Chapter 10 Solving The Brain Puzzle: The Microbiome Linking Gut and Brain Health

Please enjoy this excerpt from my book, Solving The Brain Puzzle.

For more information on enhancing the 100 trillion microbes that inhabit your gut please visit Taymount Canada Gut Flora Transplants

10: The Microbiome: Linking Gut and Brain Health  

Contributed by Dr. Teri Jaklin, ND  

As a naturopathic doctor, the gastrointestinal system is central to the recovery and maintenance of human health. Often when I introduce this concept to patients, I get one of two responses—a blank stare or total agreement, punctuated with comments like “I have always had problems in my gut” or “I knew it! I just didn’t know how to explain it!” The truth is, this understanding is not exclusive to naturopathic medicine. It is seen in many traditional medicine practices the world over. This almost intuitive historical understanding of the gut in health has been unraveling itself in the evidence base for decades. More recently, the explosion of scientific data, especially in the last decade, has put the human microbiome front and center in how we consider immunity, inflammation, changes in innate immunity (previously called autoimmunity), and ultimately the potential of the brain to heal and recover.  

In 2008, the National Institutes of Health’s Human Microbiome Project began to shine the scientific spotlight on how important the microbial environment of the gut is.  The volume of research that followed makes it arguably the hottest topic in science and illuminates the significance of the microbiome in human health. What may be most intriguing about the new science is how the brain affects the microbiome and how the microbiome, in turn, affects the brain in what has become known as the brain-gut (or gut-brain) axis.  

You may be asking yourself, what exactly is the microbiome, and how does the gut affect the brain? At its core, the microbiome has a unique fingerprint, different layers of tissues with specific functions, that do not really change from day to day. It is populated by 100 trillion microbes, referred to as the microbiota, a dynamic part of the microbiome that can easily change within just 24 hours. Its structure and function can be influenced by what you eat and drink along with the state of your digestion, whether you were delivered via C-section at birth, your geographic location, emotional or physical stress, and medical practices, such as vaccination and antibiotic use. It is different depending on age, ethnicity, and possibly even gender, and can even be impacted based on your mood, what kind of a day you are having, or if you are jet lagged! If the microbiome is altered for more than five days, a proinflammatory environment is created in the gut. In fact, studies on EAE (experimental autoimmune encephalomyelitis), an experimental model of brain inflammation in mice, suggest these proinflammatory conditions in the gut result in the onset of “autoimmune diseases,” among which is MS (Escribano et al. 2014) in the traditional manner (see the New MS chapter).  

Your microbiome contains an incredible number of genes responsible for everything from digestion and nutrient absorption to blood sugar balance, detoxification, and even the overall tone of the immune response. The microbiome produces short-chain fatty acids, amino acids, neurotransmitters, and vitamins—building blocks for every essential function of the body. Its mucous membranes protect against pathogens, and the microbiome is central to the overall immune response, determining whether an immune response is tolerant or reactive, i.e., inflammatory in nature (Kranich 2011) .  

Centered in the gut, the microbial population of the microbiome reaches far and wide from the skin and sinuses through the urinary tract and even populates a woman’s vagina. The intestines house several pounds of microbes, making it the most densely populated area of the microbiome. One gram of stool contains more microbes than there are stars in the sky! This is optimally the most diverse ecosystem on the planet, and it is exactly this diversity that is key. Bacteria, viruses, fungi, yeast, and parasitic elements, both good and bad, make up the veritable microbial soup. When there is an abundance of the different species, they work together to provide a powerful barrier between the toxins and foreign proteins within the intestines and the rest of your body and can play a significant role in disease prevention or recovery.  

