Scientifically, we are just beginning to understand that health issues do not occur as an isolated incident or event in the absence of other contributing factors. Many different factors act together to influence the development of health problems. Variables like age and gender along with other genetic and environmental factors may play a role in the onset of multifactorial conditions.

Rather than a simple case of using an antibiotic for a bacterial infection or a vaccine to prevent a viral infection or the one gene/one disease theory, the story is more complex. The infectious disease landscape itself has also become more complicated in spite of the advent of antibiotics and more aggressive vaccination programs since the 1950’s. Not only are our tools to deal with health conditions more sophisticated today but also the diseases themselves and the advent of multiple antibiotic resistant organisms emphasize that this is not as simplistic as we first perceived it to be in the 1950’s.

We now talk in terms of the “total microbial or pathogen burden”, and its effect upon an individual. It is not uncommon in this day and age for people to harbor a number of chronic bacterial and viral infections in their system simultaneously. These organisms can be seen as taking advantage of an unhealthy body to set up housekeeping in a system that has the right conditions to allow them to grow and flourish.

The issue is not just the microbial organism per se, rather multisystem imbalances in the body that create an atmosphere that allows for the growth of these opportunistic organisms. Recognize that you need to address the microbial environment as well as the specific offending microbes. Simply put, if your gut is a swamp you are going to attract offensive organisms as compared to a more pristine gastrointestinal environment.

This is not that dissimilar from termites infesting rotting wood. While this is a repulsive visual image, it makes the point that it is important to look at all aspects that affect health in your life, to prevent your body from becoming a veritable pillar of rotting wood that will allow the growth of the microbiological equivalent of termites in your system.

A slightly less distasteful way to look at “opportunistic” organisms is to think of them in terms of their ability to take advantage of you. Opportunistic organisms are not unlike invaders in your home. Opportunistic organisms invade your body when it is vulnerable in the same way that an intruder will invade your home if it is unlocked with the front door left wide open! While it is still possible to have an intruder even with the best security precautions, you are less likely to have intruders if the front door is closed and locked. In a similar manner you may sometimes become ill even if you take excellent care of your body. However, we can reduce the risk of human invasion into our homes with proper prevention, just as we can reduce the risk of opportunistic microbial invasion in our bodies with proper attention to all aspects of our health.

Supporting with a range of specific normal flora may help to populate the gut with preferred species and serve as a protective layer from nonideal organisms. Realize that your intestinal tract houses up to 100 trillion microbes. Helping to define those organisms aids in creating a positive gut environment, one that is less conducive to the growth of disease causing bacteria.

You can think of the lining of your gut as a brick wall. Assume for this example that the bricks are not held together with mortar. Like a well-built brick wall, this wall will withstand the test of time without mortar to hold the bricks together if you choose the building materials wisely. On the other hand, if the bricks don’t fit together well, if there are huge gaps between them, then water, mold and debris will begin to accumulate in those gaps. Over time the wall will begin to slowly decay as the integrity has been impaired. So too, if your gut is not lined with healthy normal flora it opens the door for less desired bacteria to inhabit the area. The gaps in the wall of normal flora allow for leakage of food particles through the gut wall, which can be a factor in allergic and inflammatory gut conditions.

“The adult human intestine is home to an almost inconceivable number of microorganisms. The size of the population— up to 100 trillion—far exceeds that of all other microbial communities associated with the body’s surfaces and is … Thus, it seems appropriate to view ourselves as a composite of many species and our genetic landscape as an amalgam of genes embedded in our Homo sapiens genome and in the genomes of our affiliated microbial partners (the microbiome)…The gut microbiome, which may contain > 100 times the number of genes in our genome, endows us with functional features that we have not had to evolve ourselves” (Backhed, Science).

My personal preference for probiotics is a mixture of normal flora that is focused on species of Lactobacillus and Bifidobacter as the main sources of normal flora. I have found that this helps to create a gut environment that is less likely to allow for the growth of nonideal microbes.

Normal flora helps to protect the gut from the growth of pathogenic organisms. Antibiotic use is well known to cause imbalances in normal gut flora. The use of antibiotics without concurrent addition of probiotics, therefore, can predispose to the growth of streptococci as well as other pathogenic organisms.

Unfortunately many individuals have issues with chronic streptococcal infection or chronic issues with other bacteria in the body. Streptococcal infection in the gut can serve as a reservoir to reinfect the sinuses. Chronic streptococcal infection has been associated with OCD behavior as well as tics, over stimulatory behavior and perseverative speech. Streptococcal infection can also lay the groundwork for leaky gut which can relate to decreased weight gain or slower growth.

“Imbalances in the flora of the GI tract may begin as early as birth. Maternal streptococci, for example, can be transmitted from the mother to the neonate during delivery. Although researchers originally believed that transmission occurred solely via vaginal delivery, more recent data suggest that streptococcal infection can also occur in infants who have been delivered via cesarean section. The rate of mother-to-infant transmission of streptococci during vaginal delivery is between 20 and 30 percent” (Yasko and Mullan, Autism Science Digest).

Studies have shown that there is an interaction between the immune system, the nervous system, and the microbial environment within the gut. In this way, gastrointestinal function not only affects digestion but also the function of other organs and systems in the body, most notably the brain and nervous system.

“Over the past few decades, research has significantly changed the way that scientists understand gastrointestinal (GI) function and dysfunction. We have come to recognize that the GI tract is, in fact, far more subtle and complex than initially thought. Studies have illuminated how the complex interaction of the immune system, the neuroendocrine system, and the microbial environment within the gut affects not only GI function but also the function of other organs and systems in the body, most notably the brain and nervous system. We now understand that body systems and organs function within a web of physiology and biochemistry, and we no longer consider each system as discrete and isolated from the others“ (Yasko and Mullan, Autism Science Digest).

