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Antibiotics and Autism

Otitus_mediaBy Kent Heckenlively, Esq.

It’s been part of the autistic canon for so long that it often gets overlooked in our discussions of autism.

That is the observation that prior to the development of autism, many of our children had multiple ear infections, which were then treated with antibiotics.  Many parents believe the antibiotic treatment in some way set the stage for their child’s autism.  I know that my own daughter had several ear infections in her first year of life which were treated with antibiotics.

One of the problems in nailing down the extent to which antibiotics may affect the gut flora is that we really haven’t had a full understanding of the bacteria which live in a typical human digestive system.

That may begin to change with the publication of an article entitled, “The Pervasive Effects of an Antibiotic on the Human Gut Microbiota” and reported in the journal PLoS Biology.  An accompanying article on the study was published in Science Daily on November 19, 2008.  (“Antibiotics can Cause Pervasive, Persistent Changes to Microbiota in Human Gut.”)

David Relman and Les Dethlefsen of Stanford University, using a technique developed by Mitchell Slogin of the Marine Biological Laboratory were able to identify changes in the gut microbial communities of three healthy people after taking the antibiotic Ciproflaxin for five days.  The scientists were able to identify roughly 3,300 to 5,700 different types of bacteria in the human gut and found that the antibiotic treatment affected about of a third of the identified bacteria.

Perhaps most ominously, the report found that while the bacterial community of these individuals recovered, many types of bacteria failed to recover within six months.

The Science Daily article noted, “This raises questions about the health effects of perturbations to the human-microbial symbiosis in the gut, such as may occur with antibiotic treatment.  Because specific microbial populations mediate many chemical transformations in the gut-and previous studies have related these processes to cancer and obesity, among other conditions-changes in the composition of the gut microbiota could have important, but as yet undiscovered, health effects.”

Parents report that their healthy babies get ear infections, treatment with anti-biotics, multiple vaccinations, and then develop autism.  Most of the time we only look at the last trigger to this disease, vaccination. 

We should also be looking at what role antibiotics may play in this disorder.

Kent Heckenlively is Legal Editor for Age of Autism.


Casey Kerrigan

The gut flora in autistic people is very different than everyone elses, thats why at least 80% ( i forgot the exact figure, but its something like that) of autistic people have gut and bowel problems, most peoples gut is dominated by "good" bacteria that help produce essential chemicals for our bodys and especially our immune system. When a 2 year olds gut flora is whiped out by over use of antibiotics, and then the immune system is overwhelmed by a vaccine, the "bad" bacteria are alowed to grow unchecked and eventually over run the gut. Alot of new research suggests that almost all mental disorders are linked directly to gut flora via the vegas nerve, which carries the chemicals made in the gut directly to tge brain. The argument that antibiotics help autism symptoms does not mean they are not a contributing factor to the disease, in fact it is the opposite. The antibiotics kill the gut flora, which in an autistic child, is dominated by "bad" or "the wrong" bacteria so symptoms improve untill the medication is stopped when the bad bacteria are alowed to flourish again. The medical industry knows all of this and autism can be cured or at least dramatically improved with the right probiotics, some fermented foods (to feed the right bacteria), and the right diet. Unfortunately once the reaserchers found all of this out, no one used it to study how to cure it. Presumably because you cant patten bacteria. Not just any probiotic will work, tgere are over 1000 species of gut flora, certin ones fight certin bad ones, some have specific functions, so research is needed to figure this out, fecal transplants are a promising treatment, but i would be willing to bet no one is funding research treating autism with this treatment.

Catherine Vanderbilt

Latest study, 2015 shows that amoxicillan, is actually HELPING kids with autism. A clinical study was preformed and all Of the children showed improvement! Although once the antibiotics were stopped, they did not continue to improve, but they DID hold all abilities acquired during the period of taking the antibiotics.

We've recently put our son, whom has autism, on a dose of amoxicillan after getting sick and I am happy to say the clarity of the words he could say improved, His eye contact dramatically got better and he started repeating 2 & 3 word phrases we Said!

So to say antibiotics hurts them is wrong! Also, parents with children of Autism who go around looking for something to blame rather than something to help them, in my opinion, are ignorant. Granted We would all love to know the 'why', but the 'what Are we going to do about it' should be more important Right now.

