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Dachel Media Review: Vaccines for Society

The Human Microbiome​: Evolution of Vaccine Exposure

MicrobiomeBy Teresa Conrick

I doubt very much that Edward Jenner, in the late 1790’s, gave much thought to the microbiome of those first patients he inoculated with his “cowpox” vaccine.  Fast forward to 2014 and the same may be true of the billion dollar companies making vaccines today.  How is that possible?  What is the microbiome? -- “A microbiome is "the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space."[1][2] This term was originally coined by Joshua Lederberg, who argued the importance of microorganisms inhabiting the human body in health and disease. Many scientific articles distinguish "microbiome" and "microbiota" to describe either the collective genomes of the microorganisms that reside in an environmental niche or the microorganisms themselves, respectively.[3][4][5] However by the original definitions these terms are largely synonymous.”

It is becoming one of the most important pieces to health in our modern society though much is still unknown, yet more and more research is showing the microbiome to be a litmus test in health, for example:

Microbiome changed by gluten increases incidences of type 1 diabetes

Date: November 13, 2013

Source: Mayo Clinic

Summary: Research has shown that the intestinal microbiome plays a large role in the development of type 1 diabetes……….These researchers demonstrated that mice fed a gluten-free diet had a dramatically reduced incidence of Type 1 diabetes. These mice were non-obese diabetic mice, or mice that grow to develop Type 1 diabetes. The gluten-free diet worked to protect the mice against Type 1 diabetes. When the researchers added gluten back into the diets of mice it reversed the protective effect the gluten free diet had provided. There also was a measurable impact of the gluten on the bacterial flora of the mice that might be one way in which gluten could affect the risk for diabetes.

Very interesting and shows how important the gut and bacterial flora are in maintaining health. Gluten is an important factor in autism and many children just can’t eat it as painful symptoms and negative behaviors begin.

We are seeing epidemic numbers of immune and autoimmune diseases.  Autism is one of them and I will add in that PANDAS, Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections and PANS, Pediatric Acute-onset Neuropsychiatric Syndrome, are also climbing these past years.  They share characteristics and many families have both autism and PANDAS/PANS, diagnosed children. Some of those children have both diagnoses, like my daughter, Megan. Why?

In the definition above, "microbiome" and "microbiota" are “largely synonymous”, so let me introduce a recent study that reflects how the microbiome and microbiota can be involved in vaccination.

This study is on the CDC website:

Volume 20, Number 2—February 2014


Seven-Valent Pneumococcal Conjugate Vaccine and Nasopharyngeal Microbiota in Healthy Children


Seven-valent pneumococcal conjugate vaccine (PCV-7) is effective against vaccine serotype disease and carriage. Nevertheless, shifts in colonization and disease toward nonvaccine serotypes and other potential pathogens have been described. To understand the extent of these shifts, we analyzed nasopharyngeal microbial profiles of 97 PCV-7–vaccinated infants and 103 control infants participating in a randomized controlled trial in the Netherlands. PCV-7 immunization resulted in a temporary shift in microbial community composition and increased bacterial diversity. Immunization also resulted in decreased presence of the pneumococcal vaccine serotype and an increase in the relative abundance and presence of nonpneumococcal streptococci and anaerobic bacteria. Furthermore, the abundance of Haemophilus and Staphylococcus bacteria in vaccinees was increased over that in controls. This study illustrates the much broader effect of vaccination with PCV-7 on the microbial community than currently assumed, and highlights the need for careful monitoring when implementing vaccines directed against common colonizers.

Let’s look at that more closely.  First off, it is a study of 97 vaccinated (PCV-7) and 103 unvaccinated (No PCV-7) children.  The study does not mention it but the name of the vaccine is Prevnar-7/Prevenar .  What the authors do mention, in quite a bit of detail, is that those children vaccinated had a shift in their microbiota. Here’s what the authors shared in the meat of this study:

“Vaccines show effectiveness against vaccine-serotype disease, nasopharyngeal acquisition of pneumococci, and pneumococcal transmission. However, nonvaccine pneumoccal serotypes fill the vacant nasopharyngeal niche, leaving overall pneumococcal carriage similar or only temporarily decreased (5,6) and lead to a gradual increase in nonvaccine serotype disease (7)….. Colonization is a dynamic process of interactions among microbes and between microbes and the host and result in balanced bacterial ecosystems that benefit health. Perturbations of these interactive microbial structures (e.g., by environmental change or vaccinations) alter the bacterial network structures and may thereby influence the presence and containment of other microbiota members, and these alterations have effects on health and susceptibility to disease (13,14).”

