flare ups and reoccurring SIBO (tested positive and tr4eated 3X) Also found to be very low in the amino acid carnitine (now affecting my mitochondria) which caused weakness with my fatigue. So I believe its all a vicious cycle…. the infections need antibiotics and cortisone which destroy your gut, turn on your autoimmunity, including celiac gene and then SIBO keeps your gut from healing; causing vitamin deficiencies, etc and a life of downward spiral illnesses/autoimmune dis-function. Oh, and I have been told by doctors not to take probiotics because I may have a negative affected because I do not have a spleen. Anyone else out there with ITP/no spleen?

  52. Your article is very enlightening! I had chronic strep as a child and (unfortunately) many rounds of antibiotics. I also had a very strong reaction to poison oak after eating blackberries covered in the oil (picked from a bush infested with it) when I was 18! I had an all-over body reaction to the poison oak and to areas of my skin never exposed to the oil, so I know that the oil was in fact ingested, and would have come in direct contact with my digestive system. I am thinking that this event is what triggered my immune system in a major way! I do have heterozygous genetic predisposition to gluten intolerance, but it was not until my early thirties that I started getting the IgA rashes, that looked, and felt, exactly like poison oak! I also do not respond well to mangoes which are botanically related to poison oak. Unfortunately, having many problems with methylation and other biochemical processes, obtaining two health degrees, and then working in a field of chronic high stress long working hours, for two decades…. I am now on a strict paleo diet, and trying to pick up the pieces of chronic fatigue, adrenal insufficiency etc. Sadly, this has cut my beloved career short, however on the positive side, I am learning so much about epigenetics! I am absolutely certain that being aware of your specific genetics and practicing health promotion in accordance with this knowledge from pre-conception on is the ONLY WAY that our people can truly be healthy! I have always known that drugs, pesticides, and food abominations are the worst enemies to a healthy body, now the scientific links are being made and the whole picture is becoming clear. Thank you for your work Chris! I am an avid reader seeking health and sharing all that I learn with those around me! Be Well

  53. Thanks Chris for starting a great discussion. It’s always hard to determine if life started with a chicken or an egg, so too what increases the likelihood someone will have celiac. I keep hearing it all starts in the gut. I wonder how much actually starts in the oral cavity. There are a lot of great information that can show that mercury, root canals etc. can lead to a bad environment in the gut which then allows so many autoimmune related reactions. I wonder if we were to compare the number of root canals, amalgams etc. that are grandparents had in their youth versus those that are now in their 50’s or 60’s. I would suspect there is a huge increase with it just beginning to decrease the past 10 years. Don’t forget if you have amalgams in your mouth and are pregnant with poor methylation, you are poisoning your child via umbilical cord. Dr. Weston Price, Dr. Meinig and Dr. Shade have some great information out there.

    Chris, do you think there is any connection?

    • I think you’re right – it does start in the mouth- and I believe there are many societies that would agree with you! Many people believe the “oral cavitiy” is the beginning of the gut. Thanks for pointing this out and adding it to the discussion. I have seen the name Hal Huggins twice recently and I just, exactly now, ordered his book, Its All In Your Head about Mercury fillings. I don’t have many fillings but I have some suspicious symptoms going on that don’t respond to all of the slow but steady improvements I’ve made. Its sur is too bad that we have the amount of people just writing here, that have to seemingly flounder around experimenting on themselves in order to feel normal, due to the medical establishment as it is today.

  54. I think you’re “right-on” with all points in this article, Chris.

    On the subject of minimizing antibiotic use, infections is one area where classical homeopathy done right in the classical manner excels, especially in acute infections.

    • Carol – What form of homeopathy can help with infections? I’ve got a recurring (systemic?) staph infection but my homeopath has not mentioned any specific remedy. Thanks

      • I just changed my mind set, i said to myself ”im getting this flu to help me cope with seasonal changes ,its mother nature rebooting my gut-with that lovely yellow/green sputum’ o and i really believe, like really believe this. So my colds and flu only last 3-4 days. Tips; reduce stress believe in the will of life. I feel beyond this; there are poor people i know who eat more gmo’s,margarine,sunflower oil and less high quality meats than me and they seem happier and healthier.This is just mental.

