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Are Vaccines Changing the Microbiome of Mankind?

MicrobiomeNote: Teresa Conrick has written a series of articles on the Microbiome.  You can read them here in our AofA Exclusives.

By Teresa Conrick

Vaccines.  The idea of them seems so good.  Inject a recipe of chemicals into human beings and animals, and they are then protected from microbial-causing diseases. The reality though for many families is something went wrong, either immediately after vaccination - seizures, death, or from that point forward, profound changes in health and development - REGRESSION.

My daughter, Megan, had subtle, regressive episodes after each vaccination but devastatingly so after her MMR vaccine. Immediately, Megan began with a fever for days, then a full body rash starting on the 10th day, diarrhea, constipation, then undigested food in her stool, then Giardia and Blastocystis Hominis infections, gluten and casein intolerance developed, nonstop ear infections (otitis media), concurrent Candida infections, Clostridium infections, Streptococcus infections, seizures when puberty hit and most recently, an autoimmune diagnosis. An autism diagnosis was placed on her before age three, based on the behaviors -- that in hindsight -- most likely manifested from all of these infections and a dysfunctional immune system. This has been the pattern and research is pointing to the microbiome as quite possibly, the epicenter of autism: NEJM, January 28, 2014, “More Evidence Links Gut Microbiome to Autism:”

If this mouse model of autism truly reflects pathology similar to autism in humans, these researchers might have identified yet another major human illness that is linked to the gut microbiome. Moreover, the identification of two specific metabolites that induce autistic behavior could provide molecular targets for therapy. Finally — although it seems too good to be true — the suggestion that probiotic therapy might cure autism surely would be a remarkable event if it proves to be valid.

I continue to investigate research on the microbiome as there are patterns that seem connected to autism and other increasing diseases that share a dysfunctional microbiome.  While investigating the microbiome, it’s important to look back into history and see that the birth of autism in the 1930’s, happened exactly when ethyl mercury vaccines and ethyl mercury pesticides/fungicides were debuting. The family history of eight found families of those first eleven reveals a toxic connection, especially mercury, and significantly the newly commercialized, ethyl mercury. Those factors  remain the most important clues for us today.

Reading about the microbiome has shown some connections that may be influencing it in a negative manner. Antibiotics used in our food supply; mercury in the environment, food and medicines; pesticides; and vaccination, all seem capable of causing insidious changes in the microbiome. Research Is showing some vaccines seem capable of causing an unintended development. I wrote about some of this before but think it’s important to include old information with new to make it more evident.

Trading ChickenPox for Shingles?   Here are live attenuated viral vaccines which show evidence of causing Shingles (Herpes Zoster) to both older folks and children actually getting the Chicken Pox (Varicella) vaccine or the Shingles vaccine or from being exposed to someone who received the vaccine. From the NYT in 2005 :

But even as the vaccine protects children, questions are arising about whether its use will increase the incidence of a related disease, shingles, in adults....The concern arises from a hypothesis, backed by some evidence, that exposure to children with chickenpox helps increase adults' immunity to shingles, which is caused by the same virus. With far fewer children contracting chickenpox because of the vaccine, that effect would vanish, and adults, who have by and large, not been vaccinated, would be at greater risk of shingles.

And here is data, done in 2005:

Between 1998 and 2003, varicella incidence declined from 16.5/1,000 to 3.5/1,000 (79%) overall with ≥66% decreases for all age groups except adults (27% decrease). Age-standardized estimates of overall herpes zoster occurrence increased from 2.77/1,000 to 5.25/1,000 (90%) in the period 1999–2003, and the trend in both crude and adjusted rates was highly significant (p < 0.001). Annual age-specific rates were somewhat unstable, but all increased, and the trend was significant for the 25–44 year and 65+ year age groups.