……. Vaccination with PCV-7 resulted in a shift in bacterial community composition and structure, with an increase in presence or abundance of several anaerobes, such as Veillonella, Prevotella, Fusobacterium, and Leptotrichia species; gram-positive bacteria, such as Actinomyces and Rothia species, and nonpneumococcal streptococci; and gram-negative Neisseria species.”

The authors’ WARNING:

“…we observed an increase in culture-proven S. aureus carriage in the original randomized controlled trial (18), as well as further increases in culture-proven S. aureus and H. influenzae carriage observed in surveillance studies 3–5 years after PCV-7 implementation in the Netherlands (8). These findings are consistent with negative associations between S. pneumoniae (particularly PCV-7 serotypes) and S. aureus (33,34) and H. influenzae (35–37) observed in healthy nonimmunized children. Nontypeable H. influenzae and S. aureus were also more frequently isolated from persons with acute otitis media after introduction of PCV-7 in national immunization programs (38–40), which indicates that carriage may reflect disease dynamics. Together with S. pneumoniae nonvaccine serotype replacement, these effects may further jeopardize the net health benefit of vaccinations with PCV.”

To sum this up:

   --   A vaccine was created with 7 types of bacteria strains it was to fight.  It has done that BUT there are many negative consequences.

   --    A more than minor shift happened in the bacteria composition of the microbiota, revealing more pathogens, more ear infections and unknown consequences.

   --    “Surveillance studies 3–5 years after PCV-7 implementation in the Netherlands (8),” revealed that not only were the vaccinated children affected but the parents as well  - “In addition to large shifts in pneumococcal serotypes, persistently higher nasopharyngeal prevalence rates of S. aureus and H. influenzae were observed among young children and their parents after PCV-7 implementation. These findings may have implications for disease incidence and antibiotic treatment in the post-PCV era.”

         --      A gradual increase in nonvaccine serotype disease.

         --      Short-term and long-term surveillance during health and disease seems important in understanding the full implications of vaccine-induced changes in microbiota structure.

--    “Because infants might be vulnerable to community disruptions and dysbiosis”, the authors recommend that new trials, “such as studies on efficacy of broader pneumococcal coverage vaccines, consider the effect of vaccination on the commensal flora in its totality instead of only on a single species.”

           --     In a nutshell, PCV (Pneumococcal conjugate vaccines) may cause more harm than good - ie “these effects may further jeopardize the net health benefit of vaccinations with PCV.”

AAP in New Jersey did a powerpoint last year  on this very subject.  They seem to understand these consequences but included many other possible sources.  They were very lite on the vaccination issue and never mentioned mercury, something I had reported on earlier . Two of their slides show hints yet they are still not totally connecting the dots:



-“The menace of antibiotics” – Martin Blaser, IDSA

- Urbanization

- Rapid global mobility

- Type of diet: processed; animal fats vs. carbs

- Sanitation/hygeine

-Child care

- Vaccines (pneumococcus vs. staph)



- Tripling and quadrupling of various diseases post World War II


- IBD, obesity/metabolic syndrome, autism, celiac, autoimmune disease, C. difficile

- Could alterations of our microbiome be responsible?

Let’s repeat that last one - “Could alterations of our microbiome be responsible?” YES , much research is showing that yet where is the alarm?

So we see CDC and AAP acknowledge this scientific significance yet how long has this concern been known?

Effect of Seven-Valent Pneumococcal Conjugate Vaccine on Staphylococcus aureus Colonisation in a Randomised Controlled Trial, Published: June 10, 2011   - “We found, even after a reduced primary dose PCV7-schedule with 2 instead of 3 primary vaccinations before the age of 6 months, a temporary but distinct 2-fold increase in S. aureus nasopharyngeal colonisation in PCV7 vaccinated infants at 12 months of age shortly after receiving a booster dose. This means that for every 20 children vaccinated with PCV7, 1 extra child is colonised with S. aureus in the nasopharynx……Increased S. aureus colonisation at a vulnerable age may have clinical consequences.”