      • Laurel, classical homeopathy involves use of the correct remedy for the person at that time, in no higher potency than needed or that their vital force can handle, and as few repetitions as absolutely necessary (dictated by symptoms and progression of healing, not a robotic schedule). Homeopathy is a lifelong study in elegance and working directly with the vital force. Many homeopaths today use too-high potencies and unnecessary and/or robotic repetitions, so it’s important to review all that with a homeopath before working with them, and I do suggest working with a homeopath in alignment with your own philosophy.
        Be proactive, don’t hesitate to interview a practitioner with your concerns before working with them, and while working with them. Heavy handed practitioners and communication breakdowns guarantee lose-lose.

        Low thyroid, even marginally low thyroid, can predispose to all manner of infections bacterial, viral, and/or fungal, recurrent infections, and difficulty in resolving infections, so optimize the thyroid to the tightest standards, beyond what is typically indicated by conventional labs.

        Further ideas and approach to staph would be beyond the scope of these blog comments, so see your own practitioner(s).

  55. I had ear infections from birth to age 14. I had respiratory infections like bronchitis and sinus infections, (anytime I got a cold, it always turned to a sinus infection) 1-2 times a year until age 34 when I moved to the desert. I had to have antibiotics to get rid of them. I was diagnosed with CD at age 41, RA at 43 and fibromyalgia at 44.

    My older daughter had ear infections constantly as a baby and a toddler. She has not been diagnosed but she noticed not feeling well after eating gluten a couple of years ago (she was 20) and she went gluten free too and feels much better. I think she has CD also.

  56. My question is how many times is considered a lot to have taken antibiotics… Compared to my husband I’ve been on them quite a bit but when I mention it to other people they say I haven’t been on them much at all compared to others… How often do you need to have taken them to have it adversely affect you?. I’m sure everyone’s different, but do you have a general idea?

  57. Chris, you’re forgetting to mention the fact that you don’t even have to take antibiotics anymore to over use them. The animals we consume are regularly fed antibiotics to counter their deplorable, disease ridden living conditions We are a suicidal species, all in the name of the almighty dollar. We poison our food, animal and plant, our air, our water, and wonder why we’re consumed by disease.

    That aside, I have found that Greek Yogurt is your best defense against candida. I will not take a course of antibiotics without it. Regular yogurt will help, but only Greek Yogurt seems to see it back to normal.
    God Bless.

  58. Wheat today contains Roundup herbicide and Roundup contains glyphosate which is an antibiotic. Organic grain only contains half as much glyphosate and organic seeds are only 2% GMO. One more reason to go organic and one more reason labeling GMOs is not enough. We need a world wide ban on Roundup and GMOs.

    • I’ve noticed that my stomach doesn’t gurgle as much after eating organic breads but it can really hurt when eating conventional breads. Could this be why?

    • My family is nothing but farmers and I am one as well. I mean I go out and buy the seed, work on equipment, seed the crop, spray it, market it and harvest it. I know the industry inside and out, in the this part of the world. I do not eat GMO, if it can be helped and buy as organic and support organic growers and stores. I read incessantly about how to turn my land over to organic in the healthiest, fastest most feasible way without going broke, and am starting the process in one field this year.

      All this said, not all wheat is sprayed with glyphosate. Even my dad, who grew up in the era better farming with chemicals, thinks this is disgusting. The problem with store bought bread is that our wheat gets blended from all over the place. When we bring it to the elevator, we get nickled and dimed to death if the wheat isn’t high protein, or has too much moisture, or this or that. Some of this is understandable but mostly its a load of BS. When you bring in absolutely choice wheat, the cost benefit is barely there. Then the elevator promptly blends off ALL the wheat they have and sells it down the road to the next buyer. So the wheat you’re ultimately eating may have all kinds of quality issues but has been blended to bring it up to a better or acceptable quality. I’m sure some bread companies are better and some companies only buy certain qualities of wheat (or barley for beer, etc). But trust me, everyone is looking out for their bottom line, over your health.