If that diversity is compromised, as it is by things like alcohol, food sensitivities, genetically modified foods, medications like acid blockers (protein pump inhibitors), NSAIDS, and antibiotics, sleep deprivation, thyroid dysfunction, or extreme temperatures, there are fewer health-promoting species and more pathogenic species. Thus, the gut is put in a state of dysbiosis, which alters the microbiome structure and plays a role in the inflammatory, functional hormone, and metabolic balance of the body. This dysbiosis can potentially enhance disease susceptibility. Dysbiosis causes different responses in different people. In one person, it may present as an itchy skin rash, while someone else may experience headaches, peripheral neuropathy, blood sugar imbalance, or inflammatory arthritis. Other symptoms common in dysbiosis can be fatigue, poor sleep, depression, brain fog (cognitive dysfunction), menstrual problems, motor function, and lack of strength. Do any of these sound familiar?  

Structurally, dysbiosis causes the tight junctions between the cells of the gut barrier to break down and render the gut barrier permeable, i.e., “leaky gut.” One of the biggest challenges of a leaky gut is that endotoxins, such as LPS (lipopoly– saccharides) and food proteins can pass through into the blood, where they activate an immune response. This is a normal response, as food particles in the blood are foreign proteins to the body. This immune response causes a release of inflammatory chemicals called cytokines, which set up and perpetuate generalized inflammation, which can turn up anywhere in the body, from rheumatoid arthritis of joints, dermatitis of skin, or brain inflammation, presenting as depression or other neurodegenerative diseases.  

The presence of LPS in the blood plasma provides a measurable value that correlates directly to the level of gut permeability. As such, it can also be considered, to some degree, a marker for inflammation. LPS has been measured and is visibly increased in mood disorders, ALS (Lou Gehrig’s Disease) (Zhang 2009), and autism (Emanuele 2010), indicating the gut has become permeable and the resulting systemic inflammation is targeting the brain, increasing the permeability of the blood-brain-barrier (BBB), causing, you guessed it, leaky brain. Once the BBB is breached, the brain’s immune cells are activated, causing one of the foundations of all brain injury, neuroinflammation. An additional link of the gut-brain/brain-gut communication occurs via the vagus nerve (Yu et al. 2014), which senses changes in the microbiome and sends cytokines and other inflammatory chemicals to the brain. The conversation between the gut and the brain is incredibly important in the control of neuroinflammation, which has become a hallmark in neurodegenerative conditions (e.g., MS, Alzheimer’s, and Parkinson’s).  

A 2015 study linked chronic intestinal inflammation to a reduction in hippocampal neurogenesis, the brain’s ability to create new neurons (Zonis 2015). The hippocampus is involved in learning, memory, and mood control. Researchers have shown that decreased hippocampal neurogenesis secondary to neuroinflammation can lead to significant behavioral changes, cognitive impairment, and depression. This neuroinflammation also damages mitochondrial DNA, affecting energy production in the electron transport chain that controls energy production in brain cells. Together, neuroinflammation and mitochondrial dysfunction further damage neurons through increased production of reactive oxygen species and are thought to play a fundamental role in the pathogenesis of neurological disorders, such as MS, Alzheimer’s, Parkinson’s, and stroke (Witte et al. 2010). Ultimately, we rely on neurogenesis, healthy mitochondrial function, and the production of BDNF (brain-derived neurotrophic factor) to keep our brains healthy. This can now all be linked to having a healthy gut.  

In case you were wishing you had never taken those NSAIDs or had not had such a thing for junk food, rest assured, that is only part of it. The formation of the microbiome begins long before neuroinflammation can actually damage the brain in an in-utero exchange between mother and fetus. It is richly inoculated as the baby passes through mom’s vaginal microbiota on the way out. Breastfeeding passes more beneficial microbes from the mother through the breast milk, and so the creation of the precious, omnipotent microbiome evolves. You can imagine then, how a C-section birth would impart a dramatically different population of microbes. Rather than picking up mom’s microbial contribution, the microbiome is instead seeded by the microbes on the skin of the attending physician and nurses, the air in the delivery room, and any other microbes the newborn may come in contact with. If a baby is born by C-section, it has been shown to be more susceptible to allergies, asthma, celiac disease, type 1 diabetes, and inflammatory bowel disease, all because the microbiome is seeded differently at birth (Funkhouser 2013).  