Clinical consequences?  That was three years ago.  More alarming, here is another study conclusion from TEN years ago but with a different spin:

“Since 2004, the invasive pneumococcal disease rate caused by nonvaccine serotypes has increased 140% compared with the prevaccine period……. Alaska Native children are experiencing replacement invasive pneumococcal disease with serotypes not covered by heptavalent pneumococcal conjugate vaccine. The demonstration of replacement invasive pneumococcal disease emphasizes the importance of ongoing surveillance and development of expanded valency vaccines.”

What that means is that these children were developing numerous infections capable of causing increased diseases AFTER receiving the PCV-7 vaccine.  They even gave it a fancy name - “ replacement invasive pneumococcal disease with serotypes not covered by heptavalent pneumococcal conjugate.”   Their conclusion was to create more vaccines to then kill more of these strains. It was a CDC funded study.

So far there are four vaccines on the market targeted at pneumococcal diseases:

•        Prevnar, contains the cell membrane sugars of seven serotypes of pneumococcus, conjugated with Diphtheria proteins.

•        Synflorix is a decavalent vaccine, meaning that it contains ten serotypes of pneumococcus.

•        Prevnar 13 is a tridecavalent vaccine, meaning that it contains thirteen serotypes of pneumococcus.

•        Pneumovax® is 23-valent polysaccharide vaccine (PPVSV23) that is currently recommended for use in all adults who are older than 65 years of age and for persons who are 2 years and older and at high risk for disease. 

Listed by CDC.

There are over ninety serotypes of pneumococcus  .  Is the plan to create vaccines to kill them all because as we are seeing, that idea has some rather dangerous ramifications?  While it is a noble idea to try and stop cases of pneumonia or pneumococcal meningitis, the reality is that there seems to be a horrendous domino effect, “This analysis suggests that a PCV vaccination programme would eradicate vaccine serotypes from circulation. However, the increase in carriage of non-vaccine serotypes, and the consequent increase in invasive disease, could reduce, negate or outweigh the benefit.”

The Bill and Melinda Gates Foundation also seems interested in this research:

Vaccination is likely to have important consequences for the NP microbiome. Current pneumococcal vaccines are directed against multiple serotypes thus potentially eliminating these from the microbiome.  Based on observations on this and other vaccines, new organisms are expected to move into the empty niches created by vaccine elimination of organisms. Thus the structure of the microbiome is altered by vaccines. The unintended consequences of this alteration remain to be seen.

It seems very possible that if the microbiome takes a hit, like mercury exposure or immune manipulation via vaccination, the more we may see the immune system diseases rapidly rise.  Autism and PANDAS/PANS and other immune-damaged diseases deserve huge concern and true research.Coldplay has some good lyrics in their song, Clocks and the message and the ticking of time seems pertinent here:

….. And a trouble that can't be named

…..Am I a part of the cure?

Or am I part of the disease? Singing

You are

You are

You are

You are

Teresa Conrick is Contributing Editor to Age of Autism and has authored a series on the Microbiome that is available in the AofA exlclusives.



A couple of excerpts from an article on today touching on staph & superantigens and inflammation/cytokeins, so if you have a vaccine that could possibly tip the microbiome balance increasing the presence of staph in the body it demonstrates what the fallout could be:

Chronic inflammation in your gut can disrupt the normal functioning of many bodily systems. There also appears to be a connection between certain types of bacteria and body fat that produces a heightened inflammatory response and drives the inflammatory process.

For example, recent research1 suggests that superantigens—toxic molecules produced by pathogenic bacteria such as staph—may play a role in the development of type 2 diabetes through their effect on fat cells. As reported by the featured article:2

“The idea is that when fat cells (adipocytes) interact with environmental agents -- in this case, bacterial toxins -- they then trigger a chronic inflammatory process... [B]acterial toxins stimulate fat cells to release molecules called cytokines, which promote inflammation...