      The other thing I think many people seem to be confused about is spraying wheat with glyphosate. We do not buy GMO wheat- there is not *supposed* to be such a thing. (although I’ve heard tale that it is out there, farmers are completely against it) I’m pretty sure if I went out here and sprayed my wheat crop with glyphosate I would be in big trouble. The only time farmers spray with Roundup is before harvest to help with the combining, so they have a uniform field of dry stalks and aren’t pluggin up their combines, which let me tell you is an awful thing to have happen. In my opinon they would get the same effect waiting a few days.

      Ultimately, I think the best option is to bet with our dollars by buying organic every time we get a chance and can afford it. Farming got to be in this position because this is what was paying and this is what was rammed down farmer’s throats as being “progressive”. To this day yet, when you see an advertisement of a farmer, you get a hick wearing bibs with a stem of wild oats hanging out of his mouth. Farm kids used to have to go to school ready to fight the city kids as they would be ridiculed for being dirty, smelly, and manure covered. Trust me when I say that technology came along and made farming “cleaner” and more “advanced” many farmers were thrilled to accept it. Most farmers around my area run a very tight ship, are very careful when spraying chemicals (and don’t overspray anything simply due to the high cost) and have immaculate, successful, family operations. Their farms should be on the cover of Better Homes and Gardens.

      I guess what I am trying to say, is that we’re not just fighting against GMO and chemicals, you’re fighting a mindset of “you want us to do what? Go back to weeds and cowsh*t? You want us to stand out in the middle of a sweltering field again when its a 100 above and fight biting flies and hoe weeds? Go to hell…” But if the farmer sees the economic benefit, he will find the ways (that are out there!) to do it.

      I’m not really religious but I hope and pray every day that I can make this organic ideal work and make it work beyond just getting by. Its the only way to get this profession to change- efficiency and money.

    • I read through all of these comments so far, and was surprised to read only a few people mentioning Roundup/Glyphosate (on GMO crops and used on Wheat) as a cause for our microbial imbalance. Like RawMilkMike said Roundup’s active ingredient: Glyphosate is an antibiotic… it is actually patented as an antibiotic – so it make clear sense to me that Roundup sprayed on GMO crops and on WHEAT in the desiccation process is doing the bulk of the damage to our gut flora. I am very surprised to see that MANY experts in the fields of nutrition, health, medicine, research are not focusing on or sharing this piece of important information in their articles (including this article from CK). WHY? What are they afraid of? Or has Roundup been tested and proven very safe? Please tell me WHY we are not hearing more about Glyphosate’s role as it relates to digestive disease?

  59. Hi Chris, I found out that I have celiac and thinning of my stomach lining last summer. I had becoming violently sick and could not figure out what was wrong. Developed Graves’ disease in my 20s during a very stressful time in my life but the biggest issue I now understand is being bite by a tic in Wisconsin when I was about 12. I remeber the hotel floor because this tic made me really sick. When we got to Colorado doctors said it was tic fever with pneumonia. Over the years I always had strep, mono etc. Last summer I started seeing a hollistic doctor which helped me discover my leaky gut. I believe this happened with a traumatic incident in my life, the death of my father and my son brought home the stomach flu. After getting off gluten I was still sick. It was like I had the flu everyday. Going to the rumatologist they labeled me fibromyalgia and tried putting me on antimalaria drugs and other crazy sleeping stuff to shut down my immune system. Going back to the hollistic doctor she found I had high levels of mold. Once I went on a serious detox I was better. I continued testing and have the antibodies for numerous auto immune diseases. I show a little sign of them at times when I have too much activity. Now, I have gone organic, non gmo, grass fed along with drinking and eating fermented foods. I have high end supplements that have helped my immune system recover. I now understand that the tic that bite me gave me Lyme. Fortunately I was treated with heavy antibiotics back when I initially showed signs of Lyme. However Lyme disease I have been told causes inflammation. I never took care of myself correctly over the years. I hope that I fully recover soon. Thank u for helping so many people.

