There has always been traditional healing methods and natural remedies that have been passed down
from generation to generation to heal a variety of afflictions, but there has never been a great
understanding of how or why they work, until now. Thanks to evidence produced by research like the
microbiome project, science has validated that while terrain and toxins like mercury play a critical role in
the microbiome, commensal and pathogenic bacteria have become one and the same that can live in
harmony within your microbiome. People used to think of bacteria as just single celled organisms that
were either good or bad when they get into our system. Now after 170 million dollars’ worth of
microbiome research we are beginning to understand that when bacteria are introduced to the
microbiome they begin to function as a group. These studies explain how when the bacteria that makes
up our microbiome come together, they act as another organ that plays a critical role in immunity,
communication with our cells, digestive health, brain health, metabolism, and just about every other
function going on in the body. Unfortunately, just like with other organs when there is a dysbiosis in that
system, chronic illnesses my arise.
Autoimmune issues have become an epidemic that can’t be dealt with in the same way as other
epidemics because they aren’t acute scenarios that are well adapted to treatment research like
influenza. They are chronic illnesses and chronic autoimmune systems that we are just beginning to
understand and make advancements in thanks to microbiome research. One of the chronic auto
immune illnesses that has now been linked to the microbiome is autism. Research shows that when it
comes to a person with autism, their body, their microbiome, and their tissues struggle to deal with
heavy metals like mercury because of low glutathione production. Glutathione is a powerful antioxidant
produced within almost every cell in the body but is primarily produced in liver cells due to its
detoxifying properties. Glutathione helps detoxify cells by chelating heavy metals, like mercury, so that
they don’t get converted to cytotoxic compounds, like methyl mercury, that can build up and wreak
havoc in the body. It’s important for everyone to consume foods or supplements rich in glutathione, but
It’s especially important for those with autism. It’s crucial for them because even though glutathione
that is ingested won’t necessarily raise the levels in the blood, it provides the microbiota with a
chelating agent that they otherwise wouldn’t have since most bacteria cannot make glutathione. By
providing their microbiome with extra glutathione it gives the bacteria a better chance at removing
extra heavy metals from the intestines before they can be absorbed and increase the already toxic high
levels inside the body.
Up until the microbiome project was conducted, research on the microbiome had just scratched the
surface on the potential benefits that these bugs have on our everyday lives. Thanks to the evidence this
research has provided we are finally beginning to understand why each strain of bacteria in the
microbiome has a specific role that they play in our body. The microbiome project showed us that the
diverse community of bacteria that make up the microbiome contains about three million genes that
allows them to make different compounds and proteins that our bodies need but cannot make. Each
one continuously provides us with their metabolites that assist mechanisms in our body to function
efficiently. They are so important because the only way to get all the wonderful things that they produce
to contribute to our heath is by colonizing the gastrointestinal tract with these probiotics and using
prebiotics to help them flourish. Even though we have been aware of normal flora, probiotics, and the
benefits they provide, we had no idea the impact bacteria could have on our world by providing us with
an arsenal of about three million genes for us to utilize in the journey to optimizing health.

A healthy microbiome with a diverse community of bacteria provides us with many unique advantages.
For example, with the technology available in modern medicine we can create synthetic compounds to
use in different medicines and treatments to alleviate a patient’s symptoms. However, people are slowly
accepting that there is really no need for these synthetic products because the diverse community of
bacteria in the microbiome are capable of producing many of the same compounds naturally. Another
huge advantage is that these probiotics can create a biofilm. Usually biofilms are perceived as a negative
property of bacteria, but in this case it’s good because it can act as a defensive shield that coats the
gastrointestinal tract, skin, mouth, etc. where everything that comes into the body must filter through
first. This biofilm limits the number of harmful compounds that can get into the bloodstream by either
utilizing them for their own metabolic processes, converting them into different compounds our bodies
can use, or breaking them down to help our bodies excrete them. In order to utilize these advantages,
we must diversify the microbiome with a variety of probiotics, fermented products, and novel enzymes
that the microbiome may be lacking. We can manipulate the bacterial populations in the microbiome
through environmental exposure. This exposure can come from subtle environmental changes like being
around new people with different microbiomes, or a more drastic change like fecal transplantation. The
interesting, yet difficult, part about studying the microbiome is that microbes are always changing and
reproducing at an alarming rate. Not only are bacteria reproducing with each other and sharing their
DNA, they are also reproducing with other microorganisms in the microbiome like yeasts. This kind of
interaction leads to the production of new metabolites that can ultimately lead to the discovery of new
medicines, antibiotics, enzymes, and compounds that our bodies can use to its advantage.