All staph bacteria make toxins called superantigens -- molecules that disrupt the immune system. Schlievert's research has previously shown that superantigens cause the deadly effects of various staph infections, such as toxic shock syndrome, sepsis, and endocarditis.

... [T]he chronic inflammation caused by the superantigens may also hinder wound healing in diabetic foot ulcers. The ulcers, which affect 15 to 25 percent of people with diabetes, are notoriously difficult to heal and can often lead to amputation.” . . .

Perfect Storm' of Inflammation Promotes Diabetes

Previous research has shown that obese people have different intestinal bacteria than slim people. Lean people tend to have higher amounts of various healthy or beneficial bacteria compared to those who carry a lot of excess weight, who tend to have greater colonization of pathogenic bacteria.

For instance, the human adenovirus-36 (Ad-36) -- a cause of respiratory infections and pinkeye – might play a role in promoting obesity by transforming adult stem cells into fat cells that are capable of storing additional fat.

Researchers have also discovered that certain gut bacteria, including Staphylococcus aureus (staph) and E. coli, trigger fat cells to produce inflammatory cytokines. Researchers have proposed that this interaction can provoke the development of diabetes, which is a well-known “side effect” of obesity.

Staph bacteria in particular appear to play an important role in diabetes, and according to the featured article, there are two primary reasons for this:

Obese people have a tendency to become heavily colonized with staph bacteria
Staph bacteria is the most common bacteria found in diabetic foot ulcers
The featured study found that when both staph and E. coli are present (both of which produce superantigens), the inflammatory cytokine response in fat cells are further amplified, thereby boosting your risk of diabetes. According to the co-author of the study, Patrick Schlievert, Ph.D:

"The E. coli that resides in our gut produces LPS [lipopolysaccharide, a toxin] and every day a small amount of this toxin gets into our circulation, but it is generally cleared from the circulation by the liver. However, people colonized by staph bacteria are also chronically exposed to superantigens, which shut down the LPS detoxification pathway.

That creates a synergy between the 'uncleared' LPS and the superantigen. All these two molecules do is cause inflammation and cytokine production. So in essence, their presence together creates a perfect storm for inflammation."

Previous studies have come to similar conclusions. For example, one study3 found that babies with high numbers of bifidobacteria (beneficial bacteria) and low numbers of Staphylococcus aureus, appeared to be protected from excess weight gain.

This may also be one reason why breast-fed babies have a lower risk of obesity, as bifidobacteria flourish in the guts of breast-fed babies.

end of excerpts
Next question: is it only a pneumonia vaccine that could cause such a shift?

So what if a vaccine during pregnancy could end up shifting the mom's microbiome? . . .
So what if a vaccine on day one of life ended up shifting the newborn's microbiome? . . .
So what if multiple vaccines at once could shift the biome? . . .
So what if kindergarten vaccines could shift the microbiome?
What happens if middle school shots shift the microbiome?
High school shots?
College entry shots?
Flu shots at any age?
Senior citizens?

How does a mercury filling in the mouth change the microbiome in the gums, periodontal, stomach/blood, etc?


Ruminococcus is under the order of Clostridium which is the same as the dreaded C diff -that we all are familiar with. It is also in the same order as the tetanus we get vaccinated for.
What could that mean? If anything.


Linda; I did breast feed mine. I suppose they could have been worse, but my own microbiome might have been messed up. I did receive a tetanus shot in my early 20s that was in fact a DPT shot - and shortly after for the first time I developed a yeast infection.

Before that happened though -- I helped my professor do his labs for his research and publishing on his paper of the metabolism of yeast -- - back in the 70s yeast infection suddenly became a major problem and research in that area was well received for anything on it was published easily.

Sutterella from what I am reading is very hard to get to grow outside the gut. Very hard to culture.

"Sutterella spp. and some other mucosa-associated bacteria linked with gastrointestinal disease (Ruminococcus gnavus and Ruminococcus torques) are also altered in the stool of these children."

So, it begins -- they are adding more types of bacteria that are growing in ASD children.