Becky Benish

I have a 24 year old son with severe autism,I'm not sure that atb's cause autism. I do know that about 3 days after my son is on antibiotics his mood is better and he doesn't have episodes of violent behavior. I would like to hear information about this.

Rick Shorrock

Hello, glad I found this site! I own a video production company in Central Florida. I was contacted by a gentleman around here about his child contracting Autism when he was a baby, even though all the medical staff at the hospital told the parents the baby was fine. And this gentleman blames the use of Augmentin in his child's Autism. We are in early stages in talking about producing a medical thriller about his case. Would you like his name and contact information?


My son is on the autistic spectrum but has never had an ear infection, nor was he given any antibiotics in his 3 years.

However, during my pregnancy, I had a non-specific vaginal infection requiring cipro cream. And since they catharized me so many times while I was in labor, I was given amoxicillin while I was breastfeeding (8 days), and it did nothing, so I was then given Cipro for 3 days (pump and dump).

But my son did not teethe normally and never puts anything but in his mouth. So to develop his flora, we have started giving probiotics including a broad spectrum acidophilus and saccharomyces boulardii...it has really improved his disposition and he seems to be more understanding of directions, etc. That and chelation with dmsa and ala have really been good for our boy.



You have put together an interesting list of 'insults' that are damaging our kids. Allow me to add a few:

-Sonograms, ultrasounds and 3-D ultrasounds for pregnant women.
-Pitocin giving to moms when in labor.
-The vitamin K shot given to newborns (Some claim this shot has aluminum in it.)
-Aprox. 50% of hospitals use silver nitrate for the newborn's eyes and the same for boy's penis if you choose to circumcise; the other 50% use strong abx for both procedures.
-Remodeling and/or adding on to your house before, during and after the pregnancy; therefore spraying the baby’s environment with lead and/or formaldehyde and who knows what other harmful substances.
-The use of Bismuth in infant drops like Mylicon to treat baby’s tummy issues.
-BPAs in plastic bottles and pacifiers.
-Antimony in baby’s clothes and bedding
-Corn syrup and genetically modified food particles in infant’s food.
-Electro magnetic frequencies in the house and nursery
-Lead in toys

And the list goes on and on, but that is OK, right? It’s all in the name of progress and convenience…


My son had 24 rounds of antibiotics in his first 2 1/2 years of life even though I questioned our then pediatrician repeatedly. They were mostly for chronic ear infections. Even though we understand now the damage this did to his gut, he is still unfortunately on a long-term antibiotic regimen for acute PANDAS and now Lyme. We struggle with this every day, but without the antibiotic, his PANDAS symptoms are so fierce he can't function. Even with IVIG, we've heard from docs that he'll have a long term course of antibiotics. This brings up an interesting question for me as we've seen a regression in his autism symptoms with the PANDAS exacerbation. I now wonder if part of that regression is due to the antibiotics which are helping to treat the PANDAS. Help. It's a never ending cycle of autism symptoms, immune issues, and gut problems. "Jane! Get me off this crazy thing!"


The greedy pediatrians are the culprit in the autism epidemic. Our insurance system pay the pediatrician a monthly stipend for each kid no matter how many times he goes for a visit. Thus, even when a kid is still sick and under antibiotics, the doctor "save money & time" by vaccinating when the kid is on-site instead of scheduling another visit. I checked my son's medical file 3 years ago and he had several vaccinations while sick and under antibiotics.
In a mojority of countries, if the kid has even a small running nose, vaccination is denied until he is healthy.
A parent told me that one of her two identical twins kid who is autistic had a flu as compared to his brother who was healthy when they got vaccinated at the same time.
Even if you believe in vaccinations, do not vaccinate when your kid is sick or under any medication and try to space the vax as long as possible instead of a six-vax cocktail.
Since relying on the medical system to do the right research is not an option, I would propose to every parent to share his autistic kid medical file(removing all personel info of course). We can put the files somewhere where everybody who share files can access them. I am sure that if we can get about 100 files, we will be able to zoom rapidly on the main causes of autism and reach a conclusion that is much more scientific than all the one produced by the so-called "Autism Experts".


