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microbiome and influenza


Microbiome Flu Bacteria

It was two decades ago that three Australian researchers published the study, The Intestine as a Sensory Organ: Neural, Endocrine, and Immune Responses, which revealed that, “the gut immune system has 70- 80% of the body’s immune cells.”  The authors went on to say of the microbiome (the bugs living both in an on you)…..

“The lining of the gastrointestinal tract is the largest vulnerable surface that faces the external environment. Just as the other large external surface, the skin, is regarded as a sensory organ, so should the intestinal mucosa. In fact, the mucosa has three types of detectors: neurons, endocrine cells, and immune cells.

The mucosa is in immediate contact with the intestinal contents so that nutrients can be efficiently absorbed, and, at the same time, it protects against the intrusion of harmful entities, such as toxins and bacteria, that may enter the digestive system with food.  The gastrointestinal tract has an integrated response to changes in its luminal contents. When this response is maladjusted or is overwhelmed, the consequences can be severe or debilitating.”

In other words, your digestive tract is considered to be part of the “external environment” because it is essentially a tube that runs through your body, allowing nutrition and water in, while allowing excretion of metabolic waste products out of the body and into the tube.  This occurred because the mucosal layer is porous.  When the mucosal layer of the “Gut” becomes too porous, the medical community refers to it as ‘increased intestinal permeability’ or something similar. 

The general public (and increasingly the peer reviewed scientific literature) refer to it simply as a LEAKY GUT.  If you are interested in seeing pics of the difference between normal permeability and increased permeability, simply click the link.

In a nutshell, INFLAMMATION from an almost endless number of potential sources can cause the “tight junctions” between individual mucosal cells to become loose, allowing things like undigested or partially-digested food particles into the blood stream, along with “harmful entities such as toxins and bacteria“. 

However, because the molecular size is so much smaller, the passage of toxic chemicals through the Gut mucosa into the blood stream is more difficult to control.  Thus, it’s important to both avoid toxins and make sure your body is doing a good job of BIOTRANSFORMATION

As for the bacteria, when you start letting uninvited bacteria or other critters into your Gut, they can take hold and begin to grow.  The result is something known as DYSBIOSIS.  And as I’ve shown you from numerous studies, dysbiosis and leaky gut are a chicken-and-egg sort of thing — either one can occur first, leading to the other (HERE). 

The bacteria living in and on our body are collectively known as our MICROBIOME.  Every day there are numerous studies published touting the microbiome as being intimately related to some aspect or another of our health.  What’s fascinating is that increasing numbers of researchers are saying that if you give your microbiome the TLC IT NEEDS to thrive, it’s like a modern superhero that can perform amazing and outlandish feats. 

And while it may not be able to jump over tall buildings in a single bound, your microbiome can do other cool things, including making large numbers of anti-inflammatory compounds and even most vitamins (HERE).

With FLU-PROPAGANDA SEASON right around the corner (you’ll soon be seeing the annual warnings to get your shots because once again it’s predicted to be the worst flu season ever), the question I want to ask is whether or not INFLUENZA and the microbiome are related to each other in any significant manner?  It seems that the answer is “yes” in more ways than you might imagine. 

For instance, a 2010 issue of Letters in Applied Microbiology (Oral Administration of Lactobacilli from Human Intestinal Tract Protects Mice Against Influenza Virus Infection) concluded that two specific strains of lactobacillus, “significantly ameliorated the clinical symptoms score compared to those of the control…  These results demonstrate that oral administration of selected lactobacilli might protect host animals from Flu infection by interactions with gut immunity.” 

Oral probiotics can be fantastic for any number of GUT HEALTH issues (and what isn’t a Gut Health issue?), but if you are chronically ill, THIS MIGHT BE SOMETHING to look into.

In March of 2011, PNAS published a study (Microbiota Regulates Immune Defense Against Respiratory Tract Influenza A Virus Infection) that showed one method a healthy microbiome uses to fight off flu viruses. Yale immunologist, Akiko Iwasaki and his team of seven researchers, treated mice with antibiotics, which weakened their immune systems, making said mice more susceptible to catching the flu.