  60. I was on 23 rounds of antibiotics about 12 years ago and have never been the same since. I have never been to a functional doctor and do not know if there is one in Arkansas. The GI will do a scope soon to follow up on the progression of Barrett’s Esophagus. Is there any other procedures/tests that can be done at the same time to diagnose gut problems? As you can imagine the only advice I have been given to date is PPI’s and cut out foods like alcohol, coffee and chocolate. No one is asking why the problems exist or testing for any kind of gut dysbiosis. Can root problems only be diagnosed through a functional medicine practicioner? I am terrified of getting esophageal cancer. Thank you

    • Conventional medicine is unfortunately primarily oriented around symptom suppression and disease management, not determining and addressing the underlying cause. That is the focus of functional medicine. In the future I hope that functional medicine will be the default, but for now, you still have to seek out a practitioner specifically.

    • As a fellow Arkansan, I would recommend looking into Dr. Mamie Burruss at Little Rock Natural Medicine. It is very frustrating trying to find holistic help in this state, but I believe it is improving. There are probably more options if you live in the NW corner of the state.

      My mom has oral lichen planus with esophageal involvement – the GI docs have not been helpful. They will certainly scare you to death with dire predictions. Spend your time and money with a practitioner who will help you find the answers you are looking for and has a positive outlook. Your body wants to heal – you just have to discover the best way to assist in the process.

      • Thank you Erin L. for that information. I will check into that doctor. Also, thank you Chris. I’m hoping one day to be seen by someone in your practice.

  61. What if it is not all antibiotics?

    What if the modified grains are more problematic for lots more of us than the grains of around 1950 or so?

    I haven’t stopped all wheat yet and HAVE reduced what I consume.

    • I’m not suggesting that antibiotics are the single cause of CD. CD, like most diseases, is multifactorial and involves a combination of genetic predisposition + environmental factors, of which antibiotic use is only one.

  62. Remember when it was thought that MS might be caused by bacteria penetrating into the brain through a weak spot behind the nose? This was based upon the data that newly-diagnosed MS cases had a higher probability of having had a severe sinus infection in the prior 6 months, compared to the population in general. Scientists in medicine tend to do this unscientific thing of not understanding association does not imply cause. They also tended to believe that antibiotics saved so many lives they had no side-effects. So they were handed out like candy. It would have been a far better hypothesis that the sinus infection caused antibiotics to be prescribed and then. antibiotics were the cause of MS, an autoimmune disease. About time those hi tech probiotics were available which fight the other battle of clearing up the collateral damage to the human organism’s essential organ, the gut flora. Isn’t replanting the gut bacteria currently the only high-success rate treatment for c-difficile

    • Not sure of the success rate, but it is possible to buy pro-biotics, including the beneficial yeast, Saccharomyces Boulardii. This was discovered on the skins of lychees and rambutan fruit over 50 years ago and used to combat C. Diff.

  63. We look back at photo’s of my daughter and can see (and remember) clearly that it was after her illness with Whooping Cough & Pneumonia (and two courses of antibiotics) when she first started to progressively decline in health. Side note, she had been vaccinated for Pertussis too, by the way and still contracted the horrible virus – age 8. Additionally, she was a former extreme preemie (23 weeks), and her “First Food” post birth was an antibiotic for suspected sepsis. She received many more rounds in her first three months of life… and they saved her life, no doubt. All was good until age 8. Now 15 and struggling – cannot eat any grains, has to avoid all dairy, eggs, soy, peanut, and artificial ingredients and her worst allergen is Xantham Gum. My feelings, perfect storm/combination of antibiotic use during the time of GMO (glyphosate) consumption causing severe gut dysbiosis.

    • Dawn consider looking at the GAPS Diet by Natasha -Campbell- McBride. It is designed to help rebuild/ restore ones intesinal track. I had a history of over prescribed antibiotics which led to chronic constipation which led to diverticulosis. The info Natashs offers has been totally right on. Best of luck to you and you daughter in finding what works.

      • Thank you for your reply Sylvia! Just reading it now 2-22-16. I have read the GAPS book and have followed the diet with her (mostly) several times. We have started it over and over after she gets really ill – thinking each event is her rock bottom. Following a contamination, I start up with GAPS, I can usually get 10 days with her, but then she jumps right back into eating sugar! She will be 16 in a couple weeks and we have been trying to convince her to stop sugar for a year and a half. I stopped eating sugar (gluten, diary and artificial ingredients too) to show her it can be done and that she will always have my full support!