From "across the pond":- Over twenty years ago, after several exposures to amoxicillin/penicillin over a period of years, my face blew up into a melon and my shocked doctor told me "For God's sake, don't take any more of those, you're allergic to penicillin. Wear a Medicalert medallion in case you're ever unconscious after a road traffic accident to avoid you being injected automatically with penicillin. Your next exposure could kill you." He wasn't the sort of doctor to be joking about my situation.

My teenage ASD daughter had several courses of augmentin as a baby (for ear infections, how did you guess?) and at five years, when given amoxicillin for a urinary tract infection, she developed an all-over red rash. Her medical records now record the distinct possibility that she's allergic to penicillin (would you be willing to take the risk?).

I wonder how long it will take the orthodox medical profession to cotton onto what's happening? How long will it take for them to believe us?


It could also be the Thimerosal in ear/otic antibiotics that is causing some of the problem. I recommend a quick google of otic( which means ear), thimerosal and antibiotics.
The combination will bring up some sites that identify thimerosal as being part of some pediatric ear antibiotics.
www.fda.gov/Cder/fdama/mercury300.htm( hope I typed that right) is an FDA website that lists a collection of, amongst other things, ear antibiotics that contain/or contained thimerosal.The website was last updated 2006, and has some information from as early as 1998.I don't know whether thimerosal was ever taken out of these antibiotics, or if it is still present.
But for a baby with frequent ear infections, there is a possible high mercury load from frequent mercury containing antibiotics.

Kathy Blanco

The measles virus is often known to cause otix media, naturally, so if it does it unnaturally, would it be forward for me to think vaccines cause all of this overuse of antibiotics?

Then again, I have seen kids go on minocycline, and lyme drugs who hae autism lyme, and they are recovered, so, what am I to think? We are talking LONG TERM USAGE, years...not weeks, so it kils off all life cycles of bacterial organisms, if not reduces inflammation in the brain...sometimes Abx's are not the enemy...

Its the vaccines!

Has anyone considered the fact that its the insane amount of bacteria and viruses we are injecting into our kids that are in actual fact *causing* the ear infections? If the immune system is unable to handle the onslaught of pathogens, where the heck are they gonna go? I suppose they piggyback the mercury into the brain, nice yummy grey matter here to chew on, don't you think?


I suppose in this way, I do agree with those that believe that "vaccines do not cause autism." However, I think it's because it is a gross (in both senses of the word) oversimplification.

Vaccines are, imo, the last straw in the complex interplay of common exposures that happen before conception, during fetal development, and early in a baby's life that can set up a cascade of biochemical problems that may ultimately result in autism.

-mother's use of hormonal birth control
-inadequate preconception and prenatal nutrition, including due to hyperemesis gravidarum
-maternal dental amalgams
-maternal vaccinations
-RhoGam (less so now than before, when it had the full amount of mercury)
-routine abx during labor for GBS
-abx post c-section
-abx for baby (esp. babies born surgically that are preterm,which many of them are)
-reflux meds, thrush meds (both of these are increasingly common)
-use of tylenol/motrin for teething pain, minor fevers, and pre-vax
-premature introduction of solids esp. grains and iron fortified, processed cereals, premature weaning from breastmilk
-abx for ear infections
-overconsumption of dairy
-fluoride drops

Most of the above listed factors are detrimental due to causing imbalances in the gut flora, coupled with inadequate vitamin and mineral consumption/absorption.


I would like to echo and underscore the posters here who point out the *possible* link between vaccines and (the likes of) otitis media, and THEN the damage wrought by the resultant antibiotic regimen. When I started studying this issue of vaccine *safety*, the more I read the more I came across references to 'glue ear' in relation to kids otherwise damaged by vaccines (ADD/ADHD, ASD etc etc). A number of vaccines are KNOWN to suppress the immune system; thus in their wake come opportunistic infections like the bacteria that cause otitis media. And then the gut gets even more damaged by the antibiotic treatment; and then:: a vicious circle.