Certain bacteria were discovered to activate pre-inflammatory pathways of the “INFLAMMASOME,” causing certain CYTOKINES to mature into cells and compounds with the ability to mount attacks against said viruses.  No bacteria, no mature immune cells, which allowed the virus to replicate unchecked.  This was a complex paper with conclusions similar to what you’ve hopefully known for years — that antibiotics foul the immune system in ways that are only just beginning to be understood (HERE). 

And to top it all off, flu is a virus, and virus don’t ever respond to antibiotics except unfavorably (see previous link).  Despite this, little seems to be changing in the prescription habits of the average physician (HERE).

When it comes to aging, the immune system, and influenza, there are a few things we know for certain.  For starters, people’s immune systems don’t work as well as they get older, leaving them not only more prone to infections of all sorts, but in an increased state of inflammation, which helps explain why flu shots for the elderly are not much better than 0% effective (HERE).  

In 2013, Cambridge University Press’s Proceedings of the Nutrition Society published a literature review called Ageing, Immunity and Influenza: A Role for Probiotics?  The gist of this study was instead of using dangerous ALUMINUM ADJUVANTS in flu vaccines, scientists should be taking a harder look at the “potential adjuvant effects of selected probiotics for vaccination against influenza.” 

For the record, adjuvants are compounds added to vaccines to create inflammatory responses in order to make the vaccine react harder / more intensely.  A year later, the journal Immunity published a similar study called Gut Microbiota: A Natural Adjuvant for Vaccination, which as you’ll soon see, is an increasingly hot area of research.

On the first day of 2014, Annals of the American Thoracic Society published Viruses and Microbiome Alterations, which went the opposite direction.  While discussing the fact that certain bacteria have been shown to help prevent and fight off the flu, this study also showed that viral infections adversely effect the microbiome.

The upper respiratory tract represents a site of overt microbial colonization, where the composition of the microbiome in this niche appears to act as an ancillary barrier and define host response to respiratory pathogen invasion. Viral infection results in a perturbation to the respiratory microbiome; in the case of the recent pandemic influenza A virus strain, infection resulted in selection for a discrete subset of bacterial species with functional capacities consistent with survival and translocation to the lower airways, where they presumably contribute to secondary bacterial pneumonia.” 

What does this mean?  It means that instead of talk of “BOOSTING YOUR IMMUNE SYSTEM,” you had better feed, nurture, and actually think about your microbiome.

Later in 2014, Immunity came back with another study on the topic, this one called TLR5-Mediated Sensing of Gut Microbiota Is Necessary for Antibody Responses to Seasonal Influenza Vaccination. The authors kicked things off by letting readers in on one of those dirty little secrets — something known by all doctors (MY BROTHER INCLUDED), but not widely admitted to.  “Influenza affects millions of people worldwide, and despite it being one of the most widely targeted viruses through yearly vaccination programs, significant rates of morbidity and mortality persist.”  In other words, the flu vaccines don’t, and never have, worked worth a hill of beans. 

In this study, researchers realized that still another type of immune system cell (this one the Toll-Like Receptor 5 or TLR5) did not work properly in making antibodies against the flu until it was stimulated by bacteria with a FLAGELLUM.  The authors concluded that, “These results reveal an unappreciated role for gut microbiota in promoting immunity to vaccination.”  What’s interesting about this conclusion is that I can think of nothing in VACCINES that aids or improves the microbiota.  In fact, I have shown you time and time again that they tend to do just the opposite (links coming).

A 2015 study from the American Thoracic Society Journal (The Bacterial Microbiome of Gut, Lung, and Blood after H1N1 Influenza Virus Infection in Mice with and Without House Dust Mite Exposure) showed us that yes, dust mites can adversely affect the microbiomes of young asthmatics (make sure to read my post on asthma as an autoimmune disease — HERE).  Then, after telling us that, “Every year in the United States approximately 200,000 people die from pulmonary infections,” authors of the Frontiers in Microbiology study, Regulation of Lung Immunity and Host Defense by the Intestinal Microbiota, revealed something I’ve been telling you in the GUT HEALTH section of my blog for years. 

