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Autism and the Microbiome: Following the Clues of Damage - PART 1

MicrobiomeBy Teresa Conrick

I have a daughter who has a diagnosis of both  AUTISM and AUTOIMMUNITY. They are connected and not just for her but for thousands like her. Megan regressed after receiving a Thimerosal-containing Hib vaccine and the MMR vaccine in 1994 – crying, fever, full body rash, GI distress, losing speech, receptive language, eye contact and skills.  It also began the devastating and ongoing health issues that continue today. The research on the Microbiome seems key to both the regression into autism so many children developed and therefore may be the key for the way out.  Many, like my daughter, are very ill with seizures, gastrointestinal disease, immune and autoimmune disorders, severe allergies and mitochondrial dysfunction. Regression then would appear to be an injury developed from vaccines:

Developmental regression and autism reported to the Vaccine Adverse Event Reporting System.  

We report demographic and clinical characteristics of children reported to the US Vaccine Adverse Event Reporting System (VAERS) as having autism or another developmental disorder after vaccination. 

And who can forget what happened to Hannah Poling in 1999

…..CHILD received five vaccinations – DTaP, Hib, MMR, Varivax, and IPV…CHILD developed a fever of 102.3 degrees two days after her immunizations and was lethargic, irritable, and cried for long periods of time.…..101-102 degree temperature, a diminished appetite, and small red dots on her chest…less responsive to verbal direction in the previous four months and had lost some language skills…complaints of diarrhea, vomiting, diminished energy, fever, and a rash on her cheek…  she had frequent bouts of otitis media, which doctors treated with multiple antibiotics ….He diagnosed CHILD with “regressive encephalopathy with features consistent with an autistic spectrum disorder, following normal development.”…..an underlying mitochondrial disorder…seizure disorder….

The issue of antibiotics is interesting in the research regarding the Microbiome but it does not seem to be the WHOLE picture. Antibiotic use did not happen until well into the late 1940’s.  Thimerosal and its use since the early 1930’s, was in the direct path of the first eleven children diagnosed:

“Since 1938, there have come to our attention a number of children……….”

In addition to Thimerosal, what about those studies linking an increase in AUTISM diagnoses to those living near an ENVIRONMENTAL MERCURY SOURCE? I think the answers are becoming clearer, as we get closer and closer to seeing that the bacterial and viral residents of the human gut appear to have an intimate relationship with toxic MERCURY. We know the BRAIN is impacted by mercury so let’s check out more about the gut.

I have investigated both vaccination  and mercury  as altering the Microbiome, and they seem to fit the pattern of candidates capable of causing regression of development and health.  The research is showing that alterations in the Microbiome might be the epicenter of many chronic diseases, such as MS, Lupus, Parkinson’s, ALS, Alzheimer’s, AUTISM and more.

For anyone new to the mercury/Thimerosal research, it may be helpful to see the connection between antibiotics AND mercury.  Mercury has a long history of use as an antibacterial. So let’s take a look at mercury and what it can surprisingly do to bacteria:

•  Concomitant antibiotic and mercury resistance among gastrointestinal microflora of feral brook trout, Salvelinus fontinalis 

Twenty-nine bacterial isolates representing eight genera from the gastrointestinal tracts of feral brook trout Salvelinus fontinalis (Mitchell) demonstrated multiple maximal antibiotic resistances and concomitant broad-spectrum mercury (Hg) resistance….The presence of similar antibiotic and Hg resistance patterns in multiple genera of gastrointestinal microflora supports a growing body of research that multiple selective genes can be transferred horizontally in the presence of an unrelated individual selective pressure. We present data that bioaccumulation of non-point source Hg pollution could be a selective pressure to accumulate both antibiotic and Hg resistant bacteria. 

Very interesting and so how does that look in humans? 

•    It is well established that some human intestinal bacteria carry plasmids encoding resistance to both Hg and antibiotics (39). In a population subgroup of 356 persons who had no recent antibiotic exposure, those individuals with a high prevalence of Hg resistant bacteria in their intestinal flora were significantly more likely to display multiple antibiotic resistance in these same bacteria.