    • Your daughter’s food intolerances look exactly like mine. I want to give you a thumbs up about all the food prep you must be doing to keep your girl nourished. I get it.

      • Thank you for your encouraging words Heather! It is a lot of work and I am getting tired of it, but will keep forging on (prepping and cooking) because I can see the light… she is learning how to cook now and that has already brought me some relief! Also, the dietary changes we had to make for her, I made for my whole family and because of that, my whole family’s health status has improved immensely! Especially my husband! No more dizziness, headaches, anxiety, or acid reflux for him AND he has lost 50 pounds, has more energy than I have seen him have in the past 20 years! Something good always comes, even out of the seemingly bad things!

  64. I have a few questions.

    1. How do we avoid Lipopolysaccharides?

    2. How is Dr. Fasano’s theory of autoimmune disease and intestinal permiability panning out?

    I ask because I am on the fence about beginning LDN. I have been giving it ALL I’VE GOT for the last 2.5 years with lifestyle and gut healing interventions. I have made some progress, but no remission. My quality of life is quite compromised with an inablitly to travel if I do not have a kitchen, and the time I spend planning, preparing and cleaning up after cooking 3 meals a day has a huge impact on my life. Wondering if I just have more gut healing to do or if LDN will finally help get my immune system off my tissues…

    • Addressing SIBO, dysbiosis, and other gut pathologies and sealing the gut barrier would reduce your exposure to LPS.

      I can tell you that in most cases of autoimmune disease that I’ve worked with (very common in my practice), gut pathologies including intestinal permeability are the rule, not the exception.

      Anecdotally, we’ve seen very good results with LDN for many different AI conditions.

      • Thank you Kris, for your timely reply. I am going to keep on keeping on, healing, recolonizing and sealing my gut.

          • Very cool Lisa. I’ll check out your site. I have a little hot plate and cutting board based ‘kitchen in a bag’ for hotel rooms that don’t have a kitchenette. We also are putting more mileage on our camping trailer, because it has a kitchen…I have often thought about an AirBnB for grain free/dairy free folks…

  65. I think antibiotics are probably part of the problem…I feel that we can ultimately solve this issue by keeping our gut flora in balance. I have had chronic lyme and done several courses of antibiotics which lead to yeast overgrowth and just the early phases of celiac’s….I have solved all my past issues with apple cider vinegar. My opinion is clearly based on personal success. I am healed!

  66. Thank you for the article, Chris. Do you happen to know if anti-biotic eye drops affect the gut? I’m considering Lasik, but I’d have to take them and a steroid eye drop after. Thanks!

    • re: … if anti-biotic eye drops affect the gut?

      If it can into the eye, it can get into the body generally, and via the tear ducts, it can into the throat pretty easily.

      The precautionary principle says: if you have to do a course of antibiotic, also do a course of a quality probiotic*, and probably take the PB for at least 2 weeks after the AB ends.

      As it happens, I just started an AB for a dental procedure, and have started a PB as well.
      * The vast majority of probiotics on room temperature store shelves are not quality products.

      • The majority of probiotics are poor quality or dead.

        I switched to Thorne shelf stable probiotics – excellent quality brand and I was tired of concerns about the refrigeration issue. Thorne are also resistant to stomach acid so they get to the gut where they can do their work. They are expensive, but for an affordable brand my nutritionist recommends KyoDophilus 9 (must have the 9 meaning 9 strains) which are also shelf stable.
        We also use OrthoMolecular probiotic powder in packets, also shelf stable. Two people can share each packet to save cost.

        The point is, switch it up using different brands (unless you find a particular one that solves an acute issue you are having). and of course refrigerated sour kraut and other properly fermented foods.

  67. I absolutely agree with all of this. I have been on antibiotics more times than I can count beginning in early childhood. I’ve also struggled with Candida, food sensitivities, and then was finally diagnosed with Celiac Disease.