“Recent evidence suggests that the gastrointestinal (GI) microbiota plays a key role in immune adaptation and initiation in the GI tract as well as at other distal mucosal sites, such as the lung. Infection of the respiratory tract represents a breakdown of the host’s immune defenses.  Most of the current therapies used in the treatment and management of these diseases are suboptimal as antibiotic resistance, efficacy, and toxicity have been difficult to overcome.

Intestinal microbial diversity and composition changes not only along the length of the intestinal tract but is spatially distributed between the mucosa and the lumen of the intestinal tract within each region. Many environmental factors will drastically alter the normal intestinal microbiota. Changes in diet, the use of antibiotics, chemotherapy, GI tract infection, and host immune status significantly alter, either transiently or permanently, the intestinal ecosystem.

Alterations of the microbiota that lead to intestinal dysbiosis (a microbial imbalance within the intestinal tract) are characterized by a loss or significant decrease in the amount of beneficial bacterial species and/or an outgrowth or population shift of other species……  intestinal microbiota is crucial for modulating the host’s ability to control inflammation. 

Numerous studies have shown that fluids, particles, or even microorganisms deposited into the nasal cavity of mice can also be found in the GI tract a short time later.   Importantly, disturbances in the intestinal homeostasis by either alterations in the host’s genetics or alterations in the microflora could have drastic effects on systemic (e.g., lung) immune responses.”

First, in light of the title of the study published a few months earlier in Medicine Sciences (The Intestinal Microbiota Helps Shaping the Adaptive Immune Response Against Viruses), we can’t be surprised.  Secondly, the fact that for two decades now we have known that 80% of the body’s immune system resides in the Gut (HERE) means that this is rather what we would expect to see.  Thirdly, if you don’t understand DYSBIOSIS and its link not only to antibiotics but to all drugs in general, you had better start paying attention (HERE). 

And lastly, simply taking probiotics; while helpful for some, will prove minimally effective or even completely ineffective (or harmful) for many — particularly those of you struggling with hardcore chronic health conditions.  Why?  Because of the fact that a normal microbiome should contain at the very least, hundreds of organisms, this study proves what I have been saying about PROBIOTICS -VS- FMT for a very long time.

“This microbial community includes autochthonous (permanent inhabitants) and allochthonous (transient inhabitants) microorganisms. Microbiota of the human GI tract contains bacterial (microbiota), viral (virome), and fungal (mycobiota) species. Surprisingly, approximately 60% of these organisms cannot be grown in traditional culture.”

Did you grasp what they said in the last sentence? This means that even the best of the best probiotics don’t look even remotely like a real microbiome.  But that’s not all.  Another study — this one from the November 2015 issue of the International Journal of Molecular Sciences (Metagenomics: A New Way to Illustrate the Crosstalk between Infectious Diseases and Host Microbiome) showed that this issue may be even more dire, revealing that “90% could not be cultivated in the laboratory“. 

This means that simply taking more probiotics (made up of strains that are easily cultured) often throws microbial ratios even further out of whack, sometimes actually causing dysbiosis (HERE).   This is why truly sick people —- especially people who have eaten really crappy diets (HERE), taken lots of drugs of any sort, or have struggled with overt Gut Health issues (IBS, IBD) or problems where Gut Health has likely been affected (AUTISM and numerous autoimmune issues, including CELIAC or NON-CELIAC gluten sensitivity) —- should take a long, hard look at FECAL MICROBIOTA TRANSPLANTS (with your doctor’s blessings, of course).

In 2016, nine researchers from UCLA published a study in PLoS Pathogens called Influenza Virus Affects Intestinal Microbiota and Secondary Salmonella Infection in the Gut through Type I Interferons, in which they determined that yes, flu affects Gut Health.  The authors started by saying, “Human influenza viruses replicate almost exclusively in the respiratory tract, yet infected individuals may also develop gastrointestinal symptoms, such as vomiting and diarrhea.” 

While this is technically true, it’s extremely rare.  Generally speaking, if you are spending significant time on or hunched over the toilet with your illness, it’s unlikely it’s caused by a flu virus, even though most of us tend to refer to it as such (HERE).  The gist of this study was that flu, as do all viral infections, increases the body’s production of interferon (a powerful immune system agent).  In people with acute colitis, interferon inhibits the body’s ability to effectively deal with salmonella infections.  Thus, certain populations who get the flu can be more prone to getting salmonella.