 From fish to humans to infants --- who also WERE NOT exposed to antibiotics, yet they became resistant to antibiotics.  What can do that?—MERCURY. :

  In two studies, a large fraction of healthy, non-antibiotic-treated infants in the first 3 months of life harbored resistant and multiple resistant bacterial strains [59,60], perhaps through maternal transmission [61▪]. Although it has yet to be evaluated epidemiologically, the growing presence of resistant microbes may be due in part to more widespread contaminant exposures from foods and the environment. For instance, several studies demonstrated that individuals exposed to mercury were more likely to possess resistance to multiple antibiotics, suggesting a coselection mechanism [62].

As we see more evidence, keep asking yourself:

  • Why do many children with an autism diagnosis have chronic infection where antibiotics are needed multiple times yet infection returns again and again? PANDAS (Pediatric Autoimmune Neuropsychiatric Disorders Associated With Streptococcal Infections) children, too have this history of infection then autoimmunity.
  • Why do children with an autism diagnosis harbor more pathogenic bacteria and less commensal bacteria than their non-affected peers?

It’s very possible that antibiotics do not cause the long-term damage we are seeing in the diversity of the Microbiome:

•  One study of 31 amoxicillin-treated infants with acute respiratory infection identified complete elimination of Bifido-bacterium adolescentis species, as well as a significant decrease in Bifidobacterium bifidum in the gut, with no change in overall counts of Bifidobacterium but profound shifts in the microbiota at the species level [56]. Indeed, life-threatening complications of empiric antibiotic use in premature neonates, including necrotizing enterocolitis and sepsis, have been observed in a large National Institute of Child Health and Human Development cohort study [57]. However, when early fecal samples from antibiotic-exposed infants were compared with a later post-weaning sample, antibiotic resistance was reduced, and overall diversity had increased [31▪]. This may have been due to the plasticity and rapid rate of change within the gut microbiota in the first year of life, suggesting that effects of early antibiotic usage in infants may be diminished over time [12▪▪,31▪].  

And more recent research, showing that antibiotics do not cause Microbiome alteration:

Although the use of antibiotics is often regarded a cause of reduced biodiversity in westernized microbiomes this is an unlikely explanation for our findings….. 

BUT look at MERCURY, capable of causing antibiotic resistant genes:

•  Antibiotic Resistance Pattern Among Gram Negative Mercury Resistant Bacteria Isolated From Contaminated Environments 

Some of bacteria have developed special resistance mechanisms against mercury, in addition to resistant to different antibiotics. These bacteria usually acquire Hg and antibiotic resistance genes via horizontal gene transfer in their habitat

•  Summers says bacterial exposure to metals such as mercury can contribute to antimicrobial resistance because many transferrable plasmids carry genes for multiple types resistance. In other words, in the process of developing metal resistance, a bacterium may also become resistant to an antibiotic it hasn’t even encountered. This is important because the result of our collective microbiomes’ gene transfers may not always be as good for us as they are for our microbiomes, says Les Dethlefsen, a staff scientist at Stanford University

They reported that there is a direct relationship between increased use of herbicides and spreading resistant to mercury in bacterial communities residing in agricultural soils (9). Enhancement of mercury contamination increases antibiotic resistant strains. This is a serious environmental and public health concern in such regions (10-12). Moreover, using mercury-containing products such as disinfectants and amalgam may cause spreading of multiple antibiotic resistance strains in hospitals and human intestine (3, 13)

•  Because mercurial compounds were commonly used as disinfectants in medical settings they selected for Hg resistant bacteria (Porter et al., 1982); in light of such observations, Hg-containing disinfectants were largely replaced by quaternary ammonium disinfectants during the 1980's. By that time, advances in the study of bacterial gene transfer had revealed that plasmids, which are small circles of DNA capable of moving themselves from one cell to another, could carry multiple genes for resistance to several different antibiotics. Plasmids were then revealed to be the major agents mediating the newly recognized spread of antibiotic multiresistance. Many of the first studied plasmids also carried resistance to mercury and organomercury (e.g. merthiolate) compounds genetically linked to the antibiotic resistance loci on these transferrable bacterial plasmids. Consequently, exposure of bacteria to any agent for which their resident plasmid provided resistance would indirectly select (co-select) for all of the other genetically linked resistance loci on that plasmid (Fig. 2). 