  68. Yes ever since I was in my early teens, I would get strep throat and be on antibiotics. I would get strep several times a year till I was in my late twenties and then got my tonsils taken out and never (touch wood) have had strep since. I do have celiac disease and have been Gluten free now for eleven years, but now I get terrible stomach pains, nausea, head aches, high blood pressure when I am around ,when something is being cooked or baked with wheat. I can not be in a house if someone is making toast or baking with wheat, cannot go to a grocery store if they are making pizza or baking in the bakery, etc…it totally limits to where I go and when. I always have to ask before I go to a friends house to see if they will be cooking or baking with wheat. Also can not go into a restaurant unless the kitchen has their own Google ventilation system so the wheat does not circulate in the whole restaurant…..urrggggg it is crippling and it sure is a handicap!! I have to wear a good mask if I happen to go somewhere where there is wheat baking or cooking and am quick as possible to get out….have you or anyone heard or know of this severe reaction? I would like to know because I feel I’m walking all alone and would be nice to have some support and some kind of education on this?! Thanks for your time…..Katri

    • Hi Katri!

      I have a similar history as you, and am very sensitive (although not like you!) I really feel for your situation and hope very much that you find the answers you need! A few of the symptoms you mentioned caught my eye, and I suggest HIGHLY that you read the book Stop the Thyroid Madness (on amazon) as well as some of the blogs on Chris’s website about the HPA access and thyroid. Thyroid and adrenal problems can greatly magnify symptoms of dysbiosis and food allergies. Chronic food allergies can in fact bring these imbalances in your endocrine system on, AND have symptoms of their own that you could be missing or mistakenly assign to just the allergy itself. Forgive me as I do not have information on your complete history, you may have already explored this angle? The book I recommended has EXCELLENT tips on diagnosis and is written by and for patients, so it makes these connections simply and clearly. I sincerely hope this helps get you in the right direction and I send you love and good wishes! Don’t give up! follow the trail, go get your health back, and then share it with others, especially parents so that people like you and I can give the ones after us a chance to have a better life!!

  69. I think the comment from Dr Jeff needs further consideration. I would advance the discussion if we would not focus on just one thing. All allergies, intolerances etc. are multi factorial with one or more triggers. Blaming the trigger isn’t very useful. In a worst case scenario you get rid of the symptoms but the real cause(s) not being addressed, it goes underground and becomes low level inflammation.
    Glyphosate has been used increasingly in the production of all our food. Yes, also on wheat, a common practice to speed the dying off.

    • As I said above, I’m not suggesting that antibiotics are the single cause of CD. CD, like most diseases, is multifactorial and involves a combination of genetic predisposition + environmental factors, of which antibiotic use is only one.

  70. Whoa, this is also based on some BIG assumptions as a bit more historical celiac testing background is needed. Missing in this discussion is that up until quite recently, CD was 1) not being diagnosed (not even being looked for) or 2) was being mis-diagnosed depending on the specialist (as schizophrenia, brain ataxia, depression, chronic fatigue, fibromyalgia) especially in the US, or 3) was only being diagnosed at end stage 3 of villous atrophy. At lot of this has a lot to do with older test methods, where only the blood of full blown celiacs were used as the sample medium. Intestinal sampling, the supposed gold standard of testing until recently, can also be faulty, as surface area of the intestinal lining is quite large, and the sample is small. Again, disturbance may not show until end stage atrophy already occurred.

      • Dunno what article you are reading, but there may not be as dramatic an increase in celiac, as it was hardly being looked for or diagnosed pre-1998 or so.

        There is, however, a clear and steep increase in non-celiac gluten sensitivity (NCGS), and autoimmune components. This one may be coming from various causes, including so-called safe gmo foods, toxic pesticides on standard produce, antibiotics, herbicides that act as antibiotics, and eating animal protein where these animals have been given repeat doses of antibiotics and also eaten pesticide laden grains.

  71. I also heard that CD is on the rise due to the higher gluten content in modern wheat and also GMO component of pesticide.

    • re: I also heard that CD is on the rise due to the higher gluten content in modern wheat …

      Modern runt mutant goatgrass (sold to you as semi-dwarf hybrid wheat) actually has less gluten than emmer, an heirloom grain. Modern wheat has different proteins, and the gliadin in particular may be different and more hazardous, but the total amount of it hasn’t changed that much.

      re: … and also GMO component of pesticide.