2017 was a particularly big year on the influenza / microbiome front, with a very cool study being published in the September issue of Frontiers in Immunology (Impact of Age, Caloric Restriction, and Influenza Infection on Mouse Gut Microbiome: An Exploratory Study of the Role of Age-Related Microbiome Changes on Influenza Responses).  The authors started by talking about THE EFFECTS OF AGING ON GUT HEALTH AND IMMUNE SYSTEM FUNCTION (“Immunosenescence refers to age-related declines in the capacity to respond to infections such as flu“), before revealing the most powerful method of anti-aging known to man — CALORIE RESTRICTION

“Caloric restriction represents a known strategy to slow many aging processes, including those involving the immune system. More recently, some changes in the microbiome have been described with aging, while the gut microbiome appears to influence responses to flu vaccination and infection.”

Because calorie restriction is such a powerful method of helping regulate PHYSIOLOGY & HOMEOSTASIS (it’s known to be the most powerful anti-aging treatment on the planet) yet difficult for most people to maintain for any length of time, we need to ask what way of eating might approximate this restriction, without forcing us to go through the emotional pain of such restriction? 

Look no farther as this is a chief characteristic of the KETOGENIC DIET (watch Dr. Seyfried’s video at the end of my post on FASCIA & CANCER).  The theme of this study was finding which strains of bacteria might be used as flu vaccine adjuvants in the elderly.  Speaking of which, a study was published in December’s issue of Vaccines (Adjuvant Probiotics and the Intestinal Microbiome: Enhancing Vaccines and Immunotherapy Outcomes).

“Probiotics comprise bacterial genera thought to provide a health benefit to the host. The intestinal microbiota has profound effects on local and extra-intestinal end organ physiology. As such, we further posit that the adjuvant administration of dedicated probiotic formulations can encourage the intestinal commensal cohort to beneficially participate in the intestinal microbiome-intestinal epithelia-innate-cell mediated immunity axes and cell mediated cellular immunity with vaccines aimed at preventing infectious diseases whilst conserving immunological tolerance. 

Equally the administration of vaccines from recent findings suggest complex mechanisms are in operation by which the microbiome impacts immune cell development and differentiation with the major implication being that the composition of the microbiome may ultimately affect vaccine efficacy. An intestinal resident immunity equilibrium is present that links the intestinal bacteria, the intestinal epithelia and the host’s immune response that leads to homeostasis maintenance.

Resultant perturbations in this equilibrium with changes in the composition of the intestinal microbiome can result in chronic inflammatory processes (e.g., IBD) and autoimmune pathologies (e.g., allergy/asthma, diabetes).”

What do we see here?  If you have dysbiosis, vaccines and immunotherapy / cancer treatment are not going to work as touted.  Furthermore, these authors talk about homeostasis (I mentioned it earlier), LEAKY GUT SYNDROME (intestinal epithelium), OUT-OF-CONTROL-INFLAMMATION, and AUTOIMMUNITY — all in the context of Gut Health, and all in the context of improving vaccine efficacy.  Why would vaccine efficacy need to be improved? 

Interestingly, our own government has shown us that vaccine efficacy is not remotely what it’s been suggested to be (HERE or HERE) — especially true of flu vaccines (200 people must be vaccinated to prevent a single case of flu — HERE). 

A study from last August’s issue of Science (The Microbial Metabolite Desaminotyrosine Protects from Influenza Through Type I Interferon) showed once again that certain bacteria can actually be protective against the flu.  The authors, from St. Louis’ Washington University, said in a study summary that…

Antibiotic treatment worsens influenza….  A microbial product, desaminotyrosine (DAT), produced by an obligate clostridial anaerobe from the digestion of plant flavonoids, is beneficial during influenza. DAT enters the bloodstream and triggers type I interferon signaling, which then augments antiviral responses by phagocytic cells. Without DAT, influenza virus causes inflammation and severe disease.” 

Instead of politely asking your spouse to pass you the vegetables, just say “Gimme summa DAT.”