I will say that after I finished my degree in microbiology -- The week before graduations -- we all stood around out in the hall and - everyone felt we knew nohting. One said she was going back for her Masters, and then maybe she would feel like she knew more. She didn't.


Great article Teresa. Your comment brought to mind that secretory IgA in breastmilk lines the baby's GI tract all the way through, acting as a barrier to invasion and setting up and maintaining normal flora. This study published this year indicates that the protection may be life long:

"Secretory antibodies in breast milk promote long-term intestinal homeostasis by regulating the gut microbiota and host gene expression

An experimental system was developed in mice to study the long-term benefits of early exposure to secretory antibodies of the IgA class (SIgA) in breast milk. We found that breast milk-derived SIgA promoted intestinal epithelial barrier function in suckling neonates, preventing systemic infection by potential pathogens. Long-term benefits of early exposure to SIgA included maintenance of a healthy gut microbiota and regulation of gene expression in intestinal epithelial cells. These findings suggest that maternal antibodies provide benefits to the intestinal immune system of the breast-fed infant, which persist into adulthood."

Teresa Conrick


Thanks for your comments. The question about Gad65 and also speciic details on asd kids and microbiome differences still needs much more exploration. This one though from Mady Hornig adds some clues:

"One mechanism by which changes in the microbiome may alter the CNS is through the bacterial production of harmful products that compromise the integrity of the epithelial barrier of the intestine, allowing entry of bacterial products or proteins with neuroactive properties into the circulation. Consistently with the potential contribution of the microbiome to the pathogenesis of neuropsychiatric disturbances, children with ASD were found to have elevated urinary levels of p-cresol (4-methylphenol), an organic compound produced by gut bacteria that contain the enzymes for its synthesis but that can also occur as an environmental contaminant.[41] A study[42] from our group identified a rarely reported microbe, Sutterella, in the adherent microbiota of the ileum and cecum of ASD children with gastrointestinal disturbances and a high rate of behavioral regression, but not in age-matched and sex-matched gastrointestinal control children. These children also have deficiencies in the expression of disaccharidase and glucose transporter genes in the gastrointestinal tract, along with abnormal representation of bacteria in their microbiota.[43] Although the contribution of these abnormalities to behavioral disturbances is unknown, abnormal patterns of intestinal microbiota are also observed in autoimmune diseases such as Type 1 diabetes."

Jeannette Bishop

Is there a similar "fermentation" process that normally aids human digestion that some "antibiotics" (ethylmercury) might hinder, changing pH, altering gut flora composition and disposition, disrupting the digestive process in one or more stages?

Jeannette Bishop

I heard something a few days past about grass fed vs. corn fed beef, something to the effect that corn changes the pH of the cow's stomach closer to that of the human stomach leading to adapted strains of e-coli that can survive in the human digestive tract.

Pertinent discussion @ 54:13-57:00 (interview begins at 39:18).

This has me thinking of what pH changes might be caused by Hg, Al, etc and what effect that might have on the gut flora, what survives, what might be adapting, etc?


Wow! Thank you Teresa. I wonder if GAD65 antibodies are at play in the type 1 diabetes/gluten association.

But to the rest, it describes my son to a T. C - section birth, shots at 2,4 and 6 months, then less than a month after his 6 month shots, he developed an ear infection that lasted the better part of over a year. 11 antibiotics in an 18 month period. We held off the rest of his shots till he was 3 years old. Then he got 6 catch up vaccines in one go and two days later, he was gone.


Thanks Teresa for bringing this to our attention.
I sent several copies to family and friends all who have recently had children ending up in the ER and to their surprise it was diabetes.

Jeannette Bishop Those are good questions -- I guess we have to stay tuned in - meanwhile -- I guess I will strain my keifer and keep on keeping on to everyone to avoid gluten.

Jeannette Bishop

Does the research showing different genetic expression in the guts of some with autism possibly suggest some kind of connection to these alterations in the microbiome?

Jeannette Bishop

Oh look, hey, we've changed something with a vaccine! And we don't know all the side effects, and we don't know if things are better, some could probably argue things are worse (we would never go there), but let's keep on keeping on! We might learn something! Have new problems calling for more vaccines! Sell probiotics along with all our antibiotics! Oh yeah, how're we coming with the newer antibiotics for these new, increasingly antibiotic-resistant bacterial strains? Anything that works?