A good study on how many cases of otitis media have occurred following various vaccinations (including the hep B at birth), and how many without that factor, is long overdue. But of course the allopathic medical profession isn't interested, for various reasons (nor their partners in the pharma industry, for one main reason). So it will probably take a reinvigorated federal agency to commission one. Though best scenario: to press for splitting up the CDC into two agencies: one researching the safety of vaccines, while the other continues its current job of promoting the vax schedule. Putting both jobs under the same hat has been the one most important reason why this issue - of vaccine damage in general, and ASD in particular - has gotten so terribly out of hand. One would think that would have been obvious from the start. So another reason why we need to keep an eye on 'the guvmint' as well...

With the change in government, maybe there's hope for a clean sweep/a cleanout of the agencies supposedly being the regulators of the drug industry, instead of their bosom buddies. But one can do more than hope. One can demand action. Letterwriters, to your stations.


I have two grandkids, 9 and 5 years old. Mostly unvaxed. Have never received antibiotics. Their parents are into the traditional foods diet and include fermented foods (think kimchi) as part of their diet. When my granddaughter was 3 the nurse practitioner was shocked and amazed to look at her chart and see that she had never had an antibiotic. At three! I was in my 40s before I took my first antibiotic. Since that time they have been prescribed for my grandkids, but never actually used. There are a lot of alternative treatments available for mild ear infections.

We have a medical system which has gone insane, IMO.


Without a doubt, it was antibiotics that gave my son the final push over the cliff and into autism.

He had a difficult birth and was given gentamycin and ampicillin within the first few hours - "just in case". The stage was set. Then he didn't stop screaming for the first 7 months of life - "colic" was a vast understatement. Of course we vaccinated at 2,4,6,12 & 18 months - my husband and I are pharmacists and had been taught in university just how incredibly "important" and "safe" vaccinations were. We were never taught to question this. Shortly after age 2 he had multiple upper respiratory infections requiring antibiotics back to back and that was the final blow. Hello autism.


My kids got a few ear infections after their shots, but never since we stopped vaccinating. They had antibiotics for those early infections. Though we can't tell if the kids got worse from the those rounds of antibiotics before ten months of age, I wouldn't be surprised if the drugs played a roll in regression.

It's why I use the Spanglish-y moniker "Gatogorra", i.e., "cat in the hat". Remember "The Cat In The Hat Came Back"-- with the pink bathtub ring that spreads and spreads with each insane attempt to remedy it? That's what we think happened to our children-- a kind of big, ever spreading pink ring induced by incompetent medical practices mopping up after other incompetent medical practices.

What made things confusing for us is that they got their shots and began teething very early, at just a month and a half. We thought the screaming was from teething and gave Tylenol-- now we realize that they could have been in pain from inflammation due to vaccines and vaccine mercury, which the Tylenol would have made much worse. Then they got ear infections right after several rounds of vaccinations and we gave antibiotics a few times. More screaming which we again thought was teething, though it was probably dysbiosis. More sleepless nights, more Tylenol recommended.

Because of all the toxic strikes against them, I'm not even sure if my twins needed to have "susceptibility genes" in order to be susceptible.

Ben's Dad

Very interesting. Add my child to the lists of those with chronic (“normal”) ear infections and a variety of routine antibiotics, with no early attention given to what all those antibiotics were doing to the digestive system. It would be fascinating to see if autism rates could be reduced by something as simple as ear tubes. After the tubes, my son never had an ear infection again and there was a huge if not compete reduction in antibiotic use.


Thanks for this Kent.

I have always wondered why this isnt part of a causation theory.

Cherry Sperlin Misra

Dan, I had always suspected the same regarding the change from Cipro to Doxy during the anthrax scare. My daughter was working in a hospital in New York a few years later and one of her co workers was given Cipro for 10 days. In her words, "His achilles tendon turned to mush and he had to be operated on, and we thought that he might lose the ability to walk" .
Regarding ear infections, one thing that could probably inferred in the case of a baby with ear infections is that that child has received mercury in vaccines which has severely damaged his immune system.Damage to the immune system has been researched at U C. Davis and in my humble opinion , this is one of the most important pieces of information that we have regarding mercury and vaccines and also one of the most widely ignored. The very long reaching implications of damage to the immune system starting right on the first day of life should have sent an earthquake through the pediatric profession, but as usual, when it comes to mercury, it went virtually unnoticed. As one "small" example, the discovery that many infants had damaged immune systems should require pediatricians to re-research so many of the studies on which they now base pediatric practise, But one can see that nothing of the kind has happened. To put this more simply- If you do a research in which you assume that you are looking at normal human infants and in fact you now discover that you were in fact looking at severely immune-damaged babies- well, arent you supposed to throw that research out the window? - rather than base your pediatric practise on it?
To take the next logical step- It would seem that the immune damaged child, who already has mercury in his body, would naturally be the first one to become autistic after subsequent mercury laden vaccines.