After studying about 40,000 pieces of feces from over 5,000 people of all ages in the microbiome
project, they have been able to divide most of the diverse species of bacteria found in the
gastrointestinal tract into two main groups: Bacteroidetes, most of which are gram-negative bacteria,
and Firmicutes which are mostly gram-positive bacteria. Some gram-negative bacteria have a bad
reputation because they produce lipopolysaccharides (LPS) that can exacerbate the inflammatory
response from the immune system and consequently trigger and autoimmune response when they are
detected in the blood. However, thanks to the microbiome project we now have proof that certain
gram-negative bacteria can actually be beneficial and live harmoniously within the microbiome without
causing any complications. For example, when Helicobacter Pylori (H. Pylori) was first discovered by an
Australian researcher, he used himself as an experiment where he proved it to be an ulcer causing
pathogenic bacteria by eating it and giving himself ulcers. It is now considered a probiotic because the
fecal biopsies done in the microbiome project showed that many people carry H. Pylori in large
numbers, but don’t have any symptoms, ulcers, or signs of gastric cancers. It’s all about balance, so
certain bacteria often only cause a problem when there is a dysbiosis from either an altered ratio of
Bacteroidetes and Firmicutes in their microbiome or there are other immune issues that makes the body
more susceptible to infection.
During the microbiome project they studied many diversities of people from all over the world and they
found that the microbial diversity and ratio of Bacteroidetes to Firmicutes of a person’s microbiome
varies depending on a variety of things including environmental factors like diet or lifestyle. In one case
they showed the microbiome of a young man from Burkina Faso Africa that mainly ate ancient grains
and compared it to the microbiome of a young man from Florence Italy that had a diet that consisted
mainly of meats. They found that the ratios of Bacteroidetes to Firmicutes were incredibly different
because the microbiome was adapting to what they were feeding it daily. After comparing these

microbiomes on a slide during this presentation Dr. Shayne Morris commented, “You are what you eat”
which Nicole followed up with, “if you are what you eat…then don’t be cheap, fast, and easy.” By this
humorous dialogue they were trying to emphasize that what we put in our bodies will ultimately
determine the diversity of our microbiome and our overall health. Therefore, if we choose to be, as
Shayne puts it, “deliberate, thoughtful, and healthy” about what we put in our bodies we can promote
the growth of healthy bacteria in our microbiomes. Whereas the more we choose, “cheap and easy”
options the more we promote growth of the wrong bacteria that can cause a dysbiosis and lead to
health problems.
Our microbiomes are self-preserving, so they are always trying to keep us healthy by continuously
adapting to its environment. That’s why diet, nutrition, and herbalomics can play such a positive role in
helping the microbiome keep people healthy because if it’s not getting any of these helpful nutrients it is
going to constantly struggle to try and keep you healthy. The more we learn about the microbiome the
more we accept that the micro-world is a critical piece when it comes to the puzzle of autoimmune
issues. Research has shown that the microbiome works just like the blood brain barrier; everything must
go through a highly regulated filtering process first to act as a line of defense by deciding what should
and shouldn’t be allowed in. If that barrier is compromised, then it can lead to major health issues in the
body just as it would in the brain. It’s important for us to fortify this barrier by diversifying our
microbiome with probiotics and nourishing it with prebiotics because as it filters through everything
coming in, it can alter those substances into a number of things that can either be good or bad for the
body depending on what bacteria are thriving.