So, if you were a C-section baby and/or not breast fed, and/or if your mom was given antibiotics during her pregnancy, chances are you have a very different and disadvantaged microbiome. To take it one step further, a recent study published in the journal Microbiome adds that early adverse life events (like trauma) can cause an altered microbiome and correlates those events with an abundance of certain microbial species and distinct changes in brain structure, suggesting a possible role for gut microbes and their metabolites in the development and shaping of the gut-brain axis early in life (Labus et al. 2017). If you were unlucky enough to have been one of those kids with constant ear infections or chronic tonsillitis, requiring round after round of antibiotics, guess what? More bad news. That negatively affected your microbiome too! As you can see, the brain pathologies we develop may actually have their grounding at the beginning of our lives in situations we have had no control over. However, despair not. We can change tomorrow by changing what we eat, probiotics, prebiotics, and, if need be, fecal microbial transplant (FMT).  

At this point in history, western cultures have largely eliminated bacterial pathogens through hygiene, antibiotics, and rigorous sanitation practices. This is now playing itself out in the dysbiosis, leaky gut, neuroinflammation, and neurodegeneration of our population. I would venture to say that the biggest issue in most neurodegenerative conditions is failure in the gut-brain axis.  

Individual studies implicating gut dysfunction with neuroinflammation and the pathogenesis of neurodegenerative conditions like Alzheimer’s (Fox et al. 2013; Daulatzai 2014), Parkinson’s, ALS, traumatic brain injury, and MS are too numerous to mention. But I encourage you to take a look at the simple search engine instruction “dysbiosis and multiple sclerosis.” This will yield a weekend’s worth of reading.  

Since the diversity of the microbial population is the most important feature of a healthy microbiome, a healthy immune response, and ultimately a healthy brain, we can begin to take corrective action under the premise “heal the gut, heal the brain.”  

While pharmaceuticals cannot improve the biodiversity of the microbiome and its eventual neuroinflammation and mitochondrial dysfunction, there is abundant evidence supporting modifiable lifestyle factors that can. What follows are five simple but powerful steps you can start to take today to begin to restore your microbiome.  

1. Food changes the microbiome for better or worse. Diet rapidly alters the microbiome. Think about your diet as eating to seed. Include prebiotic foods like chicory root, dandelion greens, garlic, jicama, and Jerusalem artichoke. Include probiotic foods like sauerkraut, kimchi, kombucha, and kefir. Eat whole, unprocessed food and strive to consume fifty different foods each week. Avoid sugar. Not only does it promote pathogenic species in the gut, consumption of it has a direct correlation to increased incidents of dementia (Crane et al. 2013). 
2. Many studies show that exercise improves microbial diversity and immune function. Some studies even show that changes due to exercise are independent of changes made via diet. This is important, because that means changing both can have an additive effect.Studies show that cardiorespiratory fitness is a good predictor of gut microbial diversity in healthy humans, and the microbiome in high cardiorespiratory fitness individuals seems tofavour decreased LPS pathways (Estaki 2016; Kang 2014; Cook 2015).  
3. Avoid genetically modified foods (GMOs) and glyphosate. This herbicide is associated with GMO foods, is used as a desiccant to harvest wheat, potatoes, sweet potatoes, and other foods, and is known to cause changes in the microbiome by acting as an antibiotic and a mitochondrial toxin, deactivating vitamin D3, and impairing liver detoxification (Samsel 2013).
4. Like every other system in the body, stress hormones change the microbiome (Panda 2014), and the anxious or negative thoughts we have during times of stress further impact it. Building stress resiliency is key. Tranquility promotes a healthier microbiome by calming the gut-brain axis. Find time each day for stillness, whether that be meditation, prayer, deep breathing, walking in nature, or any other gentle activity that will calm the brain to heal the gut. 
5. Take a probiotic supplement. If you are uncertain how to begin, speak to your health care practitioner. 

Increased diversity of the diet and more exercise independently alter the wellbeing of the gut microbiome and reveal independent associations with anxiety and cognition (Kang et al. 2014). Most of the time, the job of the immune system is to not respond! 