I am quite sure that if one does some simple investigation, it will be found that that ear infections are now much less common than they were during the heyday of thimerosal use. In fact I am sure that ear infections rates are down because a doctor told me that they are being told that it was found that some vaccines had the delightful side effect of preventing ear infections ! One more case of medical spin.
Do any of our readers have any info about the duration of the effect of mercury on the immune system? This is a very important question.


Wow. I will join the others in saying that my son was also on antibiotics many times in the first 3 to 5 years. He was constantly being treated for ear infections and he too was receiving the "piggybacking" of Motrin and Tylenol. When I began MY research into what was the culprit of my son's absence of language and various other issues... I was always searching for studies that were being done on the mix of antibiotics and vaccines. I found some answers but not enough. I also wondered which came first to cause the end trouble...or did they happen simultaneously. I would like to know if others who also had their children on Motrin alot at the time have severely autistic children or moderate. My curiosity stems from the fact that we feel using an anti-inflammatory regularly at the time(also he was on zantac for reflux which MAY have lessened any "bad" effects from the Motrin) reduced the severity of his autism. He is still on the spectrum and was hurt by something but we believe there is a connection with many different factors...antibiotics + vaccines + as someone said in another post, perhaps bottle vs. breast + the use of anti-inflammatories + all of the other poisons the babies/kids/mom's are exposed to along the way.

María Luján

There are several studies pointing to the problem of antibiotics in ASD
J Dev Behav Pediatr. 2006 Apr;27(2 Suppl):S120-7. Links
Early medical history of children with autism spectrum disorders.Niehus R, Lord C.
University of Michigan Autism and Communication Disorders Center University of Michigan, Ann Arbor, Michigan 48109, USA.

Previous studies have suggested that children with autism spectrum disorders (ASD) may have different medical histories than nonspectrum children in several areas: their reactions to vaccinations, number of ear infections, chronic gastrointestinal problems, and use of antibiotics. Furthermore, some studies have found associations between regressive autism and gastrointestinal (GI) symptoms. The present study analyzes the medical records from birth to the age of 2 years of 99 children (24 typically developing; 75 with ASD, of whom 29 had parent-reported regression). Data were coded in the following areas: frequency and purpose of pediatrician visits, frequency and type of illnesses and medications, type and chronicity of GI complaints, date of vaccinations, growth data, and whether the pediatrician noted behaviors indicative of an ASD before the age of 2 years. Children with ASD were found to have significantly more ear infections than the typically developing children as well as to use significantly more antibiotics. Typically developing children had significantly more illness-related fevers. There was a nonsignificant trend toward the ASD group having more chronic gastrointestinal problems. There were no significant differences between the groups for the age of vaccination or for number of pediatrician visits. Finally, pediatricians noted symptoms of onset of possible autism, including language delay, for 44 of the 75 children with ASD and 2 of the 24 typical children. Results are discussed in terms of needs for future research.

There are also hypothesis that have not been tested properly; of course as you know this journal is of hypothesis only

Med Hypotheses. 2005;64(2):312-5. Links

Could one of the most widely prescribed antibiotics amoxicillin/clavulanate "augmentin" be a risk factor for autism?Fallon J.