Yes, here is an adult:

Herpes zoster caused by vaccine-strain varicella zoster virus in an immunocompetent recipient of zoster vaccine. (2014)

But, also, here is a child:

Herpes zoster after varicella-zoster vaccination

A five-year-old girl, vaccinated against varicella-zoster virus (VZV) presented with clinical symptoms of herpes zoster in the 6th cervical dermatome. A VZV direct immune-fluorescence assay was negative three times but additional genotypical analysis showed a VZV strain genotype 2 (Oka vaccine strain). Therefore the diagnosis of a breakthrough varicella disease with the vaccine strain was established……

The Shingles vaccine, the one many adults are getting, appears to have the ability to shed:

Varicella Zoster Virus DNA at Inoculation Sites and in Saliva After Zostavax Immunization (2011)

Analysis of 36 individuals over age 60 years who were immunized with Zostavax revealed varicella zoster virus (VZV) DNA in swabs of skin inoculation sites obtained immediately after immunization in 18 (50%) of 36 subjects (copy number per nanogram of total DNA, 28 to 2.1 × 106) and in saliva collected over 28 days in 21 (58%) of 36 subjects (copy number, 20 to 248). Genotypic analysis of DNA extracted from 9 random saliva samples identified vaccine virus in all instances. In some immunized individuals over age 60, vaccine virus DNA is shed in saliva up to 4 weeks….

Another vaccine I reported on that showed evidence of microbiome changes:

Seven-Valent Pneumococcal Conjugate Vaccine and Nasopharyngeal Microbiota in Healthy Children (2014) 

“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…. Together with S. pneumoniae nonvaccine serotype replacement, these effects may further jeopardize the net health benefit of vaccinations with PCV.”

So again, we see a consequence that in the long run may show no benefit and possibly harmful consequences to Man.

Recently, I came across a third vaccine that also seemed to fit this pattern of causing a shift in the microbiome:

Live Attenuated Influenza Vaccine Enhances Colonization of Streptococcus pneumoniae and Staphylococcus aureus in Mice (February, 2014)

Community interactions at mucosal surfaces between viruses, like influenza virus, and respiratory bacterial pathogens are important contributors toward pathogenesis of bacterial disease. What has not been considered is the natural extension of these interactions to live attenuated immunizations, and in particular, live attenuated influenza vaccines (LAIVs). Using a mouse-adapted LAIV against influenza A (H3N2) virus carrying the same mutations as the human FluMist vaccine, we find that LAIV vaccination reverses normal bacterial clearance from the nasopharynx and significantly increases bacterial carriage densities of the clinically important bacterial pathogens Streptococcus pneumoniae (serotypes 19F and 7F) and Staphylococcus aureus (strains Newman and Wright) within the upper respiratory tract of mice. Vaccination with LAIV also resulted in 2- to 5-fold increases in mean durations of bacterial carriage. Furthermore, we show that the increases in carriage density and duration were nearly identical in all aspects to changes in bacterial colonizing dynamics following infection with wild-type (WT) influenza virus. Importantly, LAIV, unlike WT influenza viruses, had no effect on severe bacterial disease or mortality within the lower respiratory tract. Our findings are, to the best of our knowledge, the first to demonstrate that vaccination with a live attenuated viral vaccine can directly modulate colonizing dynamics of important and unrelated human bacterial pathogens, and does so in a manner highly analogous to that seen following wild-type virus infection

As you can imagine, the researchers were bombarded with negative letters and feedback.  They reported that THE VACCINE DID WHAT IT WAS INTENDED TO DO BUT THERE WERE UNINTENDED CONSEQUENCES:

While care should be taken to not overgeneralize the data described here to all vaccines, the broad implications suggest that live attenuated viral vaccines may have unintended consequences on important human bacterial pathogens unrelated to the vaccine target species. Furthermore, our findings suggest a role for laboratory models of multispecies interactions with vaccine strains to inform future vaccine monitoring and evaluation programs aimed at identifying thus far entirely unrealized “unconventional” effects, both beneficial and detrimental, of live attenuated viral vaccines and cross-species microbial dynamics.