33: Microbiome, Brain Issues, and Gut Flora Transplant (GFT) or Fecal Microbiota Transplant (FMT)  

Dr. Bill Code 

Everyone who has worked as a nurse or physician in a hospital or been a patient will know how each patient is very bowel focused. In some ways, knowing what we know now, they are more correct than anyone accepted or realized. Almost any chronic illness, immune or “autoimmune,” can be helped considerably by a healthier gut microbiome (Mullin 2011, 2017).  

Our gut (from the mouth to the anus) hosts 10 trillion microbes, which is ten times our human cells! The number and type of microbes varies for each region—mouth, stomach, small intestine and the colon, which has the greatest number. Our host-bacteria associations must be seen as of mutual benefit. In short, like it or not, we are a team. Like any team, we must work together and support each other, or every player will suffer. As the host body, without this team approach, we will become sick in a multitude of ways. Perhaps now you can see why our food diversity, fermented foods, prebiotics, and probiotics can support out team. Damage to the team comes from many sources: antibiotics, glyphosate (Shehata 2012), vaccination, major antacids (PPIs), and processed foods, to name a few. We can help our microbe team by what we put in our mouth.  

A final rescue, if needed, is possible with gut flora transplant (GFT) or fecal microbiota transplant (FMT). I will now use the new term, Gut Flora Transplant (GFT) as this term is more correct because if properly prepared there is no feces at all in the implant. I had this done in 2016 and will outline the procedure later in the chapter. Case reports of GFT (FMT) have shown good outcomes in Parkinson’s, MS (Borody 2011), and chronic fatigue syndrome. The literature to date has used FMT but the Taymount Clinics have adopted GFT as the preferred term. Taymount has now performed 30,000 implants worldwide. I suspect that this is more than everyone else combined. I will use FMT if quoting the term from a published article, but will put GFT in brackets behind it to help you help us with the more correct, safer and palatable term Gut Flora Transplant (GFT).  

According to Meng-Que Xu et al., “FMT (GFT) achieved a successful cure rate in recurrent C. difficile infection. Although there is a deficiency of randomized controlled trials for FMT (GFT), the present review reveals that FMT (GFT) could be a promising rescue therapy in extra-intestinal disorders associated with the gut microbiome, including metabolic diseases, neuropsychiatric disorders, autoimmune disease, allergic disorders, and tumors” (Xu 2015).  

Our intestinal microbiome is key in nutrition defense against nasty microbes (bacteria, fungi, and viruses), immune system development, and performance of the gut wall function (i.e., degree of leaky gut syndrome). In addition, our cells interact and cross talk. This is one of our greatest epigenetic controls. Epigenetics suggests turning genes on and off for a favorable and healthier outcome.  

Our individual gut microbiome is influenced by our sanitation, social behaviors, and genetics. Sanitation can be positive or negative. For example, chlorinated water can have negative effects on our microbiota, but it makes our water safer from some things, such as nasty strains of E. Coli. Social behavior can be as simple as a child eating and playing in soil, which is beneficial but often discouraged. Similarly, the quaternary “hand wash” units at the entry to public buildings do more harm than good. Soap and water works better against the dreaded C. difficile bacteria. The compounds in the hand cleansers are very harmful to us. In fact, the FDA has recently warned against their use (Commissioner FDA 2018).  

The four predominant bacteria phyla (groups) in the human gut are Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria. If the first two, Bacteroidetes and Firmicutes, are reduced, then chances increase for the development of IBD (inflammatory bowel disease), and CDI (clostridia difficile infection). Similarly, an increase in Proteobacteria (including a subgroup called Enterobacteriaceae) is found in IBD and MS patients. Meanwhile, the increased presence of Bacteroides fragilis, a commensal or innocent bystander, can prevent and cure inflammatory disease via the effect of its symbiosis factor, Polysaccharide A.  