The sooner we start colonizing the microbiome with a diverse community of good bacteria the better
chance we have at laying the groundwork for building up a strong defense against diseases. It’s a
common misconception that at birth babies are sterile when it comes to intestinal bacteria, but there
have been multiple scientific publications that show you are actually born with about 100 species of
bacteria in your intestinal microbiome before ingesting any colostrum, breast milk, or formula. There is
also research that shows the type of species present in a newborns intestinal microbiome is determined
by how the baby was delivered. These studies presented results showing that if the mother had a
Caesarean section delivery the baby’s microbiome was colonized with the skin microorganisms that the
mother carried. On the other hand, if the babies were delivered via vaginal birth, their microbiome was
colonized with most of the same species of bacteria present in moms intestinal microbiome. There isn’t
enough information to show what the long-term implications of this phenomenon is quite yet, but it has
been seen that this makes it exponentially more difficult for these babies to build up a thriving
microbiome capable of evolving from 100 species at birth to about 700 at weaning. Therefore, if we can
put the right practices in play at a young age, through diet, nutrition, herbalomics, epigenetics and
nutrigenetics, we can help the microbiome evolve in the healthiest way possible to prevent the onset of
health issues in the future.
While we are aware of the gut-brain axis that connects gut health and brain health, we are now seeing a
correlation between the maturation of the microbiome and the maturation of important organs like the
brain, liver, kidneys, pancreas, etc. There are even studies that show the microbiome is evolving and
maturing in the same time frame as the hypothalamus-pituitary-adrenal axis (HPA axis) that connects
the central nervous system to the endocrine system. This correlation can help explain how dysbiosis in
the microbiome of a child can hinder the maturation of other tissues and organs and lead to variety of
health problems. A dysbiosis can cause the microbiome to send the wrong information to these organs

leading to either overproduction or underproduction of hormones, neurotransmitters, and other
metabolites that the body requires to function efficiently. The more we learn about the microbiome the
more we realize that it dictates almost every function going on in the body. Therefore, preserving the
integrity of the microbiome from the get-go is crucial to the outcome of a person’s health. Even as we
age those connections cannot be overlooked when trying to treat tissues because we need that context
from our microbiome to find out where things went wrong in the first place, so we know where to start
with treatment.
A big part of having a healthy microbiome is the diversity acquired overtime. Like it was stated above,
we are born with about 100 species of bacteria in our microbiomes that depends on environmental
factors. At the time of weaning the diversity of bacteria will increase from 100 species to 700 and then
as an adult you should have about 1000 different species. This shows that a majority of our microbiome
diversity is acquired in the first few years of life between birth and weaning. The diversity of
microbiomes varies from one person to the next depending on what they got from mom and the
environment they are subjected to everyday. The environment plays a huge role in diversity because
diet and exposure to pathogens, toxins, and stresses from the environment all effect microbial
populations. These environmental factors provide the microbiome with certain things to either help or
hinder the growth of specific bacteria that would help the body thrive in a specific environment. While
there are certain bacteria and toxins from the environment that we don’t want, we also don’t want to
take it to extremes and avoid environmental bacteria all together because that can be just as harmful.
For example, there are those people that don’t want anybody touching their newborn or that make sure
everyone washes their hands before they can touch the baby so that the baby isn’t exposed to any
bacteria that could make them sick. Those practices are good to an extent, especially if someone is sick,
but exposing babies to the microbiomes of their loved ones can actually help them build a more diverse
microbiome which can in turn help them build up a stronger immune system to keep them healthy.