This was science and the authors deserve praise for pursuing it, as there is controversy.  Ethics and morals are getting too rare these days and this is a great example of gaining faith in the scientific method and in the research community.   These researchers then had to defend their work:

Reply to “No Clinical Association of Live Attenuated Influenza Vaccine with Nasal Carriage of Bacteria or Acute Otitis Media”: Specific Recommendations for Future Studies (May, 2014)

….given the strong emphasis of vaccine research on individual recipients, no trial has assessed the potential impacts of immunization on contacts of vaccine recipients with regard to a pathogen that is distinct from the vaccine target pathogen…. bacterial carriage begets bacterial transmission, and even relatively small increases in bacterial carriage density may increase bacterial transmission to bystander individuals (10, 12), a finding that has been shown in numerous mouse and ferret models of pneumococcal transmission (10, 13), as well as in studies looking at transmission of other pathogens (14, 15)…… In the context of LAIV, one could envision a situation whereby a vaccinated individual with elevated bacterial carriage titers may not himself or herself be susceptible to bacterial disease but instead may act as a reservoir for increased transmission. Such a scenario might be particularly important, for example, between young children and grandparents or other elder individuals already having increased susceptibility to pneumococcal disease (12)…

Current vaccine safety programs aim to ensure protection at the individual level, in particular, to confirm that vaccination causes no enhanced susceptibility to the pathogens targeted by vaccination and that vaccination has no immunologically relevant adverse events. Given the increased awareness of, and ability to understand, multispecies pathogen interactions within the host (which are often mediated by host immune processes), it is incumbent upon us to consider not only individual-level pathogen-specific vaccine safety and efficacy but also unintended consequences of vaccines on the dynamics of unrelated pathogens.

As we learn more about the microbiome and its integral part on health and disease, we can see how these pieces are beginning to all connect. Viruses can affect bacteria and as beneficial bacteria change, there is a domino effect and pathogens can take over. If toxins from our manmade world can do this, we can stop it by changing the process and then the outcome. The immune system of Mankind should be handled with more care.

Teresa Conrick is Contributing Editor to Age of Autism.



Is it possible all modern humans in developed countries are now severely damaged? Only those who did not vaccinate, no antibiotics, and who were breastfed, and who were not a C-Section, and who were fed organic vegan food their entire lives, minus the glyphosate, only they have a future? The humans in the primitive parts of the world will be fine though.

I am 49 years old and vaccine damaged ever since MMR at age 24 (chromic fatigue syndrome and a bunch of other gut issues, my limbs went numb after the shot). Because of how that vaccine damaged me as well as the childhood vaccines (I had chronic ear problems in childhood and severe social anxiety), I did not vaccinate my two boys (age 9 and 4), I breastfed both for almost 4 years, I feed them organic vegan and raw foods, and they are not circumcised and had natural births. My first boy was diagnosed with autism at age 4 because I believe my damaged body and microbiome dumped all sorts of toxins on him. Dr. Klinghardt says if ONLY your first child is born with autism, it is due to mercury dumping of the toxic mother. My second boy does not have autism. Both boys are very healthy. I treated his autism with organic whole food vegan raw diet and probiotics, good vitamins, and my 9 year old first son barely has autism any more. No gluten! I did not do any speech therapy. He couldn't speak much at 4 but now he speaks pretty well and his behavior is normal with some autistic personality traits like myself. Anyways I have both boys on the Nemecheck protocol which feeds the good bacteria because interestingly enough I found out I have SIBO (my damaged microbiome), and this is what Dr, Nemecheck says is the cause of susceptible children getting autism. I was floored! I had been battling SIBO for 2-3 years before I read his book. Anyways I want to share this information because my 9 year old son keeps getting better and less autistic. I hope this information helps others.

Oh I am also so damaged, I follow a vegan keto organic diet with probiotics, no gluten! I make fermented probiotic foods for all of us ( Body Ecology is a site for this), and I'm working on healing the gut, candida, sibo and removing the mercury toxicity which may be the root cause of severe systemic candida. So even us adults who are vaccine damaged can get better, or at least live a normal life with diligence on the diet, exercise, sunlight. We have had our health destroyed by the vaccines and antibiotics as well as our SAD childhood diets fed to us by our parents, but If we become saints with our diets NOW, heal the gut, restore the microbiome and remove the toxins, we can reclaim most of what they destroyed. Basically your gut microbiome wants you to eats salads. My dad was also damaged by the modern world, diet, vaccines, pesticides, antibiotics and died of dementia at age 78, but he didn't do anything to try and save himself, and so he died horribly when he could no longer swallow. The medical establishment has no help for us, we have to help ourselves.