It is beyond the scope of this book to address all possible health issues potentially impacted by improved microbiota. Suffice it to say that strong evidence suggests that FMT solves C. difficile. In addition, increasing evidence in Nature indicates that FMT may be impactful in MS (Branton 2016). There is also a strong association between MS and irritable bowel syndrome. An excellent article by Aric Lodgson describes how the BBB (Blood Brain Barrier) connects the microbiome and the brain (Lodgson 2018). Finally, brain microbiota disruption are implicated in demyelinating lesions in MS (Branton 2016).  

When my personal journey with MS began twenty-two years ago, I did not envision a link to my gut flora, now known as the microbiome. Nor did I envisage having a gut flora transplant. However, in March 2016, I had a GFT at the Taymount Clinic in the United Kingdom. I have continued with a top-up from Taymount once a month since. We now know diet changes can modulate the gut microbiome in MS patients (Saresella 2017). More on my personal experience later. For the moment, how did we get here? One of the fastest-growing topics in the literature today is the awareness, investigation, and increasing understanding of the importance of the gut in virtually all animals, including humans. The question could arise: who is supporting whom? In reality, it is an incredible synergy that changes our epigenetics, our sense of well-being, and even our longevity. I can think of nothing that treats us so simply but impacts us so greatly. The blood-brain barrier connects the microbiome and the brain (Clapp 2017).  

Over the last few years, under the leadership of Dr. Enid Taylor, naturopath, and Glenn Taylor, microbiologist, the Taymount Clinic has conducted more than 30,000 fecal microbial implants. The initial interview, when one is still at home, determines if dysbiosis is present. Anyone with a significant health challenge can apply for consideration of treatment of GFT. Clients are encouraged to become gluten-free prior to FMT. The treatment begins with a period of a very good stool softener. Clients are encouraged to have at least one colonic irrigation one to two weeks prior to arriving at the Taymount Clinic. This colonic irrigation is repeated on the first day at the Taymount Clinic. Then, immediately after the colonic, clients receive their first rectal instillation of the donor implant. Following the implant, clients are placed in several positions to facilitate movement of the 50–60 cc of fluid throughout the colon. The instillation, but not the colonic, is repeated daily. If a client is only being treated to control C. difficile, then only four more treatments are required. All other dysbiosis issues are treated by an additional five installations the following week.  

Donor implants are collected under major safety protocols. They are all evaluated with DNA typing for the numbers and diversity of microbes, thus ensuring quality of transplantable microorganisms. In addition, all donors have been comprehensively tested for critical viruses and have no chronic viral illness, such as hepatitis B or C or HIV/AIDS. Each donor unit is stored at -80°C for three months, and the original donor is tested again for all the same viruses, as some of these may be lingering and declare themselves within that three- month time frame. I believe this is the safest, most diverse, and healthiest GFT (FMT) available in the world. The Taymount Clinic also provides this same quality donor material to Taymount Bahamas, Taymount Canada, a clinic in Germany, and one in Slovakia.  

In March 2016, I had a series of ten microbiota implants in the UK. The process was done carefully and completely. I was pleased by how professional the procedure was completed. I complied with the daily Bimuno, which is a prebiotic that enhances growth of Bifido bacteria. This is superior to Bifidus probiotics, because this enhances the growth of your own “wild” type bacteria. These function and maintain much better than ordinary probiotic Bifidus. The probiotic Bifidus are typically many generations away from wild and tend to not persist within our microbiota. Kefir is a fermented food highly recommended by Dr. Enid Taylor (2013).  

The newest probiotic now taken by all the Taymount donors is Symprove. This product has been tested extensively by a quality third-party investigator in London, UK, with excellent results. Symprove is able to succeed where almost all other probiotics do not. It will soon be readily available in North America. Currently, it must come from the UK. On a personal note, I recommend the Symprove passion fruit flavour. I found the natural flavour quite a challenge to swallow. www.symprove .com has a wealth of research results from university- led studies comparing it with other forms of probiotics. Symprove outperforms all other types of probiotics as it survives the stomach acid, arrives in sufficient numbers immediately to have a beneficial effect and thrives in the large intestine, to the benefit of the host. Its actions are facultative, not being part of the microbiome, but supporting and enhancing it.  