Throughout Dr. Morris’s presentation he continuously emphasizes how a diverse microbiome is the
biggest piece of the puzzle to intracellular healing because it is connected to every cell, every
mechanism, every function and every system in the body. Before the microbiome project was conducted
there used to be a lot of speculation of how the microbiome affected the body, but now we have proof
to back up these theories. This project proved that bacteria found in the microbiome directly affects
insulin regulation, lipid composition, nutrient absorption, immunity, metabolic syndrome, brain
function, and so much more. When it comes to lipid composition the microbiome project proved that
the microbiome is able to differentiate between different kinds of lipids, like Omega-6 vs. Omega-9, so it
can send messages to the different tissues and cells to help direct your body where they need to go. It
also showed how a dysbiosis caused by large populations of highly consumptive bacteria can lead to
disease because that bacteria in the microbiome is going to use up all the excess nutrients and
proliferate before they can ever be absorbed and used in the body. Therefore, if you want to use a
supplement, like Systemic Formula’s VISTA to support cell membrane structure, it would be beneficial to
have a balanced microbiome first because if you don’t it’s going to be more difficult for the body to
receive and utilize the nutrients that the supplement provides. The gut is intrinsically linked to all these
processes going on in the body, but its most important connection is how it enables an instability to
develop all the way to an autoimmune issue; like going from having an insulin resistance that develops
into diabetes.

Genetics and toxins from unhealthy eating habits can result in an insulin resistance, but the microbiome
can also be a big factor in developing insulin resistance by affecting the mechanisms that regulate
insulin. Insulin resistance can be caused by many things, but what it boils down to is that there is either
an issue with the mechanism that regulates the insulin hormone itself, or an issue with the mechanism
that controls glucose receptors based on the mitochondria. If insulin is binding to a receptor that’s
broken in the membrane it can’t send a signal to the mitochondria to tell the cell to take in glucose from
the blood. If none of the glucose is getting taken out of the blood the pancreas will just continue to
pump out insulin to try and regulate those glucose levels. The same thing happens when you have
mitochondrial disease. If the mitochondria are damaged it sends signals to the cell to shut down the
glucose transport proteins, so they don’t let in any more glucose. While the insulin receptors may be
working fine and sending the signals to the mitochondria to tell it that it needs to take up all the extra
glucose, the cell won’t allow it because of the damaged mitochondria. Therefore, if the body keeps
producing more and more insulin and nothing changes, those response mechanisms eventually become
negated and an insulin resistance occurs potentially leading to diabetes.
Type 1 diabetes is fairly rare but is mainly found in younger people which lead people to suspect that it
was simply a genetic autoimmune disease. On the other hand, Type 2 diabetes is commonly found in
older people that have made so many unhealthy lifestyle choices that caused an insulin resistance that
worsened over time and developed into diabetes. It is still so common for people to think that if they
aren’t born with Type 1 diabetes, they can put whatever they want into their bodies without any
implications. Unfortunately, this misconception encourages people to make bad health decisions at a
younger age, causing Type 2 diabetes to begin effecting people earlier in life. These poor choices have
created a new disease called Type 1.5 diabetes that acts as a bridge between the two; it has both
autoimmune components and insulin resistance components to it. The Disney movie WALL-E depicts a
scary looking future where people ruined the planet so they escaped on a big spaceship where robots
did everything for them so they just sat in chairs 24/7, watched TV, ate lots of processed food made by
the robots, everyone became obese, and even forgot how to walk because they never used their legs.
Dr. Morris uses this movie as an example of the kind of lifestyle choices people are making that can lead
to dysbiosis in the microbiome and accelerate the development of new complicated diseases like Type
1.5 diabetes. He explains a similar future isn’t far-fetched because we are potentially facing epidemics of
terrifying proportions if we keep going at this rate where new diseases are being created or diseases are
become so much more complicated that we no longer have a simple treatment for them like we used to.