Hi Autism Mom,
I don't know about that article. They only studied about 50 preemies of various gestation ages and were looking to find what is normal flora for each age, and it seems they think they found "the" normal healthy pattern. Dr. Allen-Vercoe working in the Human Microbiome Project and who recently presented at the Arkansas Children's Hospital Conference, made the point that while there are similarities among people, that each person's microbiome is completely unique. She also said that it's very hard to know what is "normal" because of antibiotic use and other agents that affect flora. I doubt that many of these preemies did not have some antibiotic exposure. The article also says that babies are born sterile, when Dr. Allen-Vercoe stated that it is now known that the placenta has its own microbiome and that babies are inoculated in utero. The part in the article about how breastfeeding and antibiotics don't affect flora development just doesn't sound right. Talking about the normal flora of a healthy preemie - there is nothing normal about being outside the womb at 30 weeks gestation! Also, how could they really know if the study babies weren't impacted by the environment that they were born into and if the study results would be duplicated in other centers as far as type, quantity and timing of flora?

Jeannette Bishop

Thank you. There seems to be indication that vaccine components can adversely disrupt immune function and/or the avoidance of a natural infection process might be behind at least some adverse outcomes. There's not enough incentive perhaps in the medical-governmental-industrial complex to determine if vaccination actually prevents what we generally think of as disease, or mortality and morbidity, but the rest of us, IMO, can't afford to not answer that question.

autism mom

I just recieved this interesting article from
"The Scientist" about how the gut microbiome is colonized during infancy...

"Gut’s Earliest Bacterial Colonizers" -The pace at which bacterial groups take root in the gastrointestinal tracts of premature infants is more tied to developmental age than time since birth."

autism mom

I think its a combination of antibiotics + vaccines + pesticides + antimicrobials (that coat kids toys) which, taken all together, can alter a childs microbiota.

Below is an outstanding webinar about the Microbiome and Autism given by Dr. Sarkis Mazmanian who collaborated with Dr. Paul Patterson. This webinar was hosted by SFARI

Please watch:

Webinar: Sarkis Mazmanian explores probiotics for autism - SFARI

autism uncle

Seems to me the whole history of "vaccination(s)" evolved to avert serious/deadly clinical outcomes from bacterial/viral exposures. BUT, serious/deadly outcomes virtually never happen if healthy (unvaccinated) mothers breastfeed their babies and the infants have proper nutrition as they grow and mature.

Well nourished human infants/children are MEANT by Nature to go through these "disease" exposures, be tempered (and actually strengthened), to then proceed through life with a healthy gastrointestinal system into old age. AND, never getting so-called (toxic) booster shots as demanded by today's vaccination practice.

Our present culture believing in vaccines shows how malleable, and gullible, we humans are - as we damage and destroy huge proportions of our last several generations and ruin or terribly harm tens of millions of families.

But, it can get worse, if the Medical Industry cons and panics the public to think that biological entities such as human endogenous retroviruses are yet another threat -- For instance, well nourished adults who do not wreck their health with toxic "recreational drugs" have NEVER been affected by the only retrovirus HIV (out of tens of thousands of retroviruses inherent in our biological makeup) that has correlated with deadly symptoms, with even this dubious correlation vanishing if people decline the deadly, toxic antiretroviral medicines. My point is simple: Never trust the Medical Industry or our Government Leaders when it comes to disease. Never.