Autism is an ever increasing problem in the United States. Characterized by multiple deficits in the areas of communication, development, and behavior; autistic children are found in every community in this country and abroad. Recent findings point to a significant increase in autism which can not be accounted for by means such as misclassification. The state of California recently reported a 273% increase in the number of cases between 1987 and 1998. Many possible causes have been proposed which range from genetics to environment, with a combination of the two most likely. Since the introduction of clavulanate/amoxicillin in the 1980s there has been the increase in numbers of cases of autism. In this study 206 children under the age of three years with autism were screened by means of a detailed case history. A significant commonality was discerned and that being the level of chronic otitis media. These children were found to have a mean number 9.96 bouts of otitis media (with a standard error of the mean of +/-1.83). This represents a sum total for all 206 children of 2052 bouts of otitis media. These children received a mean number of 12.04 courses of antibiotics (standard error of the mean of +/-.125). The sum total number of courses of antibiotics given to all 206 children was 2480. Of those 893 courses were Augmentin. with 362 of these Augmentin courses administered under the age of one year. A proposed mechanism whereby the production of clavulanate may yield high levels of urea/ammonia in the child is presented. Further an examination of this mechanism needs to be undertaken to determine if a subset of children are at risk for neurotoxicity from the use of clavulanic acid in pharmaceutical preparations.

BMC Psychiatry. 2001;1:5. Epub 2001 Oct 10. Links
Aminoglycoside antibiotics and autism: a speculative hypothesis.Manev R, Manev H.
Department of Psychiatry, The Psychiatric Institute The University of Illinois at Chicago, Chicago, IL 60612, USA.
BACKGROUND: Recently, it has been suspected that there is a relationship between therapy with some antibiotics and the onset of autism; but even more curious, some children benefited transiently from a subsequent treatment with a different antibiotic. Here, we speculate how aminoglycoside antibiotics might be associated with autism. PRESENTATION: We hypothesize that aminoglycoside antibiotics could a)trigger the autism syndrome in susceptible infants by causing the stop codon readthrough, i.e., a misreading of the genetic code of a hypothetical critical gene, and/or b) improve autism symptoms by correcting the premature stop codon mutation in a hypothetical polymorphic gene linked to autism. TESTING: Investigate, retrospectively, whether a link exists between aminoglycoside use (which is not extensive in children) and the onset of autism symptoms (hypothesis "a"), or between aminoglycoside use and improvement of these symptoms (hypothesis "b"). Whereas a prospective study to test hypothesis "a" is not ethically justifiable, a study could be designed to test hypothesis "b". IMPLICATIONS: It should be stressed that at this stage no direct evidence supports our speculative hypothesis and that its main purpose is to initiate development of new ideas that, eventually, would improve our understanding of the pathobiology of autism


J Child Neurol. 2000 Jul;15(7):429-35.Links

Comment in:
J Child Neurol. 2001 May;16(5):387.
Short-term benefit from oral vancomycin treatment of regressive-onset autism.Sandler RH, Finegold SM, Bolte ER, Buchanan CP, Maxwell AP, Väisänen ML, Nelson MN, Wexler HM.
Section of Pediatric Gastroenterology and Nutrition, Rush Children's Hospital, Rush Medical College, Chicago, IL 60612, USA. rushstudy@aol.com

In most cases symptoms of autism begin in early infancy. However, a subset of children appears to develop normally until a clear deterioration is observed. Many parents of children with "regressive"-onset autism have noted antecedent antibiotic exposure followed by chronic diarrhea. We speculated that, in a subgroup of children, disruption of indigenous gut flora might promote colonization by one or more neurotoxin-producing bacteria, contributing, at least in part, to their autistic symptomatology. To help test this hypothesis, 11 children with regressive-onset autism were recruited for an intervention trial using a minimally absorbed oral antibiotic. Entry criteria included antecedent broad-spectrum antimicrobial exposure followed by chronic persistent diarrhea, deterioration of previously acquired skills, and then autistic features. Short-term improvement was noted using multiple pre- and post-therapy evaluations. These included coded, paired videotapes scored by a clinical psychologist blinded to treatment status; these noted improvement in 8 of 10 children studied. Unfortunately, these gains had largely waned at follow-up. Although the protocol used is not suggested as useful therapy, these results indicate that a possible gut flora-brain connection warrants further investigation, as it might lead to greater pathophysiologic insight and meaningful prevention or treatment in a subset of children with autism.

Now, the problem of the imbalance in the gut flora is one aspect and how antibiotics may treat the overgrowth of patogen bacteria in ASD is other aspect that could be related to the former one.