By the eighth day from beginning my GFT, I noted increased energy and brain clarity. This pleased me immensely. In addition, my IBS symptoms have virtually disappeared. Studies have confirmed that quality microbiota implants like these are good at persisting within our bodies. However, we must look after them by staying gluten-reduced, better gluten- free and possibly dairy-free and by avoiding antibiotics and glyphosate-containing foods.  

The Taymount Clinic makes additional implants available to purchase. I use a further GFT approximately monthly. Overall, I have been quite pleased with the results, hence this lengthy chapter discussing GFT.  

It seems that everything happens for a reason. Little did I know that when my best friend from medical school suggested that hospitals have become plague centres, he was right. By being admitted to hospital, you dramatically increase your risk of developing methicillin resistant staph aureus (MRSA) or Clostridium difficile (C. difficile). These are the two most common killing bacterial infections today despite a plethora of antibiotics. At present, your chance of a speedy death once admitted to hospital is 10 times as likely as that of dying in a motor vehicle accident. C. difficile is now found throughout our communities. In fact, only a couple of strains of this organism are particularly lethal. Almost all other strains are normal inhabitants with helpful benefits within our gastrointestinal tract. Meanwhile, these two key strains of C. difficile are difficult to treat, with the standard antibiotic therapy working about 15 percent of the time. However, four to five installations of a quality GFT have a better than 95 percent recovery rate.  

When did C. difficile become recognized as such a danger? This occurred in the intensive care units in the hospitals in the 1980s. When a patient had a severe infection or even a fever of unknown cause, without a specific organism cultured, that person was typically put on three different broad-spectrum antibiotics. This triple therapy was often lifesaving but sometimes caused the patient to develop pseudomembranous colitis. This latter condition occurs because of extreme overgrowth of C. difficile, which produces a severe toxin. In fact, during my oral exams in anesthesiology in 1988, one of my questions was about severe sepsis in a patient on the ward. This was an appropriate question, because, in Canada, anesthesiology residents spend six months in intensive care training during their five-year residency. Fortunately, I answered appropriately, the patient survived, and I passed my exam. Since that time, we have come to understand and treat the microbiome as a “virtual organ” that is equal in importance to our liver or our kidneys. So, a gut flora transplant is not unlike a liver or kidney transplant in importance. In addition, a typical microbial transplant is a lot easier, safer, relatively painless and, as yet, quite unavailable in many medical centres today. In reality, GFT is not a medical procedure and its donors are carefully selected, tested for critical viruses at least twice, then GFT has essentially no human epithelial cells and therefore virtually no immune reaction as you would with an organ transplant. 

We now know that the brain’s function is influenced by the bacteria within the intestinal tract. This is frequently called the gut-brain axis, and it is pivotal in understanding brain wellbeing. To help you understand this symbiosis, I want to give excerpts from a talk by Dr. William Shaw of Great Plains Laboratories, called “Microorganisms and their effect on mental health.” This includes all brain health, so it is very pertinent to this book.  

In 1957, a test showed that virtually all people with mental health illness had an abnormal protein in their urine. This finding in the literature noted by Dr. Shaw, and he went on to develop his organic acid testing on urine samples. In 2010, he published it in Nutritional Neuroscience (Shaw 2010). This publication was the culmination of 15 years of work and showed that there was an abnormal phenylalanine metabolite created by some bacteria. This metabolite is formed in the gastrointestinal tract relative to which particular strains of Clostridium are present. He found these proteins especially common in the urine samples from patients with autism and schizophrenia (Shaw 2010). These researchers noted that these substances were present in all mental and neurological illnesses, including MS and Parkinson’s disease. The two proteins that Dr. Shaw especially concentrates on are HPHPA and 4-Cresol. These are not produced by Clostridium difficile but rather by some of the other strains of Clostridium. This means that by using a sophisticated urine test, we are able to confirm that an overabundance of certain Clostridium species may be dramatically affecting our mental health or neurological brain health.  