Cherry Sperlin Misra

Bob Moffit- So true- and not only the immune system, but also our entire body must be treated with more care. We have allowed modern life, commercial interests to surround us with toxins and now we more often allow medical- pharma products to but put into our bodies.
My new and personal approach is to think not of "my body", but instead think of each and every cell of my body. What does each cell want? It merely wishes to go on living and operating unimpeded by infection, toxins and inflammation. Is that too much for a little being to ask?
Surely if we treat each cell kindly, it wont turn cancerous or make anyone autistic. Think about what you eat; think about what you apply; think about what you breathe- and before you vaccinate, think of the poor little cells at the injection site getting bombarded with mercury and aluminium atoms.

Maurine Meleck

Josh and I are living proof of the Chicken-pox/shingles conundrum. Years ago and shortly after I moved him in with me, I contracted the shingles. 14 days later Joshua got the chicken-pox from my shingles virus. However, he had been vaccinated against the chicken pox as a toddler.
Yay, wasn't that swell? The only good part was that we got his younger, unvaccinated for the CP younger brother to party and 21 days later he got the worse case of the chicken=pox I have ever seen. Whew-that's over.
Thanks Teresa and ruff-ruff, yay dog.

Stand Up!

Thank You Teresa,

Germs are not the cause of disease...the concept of pleomorphism and the physiologic law of adaptation comes to mind which generally speaks to the evidence (overwhelming in my view) that the environment is everything!!...purity & sufficiency is required for a healthy microbiome...the vast majority are suffering from toxicity(vaccines unequivocally)& deficiency resulting in an injured & subsequently weakened ecosystem (within).


I would like to nominate you for an award for excellence in health care journalism for this series. Because of you, I learned about the book, _Missing Microbes How the Overuse of Antibiotics is Fueling Our Modern Plagues_ by Martin J. Blaser, MD. Quote from p. 197 (caps my emphasis):

"The modern epidemics - asthma and allergic reactions, obesity, and metabolic disorders - are not only diseases but also external signs of internal change. We may see the problem when a child with an altered microbial ecosystem and diminished immune status encounters a MILD PATHOGEN that can easily damage the child's pancreas and lead to juvenile diabetes. Or the problem can show up when another child encounters a peanut or gluten, which are relatively recent additions to the human diet. Changes in their resident microbes and immune maturation similarly conspire to put them at risk, in this case for severe allergies to nuts or gluten."

A mild pathogen such as those delivered attenuated in vaccines?

autism mom

The autism-microbiome research is very exciting. Dr. Paul Patterson and his team at California Institute of Technology found that Polysaccharide Peptides (PSA) derived from Bacteria Fragilis (B. Fragilis) has healing properties on the GI and that PSA is neuroprotective and and can heal/correct leaky gut and reverse autism symptoms in mice.

This to me is breakthrough research and the type of research that deserve to be funded.

"Probiotic Therapy Alleviates Autism-like Behaviors in Mice"
CalTech" 12/05/2013

"Bacterium can reverse autism-like behaviour in mice
Findings support idea that gut microbiome has a role in disorder." - Nature; December 5, 2013

'Good' Bacteria Ease Autism-like Behaviors in Mouse Model' -Autism Speaks

More research on B.Fragilis PSA...

Intestinal antimicrobial peptides during homeostasis, infection, and disease

A polysaccharide from the human commensal Bacteroides fragilis protects against CNS demyelinating disease

The yin yang of bacterial polysaccharides: Lessons learned from B. fragilis PSA


So, the immune system can be manipulated into attacking a virus, - but not just one type of virus - a group of similar viruses -- some of which keep down the population of strep bacteria ( just an example)

To fight off a strep infection - we have to depend on our own immune system with out the help of these viruses.

This is unlimited at the possibilities -- they are trying to raise good bacteria in robo guts -- well they better start adding good viruses to the brew -- and how many kinds of fungi are there.

And when it comes to Helminths, protozoas

Well - even in a 1000 years would human beings be able to straighten it all out? It sounds more impossible than traveling to some distant star. The distant star travel would be easier.

Jesus Christ had it right -- fast - don't eat anything - and pray to God -- cause it would take God to fix the problem.

I better get off of this computer and go plant my nappa cabbage -I got to make some kimchi this fall -- and do some praying.

BoB Moffitt

"The immune system of Mankind should be handled with more care."

Amen to that ....

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