      There are no GMO wheats on the market [yet], if that’s what you were trying to get at.

      But yes, pesticide uptake is a problem. Even though there is no RoundUpReady wheat on the market, glyphosate is still used egregiously for “dessication” of wheat (terminating growth for harvesting convenience). The RoundUp obviously gets into the plant, because it kills it.

      Just another felony on the wheat rap sheet.

  72. Interesting article.

    Reading it makes me wonder if people should get a sample of gut bacteria taken before a course of antibiotics so that they can get the bacteria back in to their gut once they stop the course. Of course, that kind of relies upon being able to conserve the bacteria while on the antibiotic course and then being able to get them to repopulate the gut.

    From a personal perspective, I’m also wondering if the wrong types / balance of gut bacteria can significantly influence the cholesterol levels in the body.

  73. I am celiac, and previously had antibiotics (very strong ones) to help fight a gum infection. They made me feel really ill at the time, and I chose to stop one kind (they gave me two different ones). Previous to my diagnosis I had lots of antibiotics for strep throats etc. I noticed that severe symptoms occurred after I had Rota Virus. I was never the same, took me a long time to get over it. I think antibiotics exacerbate, but personally for me, I believe either pregnancy or Rota Virus trigger a celiac response….

  74. Definitely the cause in my case. I had continuous courses of antibiotics as a baby and until 7 years old and lots as a teenager. I noticed that I always got candida after taking them so avoided them as an adult. I had a course 6 years ago for a bad infection and immediately my health started to break down and I’m still fighting to get back to health. Lab tests show my beneficial bacteria are almost non existent and I have leaky gut. I’ve been clinically underweight all my life and I think that is due to the damage to my gut flora caused by antibiotics.

  75. My serious celiac symptoms started after a colitis infection. But after I had been gf for a while, I noticed that symptoms that had been mildly annoying my entire life had disappeared. I also had a negative blood tests (multiple one, actually), but a positive endoscopy. So I often worry that people are going undiagnosed, especially my children. I keep them mostly gf, just in case. Sparing them the trouble I’ve endured is worth the trouble and the expense.

  76. My daughter was diagnosed with Celiac at 2 1/2 yrs. she started exhibiting symptoms when she was about 22 months. I was on many antibiotics as a pre-teen and teenager. Could a mother’s antibiotic use contribute to her child’s development of the disease?

    • My daughter was diagnosed with Celiac at age 5. She started showing symptoms possibly as early as 19 months. She has only been on antibiotics once in her life when she was 5. However, I was on lots of antibiotics for strep infections in my life. I also wonder about a mother’s antibiotic use and/or antibiotics in the food supply.

      • can you provide some direction of what to take instead for ear infections for children under 5 instead of antibiotics? Are there antibiotics brands that are “safer”?

      • Yes. It is due to antibiotics. I take massive amounts of probiotics daily (if the bottle says “one a day” I take 5, 3 times a day, and so on) and try to eat fermented foods. While I don’t think I will ever be able to completely heal my stomach due to antibiotic “abuse”, I feel like I can eat a piece of (organic/homemade/”clean”) toast now without becoming “drunk”. Sure, spraying roundup on wheat getting ready to be harvested is an abomination, and other factors are contributing, but when the body is in a state of constant dysbiosis, when the microbiome is not at its best, the whole world is going to be a threat.

    • re: This also implies that CD could resolve if intestinal barrier function is restored.

      Probably not, sort of by definition. Fasano has shown that the gluten-bearing grains cause intestinal porosity in everyone, not just those predisposed to CD. If the leakage stops, and you think you’re CD-free, re-exposure to wheat & its co-conspirators just starts the whole cycle all over. By the way, lectins in other grains may be nearly as troublesome.

      re: Are there any cases of CD resolving?

      The symptoms and side effects subside by going GF. Cured? perhaps not, but does it matter? Rhetorical: why would anyone want to consume wheat again if it did? CD is only one of the many charges on the wheat rap sheet.