More clues from “medical settings”:

•  "Mercury-resistant strains of bacteria became a significant health problem in US hospitals in the late 1960's because organomercurials including Thimerosal were used at high concentrations (10-30 mg/L) in hospital detergents to inhibit bacterial growth.  After the U.S. Environmental Protection Agency prohibited use of mercurials in hospital antibiotic preparations in 1971 the frequency of mercury resistance in bacteria declined.....It has been suggested that the widespread use of Thimerosal in vaccines and various other products for medical use may account for the fact that thimerosal usually produces the highest frequency of positive skin reactions in the general population in dermal patch tests [54]."  http://tinyurl.com/pwjmeux

There are patterns and much research showing that Mercury and specifically, THIMEROSAL, can damage both BRAIN and MICROBIOME. This is a clear example:

Due to the facts that thiomersal-containing vaccine is still in use in many developing countries, and all forms of mercury have recognised neurotoxic, nephrotoxic, and other toxic effects, studies on disposition of ethylmercury and other mercury forms are still justified, especially at young age. Our investigation aimed at comparing mercury distribution and rate of excretion in the early period of life following exposure to either thiomersal (TM) or mercuric chloride (HgCl2) in suckling rats…….. In a recent overview Dórea [20] integrated experimental neurotoxicity studies of low-dose thiomersal in vaccines and concluded that doses relevant to thiomersal-containing vaccines exposure possess the potential to affect human neurodevelopment. A recently published experimental study in thiomersal-exposed infant rats reopens the debate on thiomersal-induced neurotoxic threat showing perturbations in the balance between excitatory and inhibitory amino acids in the brain, shifting it towards excessive neuroexcitation that may lead to neurodevelopmental disorders [21]….. total mercury in TM-exposed group was significantly higher both in blood and in brain than in HgCl2-exposed group…..Concentrations of mercury in small and large intestine given as thiomersal, in spite of being lower than those given as inorganic mercury, show significant enteral mercury excretion. Such data in rodents have not been revealed in the literature so far, especially not at this early age. The latter is in line with finding of increased rate of mercury excretion in infants' stool after parenteral administration of thiomersal during intramuscular vaccination, which lead to an assumption that ethylmercury might be excreted through gastrointestinal system [7]. Our finding of high mercury mass fraction in the small and large intestine of pups proves that endogenous faecal excretion given in the form of ethylmercury or thiomersal is an important route of excretion and it is probably more important than urinary excretion…… Past research confirmed that under same exposure conditions higher mercury retention is found in the gut and the brain of young compared to adult experimental animals

As we see that THIMEROSAL travels to the brain where it can damage, it is interesting to note that it also makes its way to the intestines as it exits the body, through the gastrointestinal system.  It is not difficult to see how the gut bacteria, the MICROBIOME, could be affected.  

The gut-brain-axis of Autism is a devastating reality.



Yes, it's a pretty interesting study, interesting that they focused on one particular type of bacteria, too. So that it seems to me that vaccines need to be tested to see how they affect a pregnant woman's microbiome, and if there is a shift, how long would it take to repopulate the gut with the right strains prior to pregnancy, and during pregnancy. And, of course, not give newborns under six months old any vaccines that are shown to shift the baby's microbiome during that time, maybe even until the blood brain barrier formation is complete (starts at 6 months and goes until around 2), or even until age 3 older, as 85% of brain development happens by the age of 3, or so a certain commercial was mentioning recently, for how much that is worth.

13 year followup trial re: probiotic administration in the first 6 months of life.

"A possible link between early probiotic intervention and the risk of neuropsychiatric disorders later in childhood: a randomized trial"



Thanks Jenny for the link!


13 year followup trial re: probiotic administration in the first 6 months of life.