What do you think?

Maurine Meleck

Some researchers have opined that vaccinations can actually cause ear infections. My autistic oldest grandson, of course, had numerous ear infections as a baby. The youngest one, now recovered, had his first ear infection at 5 days old(the youngest one they said at medical College of Ga, to have an ear infection. Could it have been the HepB vaccine he had that did it?
Thanks for this post.


I spent a couple of years at the beginning of my "journey" into the autism mystery thinking that microbes might be at the root of what was wrong with my own kids. I learned a lot of interesting things in my quest to understand what might be wrong with their gut flora and how to fix the problems.

I became convinced that antibiotics are part of the picture of causation in the health problems of many, many kids with autism--and likely for many other health problems, including asthma and obesity. There is also no question in my mind that the microbial differences among us are a part of the reason that we are all different--and react somewhat differently, and often unpredictably, to toxins as well as foods, medications, vaccines.
These differences are not just due to our genetics!

I think modern medicine's continued "war on microbes" approach to health does not seem wise given what is now known about microbes and our interdependence with them. Narrow focusing on the minor genetic differences among us also misses the big picture.

Microbial cells in our bodies actually far outnumber the genetically human cells in our bodies, and for the most part we don't know their functions, or even understand how they interact. (Due to new understanding of how "quantum sensing" can result in changes in the structure (e.g. flagellated or not) and behavior (free-swimming versus stationary) of many microbes that are in the human gut, it has become clear we humans do not have much knowledge at all about microbes.

Our entire "species" classification system seems questionable in regards to microbes since it turns out they can (and do) change shape and behavior (the basis of most current species classification), AND they can (and do) exchange genetic material among and between what we call "species." So our whole biological definition of a "species" does not really seem to work all that well as a framework for understanding microbes.

Given these very significant limitations of our understanding of our microbial symbionts, it seems crazy to continually attack "ourselves" with antibiotics.

One particularly worrisome aspect of microbe ecology that I came across is that many microbes are tolerant of mercury, and some actually use mercury as part of their self-defense. Curiously, many of those microbes that are "antibiotic resistant" are also mercury tolerant "species" (term used loosely).

Hmmm. Anyone suppose there is any connection to increasing levels of environmental mercury, and increasing levels of mercury in our bodies, to increasing incidences of antibiotic resistant bacteria? Could it be that by raising or lowering the mercury levels in our bodies, we affect our symbiont microbial communities?

It seems reasonable to me to guess that changes in diet, changes in the mixture of vitamins and minerals available, changes in the levels of toxins in the body might also affect the microbes which live within us. Part of the reason that so many kids respond to diet changes, supplements, and the use of probiotics may be because these treatments result in positive changes in the mixture of microbial flora in their guts.

There was a small study done showing that a group of kids diagnosed with autism actually had detectably different gut flora than NT kids.

One study on mice showed that gut flora actually can affect food selection--with mice who had one particular microbe actually preferring carbohydrates.

Microbes are also involved in the production of B-12 (and possibly other vitamins) in our bodies.

There are many, many reasons to suspect that what happens to our symbiont microbes affects human health and behavior.

Current knowledge indicates we need to view and treat our bodies as individually unique ecosystems.

Changing the composition of the flora that inhabit us is similar to attempting to change the composition of the flora/fauna that make up an ecosystem. It is lot easier to destroy than it is to fix it once it is messed up. Maintaining a healthy ecosystem is also easier than repairing or restoring a damaged one. The fewer the species in an ecosystem, the less resilient it is to change, and a monoculture is the least resilient of all.

In regards to managing ecosystems, Aldo Leopold wrote, "The first precept of intelligent tinkering is to save all the parts."
Given that our bodies ARE ecosystems, it seems we would be wise to apply that precept to managing our health, too. Antibiotics as "prophylactics" for possible exposures to potentially harmful microbes seem highly questionable. And repeated "slash and burn" antibiotic treatments for minor illnesses seem unwise in the extreme. Antibiotics can be miraculously effective, but we need to use them far less often and with far greater caution.