Sutterella does not break down carbohydrates.
Sutterella does not produce succinate.


When I was small I use to read a lot of science fiction especially Alan Nourse's books because those were what the public library had on hand.

Alan Nourse was doctor (I think) or at least had some medical training. In his book "Star Surgeon (1959)" Doctors were sent out from Hospital Earth to doctor the sick in the entire galaxy.

Hospital Earth -- To think we could bring all of this mess to the entire galaxy.

Or medical heroes were called to a planet of intelligent human looking apes, and after examining them with their fancy equipment -they decided they were being made sick by a virus.

They then put them inside a machine that could rid the body of certian microbes in the body, dumping it on a grate at the bottom of the machine. They had the apes step into this grate by the 100s.

After the treatment they noticed that something was now wrong. The apes had stopped speaking, had a vacant look in their eyes, was not responding.

Turns out it was the virus that was intelligent and it was the virus that needed help since the host's immune system had began to attact the virus.

In the end the space doctors helped the intelligent virus by depressing the immune system of the apes.

Far fetched story -- but even a science fiction writer did not have enough imagination to consider ALL what could happen when you mess with microbes. When you leave a space ((niche) open from getting rid of one microbe -- what will it be replaced by -- a microbe that is yet another pathogen -- for strep throat, ear infections --

or something worse -- the vaccine not only targets pathogens but good bacteria too. Good bacteria then being replaced by a harmless microbe, but still does not do the job that is needed; Like breaking down carbohydrates and turning them into vitamin Bs or into something called succinate - the same thing that couples with Co enzyme Q 10 in energy produciton-- to capture electrons all occurrying in our mitochondria esp, in the complex 1-- which effects complex 3. It does not got to 1 then 2 then 3 then 4.

Not breaking down carbohydrates in the stomach by these bacteria could even allow too much unused food laying around thus causing an overgrowth of fungus - -and that may not kill us, but is not comfortable either.

Or maybe -endless maybe - endless.

Joy B

This is the type of thing that should be breaking news on CNN, but isn't. Instead, we have the entire media spectrum, from the corporate to the pajama-clad 'activist', all shouting down what has been spun as 'anti-science quackery'. In the more educated sectors of America, it's simply lumped in with Creationism and Holocaust denial, the lone 'fact' being that there was this guy who tried to prove it and was found to be a fraud...or something.

Sometimes I think there is hope but today is not one of them.


Great article/great references. Thanks for using your brain to help others, Teresa.

It almost implies that the pneumococcus strains could actually be critical in controlling staph. And staph & other bacteria are becoming antibiotic resistant. So prevnar may be contributing to the increase in deaths from staph infections, no? Let's see a graph showing, for instance, reported MRSA numbers, compared to when prevnar hit the markets, and then when the increased strain prevnar came along. What is the net effect of lives saved, hospitalizations prevented when it's all put together.

And w/the gluten, again, if that shifts the microbiome (and affects hormones), and vaccines shift the microbiome also, our society would have had a double hit in both the early 1900's and then again in the 1980's (when wheat was cross bread both times increasing the gluten content) putting it in the same place in history the advent of vaccines & mercury pesticides (pesticides cause microbiome shifts themselves) and at the same time as the increased mercury load in the HEP B vaccines.

 Bob Moffitt

It is hard to accept the reality that .. for at least ten years .. credible .. though reluctantly reported .. scientific research .. began raising numerous warnings regarding the "unknown consequences" regarding vaccines .. as they impact what science determined to be the microbiome .. described as "the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space."

What in God's name will it require before the "scientific community" .. now fully armed with dire warnings regarding the fragile state of the human microbiome .. finally begins exercising their "precautionary duty" .. to "do no harm" .. as they relate to the ever increasing numbers of vaccines recommended and approved for children .. during the most critical stage of their physical and nuerological development?

This is pure "scientific maddness run amok".

John Stone


Most interesting. 'Primum nocere' seems to be the motto. Somewhat bears on Sandy Gottstein's epic battle with Dorit Reiss in Anchorage Daily News.


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