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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 an 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 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 transplants.

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.