Thanks Kent for this important piece. I know my son was an avid anti-biotic abuser. As well as prescription cough remedy (Donatussin). And, we should have had stock in children's Tylenol and Motrin. We "piggybacked" the Motrin and Tylenol when he always had those fevers that went along with his coughs/cold/ear infection/ Upper-respiratory ailments.

As a very unaware trusting mother I didn't question all these "meds" my son was living off of. I thought it was normal to be in the doctor's office every other week for either an initial examine to determine if he had an ear infection or the subsequent re-checks.

My son's body was loaded up with a lot of medical garbage as an infant and a toddler. I wonder how the years of almost constant if not frequent anti-biotic use interacted with all those other meds and vaccines.

I hope we will learn more about the role anti-biotics played in our children developing autism. It was a huge factor for my son and I'm certain it had to have a negative effect on him. Anti-biotics have to be a key factor for those kids who used them frequently. They can't be these powerful tools to knock out infection, yet have no negative side effects. Kind of how vaccines are looked at too? I guess our kids got a double whammy.


My son too was on antibiotics a ridiculous amount of times his first two years of life, never once were probiotics recommended to help restore healthy gut flora. I realize people will say, "Oh give me a break, ear infections, antibiotics, vaccines are just part of normal infant health." And, I say, "give me a break, we are destroying our children's immune systems, period.


These are interesting observations regarding children who ultimately are diagnosed with Autism.

It should be noted that normal gut microflora can significantly modify the host response to mercury toxicity. This has been shown in newborn animal models. This is a long neglected field of medicine of how tinkering with the normal bacterial flora may be a bad thing.

The name of Dr. Ann Summers always seems to come up as a leader is this research. http://myprofile.cos.com/summersa70

also see this book pages 206-208


Very interesting! My hubby has a degree in biology so we often have casual conversations about gut flora :)

Not to throw a stink bomb in the room but has any study ever been done about the rates of formula-fed babies with breastfed babies in regards to autism? The communities you mention Dan ("One thing I've pointed out about Homefirst in Chicago -- with virtually no autism or asthma among thousands of never-vaccinated, home-birthed children -- is that antibiotics and also used far less, as are pain relievers.") would also happen to have sky-high rates of breastfeeding compared to the general population.

The Amish? I would have to guess that formula is extremely rare.

Back to the gut flora thing.....breastfed babies have very different gut flora that formula fed babies. Plus the gut flora is more easily replenished if the baby happens to need antibiotics (though the rates of illnesses requiring antibiotics is much lower among bf babies if the baby continues nursing after the course of treatment).

"Formula feeding is the longest lasting uncontrolled experiment lacking informed consent in the history of medicine."
— Frank Oski, MD
retired editor, Journal of Pediatrics


dan olmsted

Kent, this is a really interesting and important post. One thing I've pointed out about Homefirst in Chicago -- with virtually no autism or asthma among thousands of never-vaccinated, home-birthed children -- is that antibiotics and also used far less, as are pain relievers. This could be the troika of the autism epidemic. Also, the first piece I wrote about drug side effects involved Cipro, which was given to victims of the anthrax attacks. It's usually a 10-day course but on the CDC recommendation they were giving it to postal workers etc for weeks and weeks. Then, in mid-course, the CDC said, let's use another antibiotic instead, doxycycline. The latter is much less toxic as antibiotics go -- Cipro is known as the nuclear bomb of antibiotics, and it's chemically related to the anti-malaria drug I've written about that does all kinds of heinous things to mind and body. The piece that Mark Benjamin and I wrote at UPI was about how so many of the survivors were having unexpected long-term health problems, and so were some of the postal workers who did not get anthrax but were treated preventively with cipro -- kind of the vaccine concept, eh? we wrote that the long-term effects in these survivors seemed much more similar to cipro side effects than to any known long-term sequelae of anthrax. as far as i know this extended use of cipro -- weeks and weeks instead of 10 days -- had never been tested; the cdc just decided to carpet-bomb the bug. they never said so, but i've always suspected that they switched the recommendation to doxy mid-course because they were seeing the effects of this untested cipro regimen. of course, nothing happened as a result of our writing about this, as far as i know, but it was my introduction to the ways and means and ducking and covering of the cdc and unintended consequences of massive public health intervention in the midst of hysteria. -- dan

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