      Contemplating more broadly, there is anecdotal evidence that some auto-immune conditions can be arrested or reversed by first fixing the leaky gut. This very likely requires that antibody titers recede. That’s a very slow process; months at least if not years. How long is a tetanus shot effective?

      But to circle around to the article topic … antibiotic use probably has multiple hazards due to nuking the gut biome, with a hypothetical enabling of CD being a relatively minor one in my view. And it’s not just prescribed ABs that are a problem – gratuitous OTC ABs abound (like triclosan in oral products). Many foods also are gut biome antagonists (and I’d include wheat on that list, entirely apart from it’s effect on tight junctions).

      • “Probably not, sort of by definition.”

        Definitions change. See Fasano’s work. Celiac used to be, “by definition” a rare disease. Until he changed the definition.

        • Even before I read some of Fasano’s papers, my position was:

          We are all celiac; it’s just a matter of degree and decades.

          Even if Big Gene™ mutates a gluten-free wheat (and they are working on it), I wouldn’t eat it. There are just too many other problems with it, going back to einkorn.

  77. My own personal story starts when I still lived in the UK, sometime in 2000. I became infected with something in my stomach/gut that made me sick for 2-3 days. The doctor prescribed antibiotics. It could have been a run of the mill bug, if it wasn’t for a very weird… dream I saw during the infection: a serpent taking rooting place in my stomach. I took that as a sign, and I wasn’t wrong.

    After that infection, everything changed in my life.

    Fast forward 11 years, I now live in the US, and I’m near death. It’s been 11 years of severe illness. At that point, in 2011, I had given up, and was even thinking that “I lived a good life, whatever comes, comes, I accept it…”. Death was looming and I still didn’t know what from. The blood test for celiac had come negative in 2003 (only to be told many years later that the blood test is not accurate), and the *various* doctors telling me that “it’s just stress” (really??). In the years followed I tried a gazillion antibiotics, got C.Diff, etc etc etc. Nothing worked.

    I went Paleo as a last ditch effort, and voila, all my symptoms disappeared within 3 days! I felt so good, as I haven’t felt for many years! I clearly remember the day No 3, I was coming back from Europe (I was there to say a final goodbye to my family), and in the airplane everyone looked tired and sleepy. I was full of energy, listening to music, and banging my head to the rhythm!

    My husband, looking at me that day, told me afterwards: “after seeing how you felt in the plane, I suddenly knew that this was the solution for you”.

    A year later, in 2012, 23andme’s DNA result revealed that I was 30x more likely to have celiac than the average population.

    Looking back, I should have seen that it was just plain old celiac, given that I had ALL the standard symptoms, but I chose to believe that darn inaccurate blood test. Doctors never asked me to do an endoscopic biopsy, which would have shown the problem, no doubt.

    So anyway, all is good now. I’m now 42 years old, and I’m hoping to become a mom. I could not become a mom earlier because my health had taken such a beating that I would either die giving birth or the baby would have been super-unhealthy (or both). I’m just hoping I didn’t make it out of hell too late.

    • @Eugenia
      I have all the complications from Celiac but don’t have Celiac. I also have the gene for Celiac. Now they are saying SIBO causes malabsorption, with the same complications/symptoms as celiac which is osteoporosis, autoimmune diseases, etc. But celiacs also have SIBO. My allergist says I have gluten sensitivity, but Dr Fasano says gluten sensitivity doesn’t produce autoimmune diseases. My daughter has Hashimoto’s and I have an undx’d thyroid condition with intermittent Lupus diagnosis and Spondyloarthritis (Inflammatory arthritis). I’m too sick to work yet I can’t go on disability without a diagnosis of something. It’s hard to heal your stomach when you have SIBO and multiple food allergies cause you can’t eat fermented foods.

      All of this started after I was hospitalized for an infection and given IV antibiotics.

    • Cheryl, was your 23andme done when they could still do some interpretation? I just got mine back and I have run it through a few online filters, but I am curious to get more information from it. Thanks!

      • I know this isn’t what you’re asking but Prometheus are quite a good on-line service for interpreting 23andme’s data.

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