"A possible link between early probiotic intervention and the risk of neuropsychiatric disorders later in childhood: a randomized trial"



Another weedkiller that likely affects human gut - glufosinate.
Also in some gmos.
"Kills plants by inhibiting the enzyme glutamine synthetase, an enzyme also found in animals including humans.
Several speciies of disease causing fungi are resistant to glufosinate, while a beneficial fungi that parasitizes disease causing fungi is very susceptible to glufosinate. This means that use of glufosinate can have "important microbiological consequences."
Journal of pesticide reform winter 96 vol 16 no 4


I hear you.
If you damage the brain in animals - a few hours to days after they will have GI problems.

The hypothalamus is part of the brain - although very low on the brain stem and it influences the metabolism and which in turn can influence the stomach.

But the stomach can influence the hypothalamus.

Dr. Pol on TV, a vet in Michigan went out to doctor a calf that was not eating, had a lot of gas on his stomach - had the runs.

He found it had a fever and pneumonia. He gave it some antibiotics but also said that it had a nerve that ran from the brain to the stomach and the fever had damaged that nerve. So, it might not be brain injury but just that nerve.

So he gave it a vitamin B 1 shot. Thiamine and said that should help help up that nerve.

Human children I don't think is getting as much care as a calf! Well, that calf at any rate.

And speaking of thiamine - vitamin B 1 - sulfites interfere with the vitamin.



A lawsuit filed in los angeles ca claiming false advertising that glyphosate only targets plant enzyme EPSP SYNTHASE. It is found in the human gut and stomach according to the suit.
Californians can join the suit.


Teresa, one of your references had this:

"One study found that dysbiosis can potentially result from bismuth exposure, commonly found in cosmetics and Pepto-Bismol, when Methanobrevibacter smithii, a normal gut inhabitant, transforms bismuth into a form that is toxic to Bacteroides thetaiotaomicron, a beneficial resident that mediates infant dietary transition from breastmilk to starches, and aids the formation of the intestinal mucosal barrier that protects against pathogens [44▪]. Hence, early-life toxicant exposure could shift the microbial balance, potentially affecting both immune and microbiome development."

So, why then is Pepto-Bismol still on the market?

(page 8)

Tim Lundeen

@Teresa, I agree with what you've written too, all good stuff.

But, we don't know how much aluminum is a factor for the gut. There's some evidence it affects parathyroid, which could affect thyroid and hence affect metabolic rate and the gut. We know it causes inflammation, which will affect the immune system and through that the gut as part of systemic feedback. Aluminum also kills neurons, and if it affects muscle tone and motility in the gut, that will be a major negative.

Carol Willis

In many infections in autism, check also C3 deficiency (C3 gene mutations), and thyroid not optimized to tightest standards.

Teresa Conrick

Hi Tim,

Yes, aluminum is a bad player and much research shows it can cause damage, immune and brain. As far as Microbiome damage though, I find really not much and since my focus is on the Microbiome, I stand by what I have written here.

Tim Lundeen

Thanks, Teresa!

It's not just mercury/anitbiotics, though -- aluminum adjuvants were first used in 1932, so they fit the same timeline as ethylmercury/thimerosal.

Lots of good info at vaccinepapers.com, and there is a ton of other papers. Epidemiology (major increases in autism correlated to aluminum adjuvant usage), toxicology (the alum nanoparticles in a vaccine are engulfed by macrophages and carried throughout the body and brain, causing damage everywhere), and auto-immune consequences.


How many members of the AAP and AMA would ever take the "well baby visit" vaccines / adjusted to their body weight ?

Dr. Marc Siegel again on yet another "tobacco science" MMR study...


Angus Files

Very good article Teresa plenty food for thought.



And as a side note.

Right after this last vaccine reaction for my daughter in 2012 three months later she could not tolerate onions and garlic.

If I was cutting them up she would gag and had a hard time getting her breath.

Now she can eat them if they are cooked first.

She cannot eat Kale either - it makes her throw up

And guess what - I cannot eat raw sauerkraut unless I want my legs and bottom of my feet hurt - just like they do when I eat gluten. How on the earth did this all come about?

So I join the rest of you all on knowing that there are such things as sulfites and sulfates - probably some missing microbe there too.

Probably the same one that helps digest gluten.


They all knew at the time that MERSA started in the hospitals. My gosh, if you read all the research they were even looking at the water in flowers delivered to patients -- But there was already research as in this 1982 paper.