Dr. Gordon, from Washington University School of medicine, published a study that compared the ratios
of phyla present in the microbiomes of healthy controls to the ratios in patients dealing with
autoimmune diseases and related chronic issues. In the literature of the study he provided pie charts for
every healthy control and autoimmune disease to show the major differences between the two. When
comparing the ratio of Bacteroidetes to Firmicutes in a healthy control microbiome to the microbiome
of a person affected by an auto immune disease, there is a significant difference in ratio. We are trying
to combat autoimmune issues by manipulating the ratios of bacteria in the microbiome to try and
achieve that ideal balance of Firmicutes and Bacteroidetes. Bacteroidetes are very important to have in
our microbiome because, even though they can act as opportunistic pathogens when there is a
dysbiosis, we need them to balance the ratios in the microbiomes of patients with auto immune
diseases. Unfortunately, we don’t have the ability to share Bacteroidetes like can with Firmicutes, that’s
why when looking at the ratios in healthy controls there are significant amounts of Bacteroidetes

compared to those with autoimmune issues. The only way to get them is through your diet or fecal
In Dr. Gordon’s study on the microbiomes of obese patients, their analysis showed more Firmicutes than
Bacteroidetes, while thin patients showed significantly larger amounts of Bacteroidetes. For his study he
wanted to see if he could reverse the side effects by reversing the ratios of Bacteroidetes to Firmicutes
in hopes of helping obese patients start losing weight. He proceeded his experiment by using a
polyethylene glycol solution to flood their colon in order strip their lower intestine of all bacteria so that
he could then transplant the desired ratios from obese patient to thin patient and vice versa. His
experiment was successful resulting in the obese patients beginning to lose weight and the thin patients
gaining weight. In patients that suffer from obesity, lipopolysaccharides from bad bacteria are getting
through broken tight junctions that then triggers a process in the cells to take up fat and create adipose
tissue. The bad bacteria in their microbiome is driving this fatty acid depositing mechanism in an
unfavorable direction that is unrelated to caloric intake. An individual that has these bad bacteria in
their microbiome can have a lower than normal caloric intake and still not see the results because of the
mechanisms being driven by certain microbiota.
He saw similar results with the success of another experiment he conducted to test malnutrition. There
was a set of twins with one showing signs of malnutrition. He took the microbes from that twin,
transplanted them into healthy sterile mice, and was able to induce malnutrition in those mice despite
giving them all the nutrition they needed. The goal is to be able to control the gut-brain axis and
behaviors of the body by manipulating the bacteria in the microbiome because all these studies have
solidified the theory that if you have a bad microbiome you are going to have bad health no matter the
amount of nutrition you provide it with. The hard part is finding a way to do that without doing more
harm good to the existing good bugs. Although Dr. Gordon was able to get a few patients to agree to do
the PEG treatment, we probably wouldn’t want to remove all bacteria from a patient’s microbiome just
to treat one issue because that would create a huge dysbiosis potentially causing even bigger problems
for the patient. From studies like these we have been able to take notes to try and come up with a way
to revolutionize this concept of microbiome transplanting by creating a protocol that will allow us to
remove a little bit of the bad stuff at a time so you can add to the good that’s already there.
Dr. Morris explains what he calls, “life’s process” by drawing a lot of nutrigenomics maps to show how
signals are constantly coming into membranes, those signals get translated through the membrane to
the nucleus, the DNA gets activated, which sends out a messenger RNA, that becomes a protein, that
then becomes a signal, which initiates the action that happens. This process is continuously happening
in every aspect of our lives including in our microbiome. Every part of the human body is constantly
communicating back and forth with this community of specialized microbiota that make up our
microbiome, just like it does with the nervous system. Without our microbiota we would lose important
body functions like our innate adaptive immunity because our microbiome is sensing everything in your
gut 24/7 to act as that first line of defense against environmental toxins and pathogenic material. When
that defensive line is compromised by a dysbiosis, or leaky gut, it corrupts that vital communication and
triggers the production of T-helper cells in the wrong direction that leads to autoimmune issues. People
are now starting to look at treatments for autoimmune issues in a different way because now there is
information and evidence that finally explains why these ancient methods, like Ayurvedic medicine and
traditional Chinese medicine, that were once based upon empirical evidence, actually work so well. This
information has made it clear that personalized treatment is required because if every patient with the

same symptoms is treated the same way, we can potentially exacerbate their problem if we aren’t
taking the microbiome into consideration. The more information we get on how the microbiome,
probiotics, and prebiotics affect our bodies, the more it helps drive the development of more natural
alternative approaches to treating patients in the future.