Just a few short weeks ago, a dozen researchers from UC Davis published a study in the Journal of Virology called Subclinical Cytomegalovirus Infection Associates with Altered Host Immunity, Gut Microbiota and Vaccine Responses.  I’ve done a fair amount of work on this site showing you the problems associated with occult infections, and how particularly destructive the CMV / EBV viruses can be. 

This study showed something we’ve seen previously — that a viral infection (in this case Epstein Barr or Cytomegalo) can cause dysbiosis and subsequent immune system dysfunction.  A study published in January’s issue of Current Opinions in HIV and AIDS (Utilizing Gnotobiotic Models to Inform the Role of the Microbiome in Vaccine Response Heterogeneity) took this a step further, trying to figure out which specific bacteria in the Microbiome are most contributing to vaccine dysfunction, with an endgame of figuring out which bacteria might be used as vaccine adjuvants. 

“Clinical data have suggested that numerous vaccines’ effectiveness are regulated by the microbiome and often correlate with the abundance of specific taxa. Gnotobiotic and other animal models are beginning to illuminate the complex effects induced by the presence of particular microbial groups and communities. Such models have identified microbial groups that improve vaccine response to rotavirus vaccine and identified pathways by which the microbiome influences response to influenza and other vaccines.”

What this reminds me of is the fact that people want to have their cake and eat it to (literally — HERE).  We don’t want to do the heavy lifting needed to take care of our microbiomes, when someone could do it for us WITH A NEW FANGLED SHOT (even better, when SOMEONE ELSE IS FORCED TO PAY for the new fangled shot).  What are my final thoughts on this post and how would I summarize this mountain of information? 

Firstly, it’s important to realize that in the big scheme of things, a very small percentage of respiratory infections are bacterial (100% of colds and flu, and about 95% of all SINUS INFECTIONS and upper respiratory are viral, with allergies and asthma considered to be inflammatory and autoimmune, and not caused by infection one way or another). 

Secondly, as we’ve seen repeatedly in the scientific literature; ANTIBIOTICS DESTROY IMMUNE SYSTEM FUNCTION AND OVERALL HEALTH — in many cases permanently (HERE).  It’s that simple. No debate, no argument.  This creates an interesting dichotomy considering I’ve repeatedly argued that the number one form of treatment in America is IMMUNE SYSTEM SUPPRESSION.

Thirdly, remember that when it comes to your microbiome, ratios rule.  The hundreds of different species and strains of bacteria, viruses, mold, fungi, etc that make up your normal / healthy microbiome are found in fine-tuned ratios.  How in the world is taking a probiotic with a single species (acidophilus), three species (add lactobacillus and bifidus to the mix), eight or even twenty species, going to approximate what’s going on in a healthy Gut — especially your healthy Gut?  That’s right; it can’t. 

I don’t want to sound like a party-pooper, but probiotics are something to be taken carefully.  And truthfully, there are other things that should be promoted as solutions for dysbiosis that typically are not (SUGAR FEEDS INFECTIONS / DYSBIOSIS).

Fourthly, since when is a vaccine going to solve the dysbiosis issue?  Sorry folks, vaccines are a known cause of dysbiosis — a major known cause (HERE is a great example).  MERCURY, ALUMINUM, and FORMALDEHYDE, which are all common ingredients in numerous vaccines, have serious antimicrobial properties — and they don’t pick and choose which bacteria they kill.  It’s that kill-em-all-and-let-God-sort-em-out mentality (HERE). 

Fifthly, remember what today’s studies showed us?  Depending on whose research is more accurate, only between 10 and 40% of the bacteria in a normal microbiome can be cultured in a lab, which is why there are no probiotics that even remotely approximate a normal microbiome.

While I certainly think that we can glean a lot of valuable information from this sort of thing, the bottom line is that scientists and institutions are searching for the jackpot — bacteria that can be used as a drug or vaccine, or added to a drug or vaccine as an adjuvant. 

If you are one of my readers who is struggling with severe chronic issues, you’ll notice that Gut Health is the cornerstone of the ONLINE HANDOUT I give patients to help them start resolving their problems.  If you know people who could benefit from the information in today’s post, be sure and like, share, or follow us on FACEBOOK.  Short of a phone call, it’s still probably the best way to reach those you love and care about most.


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