Because mercurial compounds were commonly used as disinfectants in medical settings they selected for Hg resistant bacteria (Porter et al., 1982); in light of such observations, Hg-containing disinfectants were largely replaced by quaternary ammonium disinfectants during the 1980's.


First of all, Thank-you, God, for Teresa Conrick.

I think the Amish do not use chemicals on their farm land, though I could be wrong. I asked the question 7 years ago from someone else and never followed up on my own, though now I wish I would have. If they don't then their families would not be dealing with antibiotic and mercury resistant bacterial (viral/fungal) colonies in their home and farm lives from 1st generation pesticides/fungicides, maybe just fallout from coal burning power plants, possibly preventing the Amish from being as predisposed to autism. Either vector - from contaminated food and land, and vaccines, is of critical importance. And double dipping may be synergistic toxicity.

I think it shows that the problem could happen in one generation, and be greatly compounded in two or more, and the problem will be compounded, because I am sure mercury is not the only source. I suspect Roundup is already there, too, compounding away. Bacteria, like humans, only have a limited number of pathways to deal with an infinate number of toxics.

Need to show whether antibiotic resistance of this nature can be overcome or reversed with specific non-resistance bacterial strains, and how much, and how long would it take, and how many bacterial generations.

Supports the old saying: the germ is nothing without the environment, and Dan/Mark's polio hypothesis.

Could explain why eating organic and Non-GMO is protective or preventative.

Are they toxic by creating VO2max capability polymorphisms that prevent the body from taking up and using oxygen correctly? Have some antibiotics worked by exposing traditionally anaerobic bacteria to low levels of oxygen, which would kill them in the old days, but now they've mutated to withstand and survive in slightly-oxygenated environments?
Is it possible that exercise non-responders have the highest level of these mutated bacteria in their guts and bodies, so much so that exercising actually causes medical problems? Are exercise non-responders with VO2max polymorphisms the same people who have MTHFR SNPs?

If so, can VO2max polymorphisms (or even a blood oxygen reading) be used as an indicator of who will be most likely to suffer adverse reactions from vaccines as well as who will suffer immunologically from antibiotic resistant infections, or whether a person is in a position to survive a vaccine, and are they one and the same population?

Would this imply that the same people who are most likely to get sick from germs are also those most likely to suffer vaccine adverse events. And if one knows that herd immunity from vaccinating healthy people is a disproven hypothesis AND can create antibiotic resistance in each generation leaving people MORE vulnerable to infection, then there is no reason left to vaccinate people. It will hurt people already susceptible (low oxygen), and damage previously healthy individuals by creating an ever expanding generation of susceptibles in an epigenetic progression.

Doesn't it seem like a lot of the biomed non-pharm solutions that revolve around managing and remediating autism and brain damage involve oxygen? Eileen Nicole Simon?

Do any of the 100+ articles generated from the Heritage Study shed any light on this?


When my children were growing up - there was a big concern about doctor prescribing to many antibiotics.

Big Brother of the CDC or NIH or Medical Board kept records of the amount of antibiotics that doctor prescribed.

So that meant that my kids that just kept strep - were delayed treatment and twice they came down with scarlet fever.

And antibiotics were slow to get it all under control even at that.

It just burns me that I found out that Professor Dr. Otero of Eastern Kentucky University - moonlighter of a Merck - big pharma subsidies medical lab - some how got himself involved with the CDC and was sent around to local hospitals to see what could be down for MERSA. And being the smart genius he was he came to the conclusion there was nothing that could be done. And I admired him - What a fool I am.

Bob moffitt

How many members of the AAP and AMA have ANY knowledge of the consequences of altering a child's "Microbiome"? I suspect the answer to that question would be a resounding NONE.

Yet .. the loudest voices "promoting vaccines" are the voices of the AAP and AMA ..

I know I have begun beating this drum of late .. but .. why haven't toxicologists, immunolgists, gastroenterolgists .. who have a far better "scientific" understanding of our aggressive vaccine policies on the child's "microbiome" .. spoken OUT?

Are we to consider them "scientists" .. or .. "cowards"?

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