Infection with a particular type of streptococcus, group A beta-hemolytic Streptococcus can result in a pediatric syndrome labeled pediatric autoimmune neuropsychiatric disorders (PANDAS). Individuals with PANDAS develop tics, OCD symptoms, and, in some cases, psychosis.

Chronic streptococcal infection, and possibly Escherichia coli infection can lead to a variety of inflammatory mediators as well as depleting neurotransmitters. Streptococcal infection leads to elevated levels of the inflammatory mediators that have been directly implicated in Tourette syndrome, facial tics, OCD behavior, and schizophrenia. These same inflammatory mediators can also allow for elevated levels of glutamate, an excitotoxin; excess excitotoxins can excite nerves to death.

Lack of Vitamin B12 is well documented to cause a range of neurological symptoms. There is a close relationship between gut health and vitamin B12 levels. One of the factors that contribute to increased gut acidity and gut flora imbalances include vitamin B12 deficiency. Excess stomach acid in the system can cause loose stools and severe stomach pain, increased gut acidity also can predispose to microbial imbalance. This deficiency in B12 can stem from particular Methylation Cycle SNPs or the presence of Helicobacter pylori, the bacterium that causes stomach ulcers. In addition, the use of antacids and medications for acid reflux can also decrease B12 levels. Intrinsic factor is a substance produced by the gastric lining that helps the body to absorb vitamin B12. Sufficient stomach acid is necessary for intrinsic factor activation. Efforts by the body to increase B12 levels lead to increased intrinsic factor and would be expected to increase stomach acid. Thus, Methylation Cycle SNPs that decrease the level of B12 in the body can contribute to an environment that is conducive to the growth of microbes that can flourish in an acidic environment.

While the growth of many bacteria is inhibited in an acidic environment, several bacteria can survive and flourish in a more acidic environment including Streptococcus (the bacteria that is a culprit in strep throat), Escherichia coli (the bacteria that can cause food poisoning and urinary tract infections) and Helicobacter pylori (the bacteria associated with stomach ulcers and cases of acid reflux). Increased stomach acid secondary to B12 deficiency, therefore, leads to a gut environment that predisposes to the growth pathogenic bacteria that can survive in an acid milieu. This is a key example of why you want to work on both the gut environment as well as the specific offending organisms. Until you change the environment you will continually battle the same nonideal organisms.

Helicobacter pylori itself has been reported to be a factor in B12 deficiency. This lack of B12 creates a catch 22, such that it contributes to the more acidic environment that can then attract the presence of H. pylori as well as other nonideal organisms.

Helicobacter pylori is an ulcer-causing gastric pathogen that is able to colonize the harsh acidic environment of the human stomach. Reportedly one third to half the adult population harbors H. pylori in their systems. Recent findings suggest that children with autism have a much higher than expected incidence of H. pylori (Yasko). Although the stomach is protected from its own gastric juice by a thick layer of mucus that covers the stomach lining, H. pylori takes advantage of this protection by living in the mucus lining itself. In the mucus lining, H. pylori survives the stomach’s acidic conditions by producing ammonia. The ammonia creates a cloud around the bacterium, making it possible for H. pylori to escape the harsh acid environment. Because H. pylori burrows into the mucus layer of the stomach and is very persistent there, it is difficult to get a positive test for it when it is present and is extremely difficult to eradicate. H. pylori affects neurotransmitters and brain neurochemistry. H. pylori infection increases the incidence of food allergy by facilitating the passage of intact proteins across the gastric epithelial barrier. H. pylori also decreases levels of B12 in the body and increases ammonia which in turn can decrease BH4. H. pylori infection is not just an immediate acute infection. Rather, it is a long-term chronic problem that may take months or years to eradicate. Chronic H. pylori gastritis alters feeding behaviors, delays gastric emptying, alters gastric neuromuscular function, impairs acetylcholine release; these effects can persist for months after the infection has been eradicated.  Click here for Dr. Amy’s thoughts on H. pylori testing.

Multiple factors impact the ability of bacteria to survive and flourish. In addition to taking advantage of an acidic environment, many microbes require the presence of iron for growth and/or virulence. Recall that iron also helps to cause a detour to nowhere described above in terms of the SHMT SNP in the Methylation Cycle. If addressing chronic microbial issues are goals of your personal Roadmap to health, then a strong consideration would be to use a general vitamin that is not high in iron.

As chronic bacterial infection is addressed it should help to aid in aluminum excretion since bacteria appear to retain and sequester aluminum. Aluminum is known to have a range of toxic effects in the body, including interfering with pathways that help to decrease excess glutamate. In addition, aluminum interferes with the production of BH4 regardless of the presence of specific MTHFR SNPs that negatively impact BH4 levels. Therefore, the presence of aluminum may be indirectly affecting levels of serotonin as well as dopamine in the body through its effects on BH4.

One of the overall impacts of chronic infection in the body is to increase oxidative stress and stimulate the immune system. Both of these factors can negatively influence BH4 which, again, can decrease the levels of your ‘feel good’ neurotransmitters, serotonin and dopamine.

A very high protein diet can also affect BH4 levels. Ammonia is generated from the intake of high protein foods. The body uses two molecules of BH4 to detoxify one molecule of ammonia to urea. This is an ‘expensive’ way to use your BH4. Again, recall that BH4 is also needed for dopamine and serotonin. This is just another example of looking at the multifactorial factors that come together to play a role in health. A high protein diet combined with chronic bacterial and viral issues that cause oxidative stress and immune activation, along with SNPs that decrease BH4 and aluminum retention by nonideal microbes…can all contribute to a perfect storm of complex health conditions

Next Chapter:

Environmental Burdens

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