The evaluation of the organic acid test is, in many ways, like the testing we do in newborns to check for inborn errors of metabolism. Dr. Shaw’s initial interest was in a young child who had developed psychosis during hospitalization. He confirmed that the patient’s urine demonstrated an excess of these abnormal proteins. These are from six different strains of Clostridium, with the dominant ones being Clostridium sporogenes and Clostridium botulinum. This is the same botulism that is significant in food poisoning. People can be carriers of this particular organism, and it may not cause problems in them. Alternatively, these individuals have a low-grade infection, and it may be noted simply as a “bad cold.” This means they do not get severely ill, and rarely would they be diagnosed as severe food poisoning or botulism. You may know much more about Clostridium difficile or it’s more popular name, C. diff. However, there are six critical strains of Clostridia that are actually much more common than C. diff. I will now outline how these can make such a difference to one’s health.  

The structure of the protein HPHPA is similar to the catecholamine neurotransmitter dopamine. You may remember hearing the importance of dopamine in Parkinson’s. If the proteins HPHPA or 4-Cresol are in excess, then they dramatically block the conversion of dopamine to norepinephrine (noradrenaline). The secondary effects of this are an excess amount dopamine and a reduced or inadequate amount of norepinephrine. It is the excess of dopamine that psychiatrists are trying to block when they prescribe antipsychotics to control hallucinations. These drugs block some of the effect of excess dopamine. Dopamine is a very reactive molecule compared to other neurotransmitters. In addition, dopamine degradation or breakdown naturally produces a large number of oxidative species, otherwise known as free radicals. Ordinarily, over 90 percent of dopamine is stored in the little vesicles or sacs at the end of nerve terminals. When there is an excess of dopamine, some of it leaks into the cell space, where it creates toxic issues. The breakdown products of dopamine injure neuron structure and function. This excess amount of dopamine especially injures the cells that ordinarily produce dopamine, such as the Substantia Nigra. These cells are critically destroyed prior to Parkinson’s symptoms developing.  

Once one uses an organic acid urine test to confirm that these patients have a dramatic excess of these particular strains of Clostridium bacteria, treatment is possible. The first published treatment of these organisms was reported in the Journal of Child Neurology (Sandler 2000). Eight of these 10 patients got better with the use of oral vancomycin, an antibiotic. The treatment of these Clostridia organisms is particularly challenging, because many of them live as spores as well. These are tiny pieces of protein that are very resistant to treatment and can linger on surfaces. According to Dr. Shaw, today’s preferred mode of treatment is more of a pulse treatment of either vancomycin or metronidazole. In this instance, one takes the regular amount for two to three weeks and then for one day and then stops for two days and then uses it every third day up to a month. The amount of antibiotic is no different than treating it daily for 10 days, but it has a much better response by eliminating more of the spores because of the longer duration of pulse therapy.  

I may sound ridiculous with my above comments when compared to the microbiota heath concepts in the previous chapter. However, please allow me to explain. First, antibiotics can still be lifesaving and life altering, if used judiciously. Second, if we can help resolve a mental or neurological illness with a course of pulse antibiotics, then we should use them. Then we can focus on helping the microbiota recover to a more optimal one, as this is a large part of how the illness began in the first place. All the suggestions in the previous chapter still apply. In many cases, these should be enough. However, if the above-recommended choices are not enough, the newest option is GFT.  

Before closing I want to emphasize that I believe improved microbiome diversity is critical to the recovery of any neurodegenerative disease including MS, Parkinson’s and Alzheimer’s. Furthermore, it is being shown to have an impact on our mental health challenges, TBI, diabetes mellitus and even cardiovascular disease. The recent article by Menni “Gut microbial diversity is associated with lower arterial stiffness in women” and hence reduced atherosclerosis helps highlight why so many health problems improve as the blood vessels and therefore blood flow improve (2018). Better blood flow means better oxygenation and less hypoxia and less inflammation. The latter two are cornerstones to illness recovery. 

For more information purchase my book Solving The Brain Puzzle.