Wednesday, February 25, 2015

The Human Microbiome: Cleaning it Up (Part 1)

Through the Human Genome Project, completed in 2003, scientists finally sequenced and mapped the 23,000 genes of the human body. After this world-changing feat, the scientific community has begun the arduous task of identifying the genetic makeup of the non-human genetic forms in our body. You didn’t misread that… according to the National Institutes of Health (NIH), 90% of cells in the human body are not human. Advances in DNA technologies have birthed an amazing new field of research called metagenomics, allowing comprehensive examination of the microbial communities in and on our bodies. As a result, the Human Microbiome Project (also referred to as the Human Metagenome Project) was initiated in 2007.

The Project is a global initiative with multiple countries participating, whose aim is to characterize microbial communities found at multiple human body sites and to look for correlations between changes in the microbiome and human health. They are doing this by studying the human microbiome. Simply defined, the human microbiome is the total inclusion of every microorganism living in, on, and perhaps even around the human body. It not only encompasses the trillions of microorganisms themselves (bacteria, fungi, yeast, protozoa, and other viruses); it also includes all the combined genetic material of those microorganisms. This genetic material – both the “good” and the “bad” – makes up the building blocks of our DNA that live on our skin and in our nose, mouth, esophagus, lungs, intestines, genitals, etc.

The microbiome is a gift from the mother. When babies are delivered through the birthing canal, they are exposed to their mother’s microbiome, giving their brand new immune system a leg up on cesarean-birthed babies. According to Dr. David Perlmutter, in his new book, Brain Maker, statistics suggest there is an increased risk of disease for infants born by cesarean section. The rate of autism is doubled, Celiac Disease increases 80%, adult obesity increases 50%, Type 1 diabetes increases 70% and ADHD is tripled. Clearly, our healthy germs are critical for our mental and physical health.

Amazingly (or maybe not so amazingly), different diets, families, cultures, and places of residence are reflected in variances in the human microbiome. A study, published in Nature, indicates that changes can happen incredibly fast in the human gut—within three or four days of a big shift in what we eat. Our microbiome is continually adapting to a changing environment.

MarĂ­a Gloria Dominguez-Bello, a microbiologist at New York University, is studying the gut microbiome of hunter gatherers in the Amazon in order to determine what a clean microbiome would look like. “We want to see how the human microbiota looks before antibiotics, before processed food, before modern birth… These samples are really gold.” She is finding that these samples have much greater biodiversity and higher levels of prevotella bacteria… than in the West. Interestingly, these Amerindians have much lower rates of allergies, asthma, atopic disease and chronic diseases.

A Fine Balance
Within our microbiome lies an ecosystem with thousands of species of microbes (microorganisms, especially disease-causing bacteria) living in the cells and tissues of the human body. It is estimated that the combined microorganisms and microbial cells that live inside or on the body outnumber human cells by about ten to one! There are approximately 100 trillion microbial cells in the human microbiota (all the microbes of a particular site, in this case the human body); the human gut alone contains 40,000 bacterial species. It is not surprising that our microbiota influences our health. The symbiotic bacteria in our microbiome can be considered good bacteria, those that benefit us. These bacteria – “the good guys” – escort out the “bad bacteria” and rid the body of digested food and inflammatory molecules. There are also compensatory bacteria, which can be considered neutral; however, these so-called “neutral” organisms can be influenced into becoming good or bad. There are also potential pathogenic microbes (aka pathogens – bacteria capable of causing disease) and we all have them in our bodies. They include popular offenders like Candida, E-coli, and H-pylori, just to name a few. Microbes become pathogenic when they are not kept in check.

Our microbe DNA outnumbers our human DNA 99:1. Pathogens and symbiotic bacteria work and live together, making a sticky, slimy protective matrix in the gut and sinuses called biofilm. The biofilm is like a city where the microbes live, eat and multiply. It is a complex structure that includes channels where food is transported in and waste is transported out. The sticky matrix also helps protect the bad microbes from antibiotics, antifungals, and our immune system. They also communicate via quorum sensing, a sophisticated stimulus/response system that allows them to alert each other of an adversarial event. Pathogens respond and protect themselves, sometimes through mutation, multiplying and becoming more resistant.

In spite of such an overwhelming majority of potential offenders, our microbiome inhabitants coexist on basically friendly terms… that is, until imbalances in the body disrupt the natural order of things.

Gut Microbiome
The gut microbiome influences tissue building and hormone regulation through nutritional absorption, but it also influences how we metabolize the food we eat, and how herbs, vitamins, and medicines work in our bodies. Nutritional absorption is affected by our gut’s health and bacterial composition. The bacteria make metabolites that feed the good bacteria and, in turn, make certain vitamins and help metabolize drugs. They also manufacture enzymes, amino acids and short chain fatty acids. The gut microbiome influences inflammation by up regulating or down regulating the immune system, and it produces hormones that have a direct influence on fat storage. Who would have thought gut bacteria has such a huge influence on whether or not we are overweight?

Let’s look more closely at the variety of ways that our gut microbiome affects our health. Ideally, when we eat food we chew it into small pieces in a process called mastication. Our saliva plays a role in liberating certain nutrients; healthy germs in the mouth are fed by these nutrients and, in turn, support our dental health. Patients with periodontal disease have an abnormal collection of germs that damages the gums and triggers inflammation, contributing to an increased risk of cardiovascular disease.

From the mouth, the ball of partially broken-down food enters the stomach. The stomach acts like a blender, churning and mixing the food with digestive juices. Helicobacter pylori (aka H. pylori) is a germ that lives in the stomach and can cause stomach ulcers if it is not balanced by other germs in the stomach; however, it also helps to signal the brain that we are full – that we are satisfied when we eat. It affects our caloric intake and our mood. The proper balance of these germs is the key.

The stomach action and stomach acid signal the pancreas and the liver to gear up for digestion. Healthy germs in the small and large bowel (again, components in our microbiome) influence the action and health of both organs. If people eat too many carbohydrates, it changes the proportion of two populations of germs in the bowel so that Bacteroides decrease and Firmacutes increase. Firmacutes produce more inflammatory chemicals, and extract more nutrients from any given food than Bacteroides. This is another way these different germs contribute to obesity, which puts extra strain on the liver and pancreas.

The small intestines are lined with a one-cell layer made up of brush border cells. These cells have small finger-like projections call villi and microvilli, which add more surface area for absorption of fluids and nutrients. This is where Lactobacillus bacteria live. They protect and help to manufacture the mucous that protects our gut cells. Without them, our cells are more susceptible to damage. The brush border cells have tight junctions between them that prevent foreign particles from passing through the intestinal wall into the bloodstream. 


Some nutrients are allowed to pass through these openings, but the junctures are too small for undigested food. When these unbroken-down food molecules are able to leak between the cells and enter the blood stream, inflammation is triggered and antibodies, lymphocytes, and cytokines are made, leading to food allergies and sensitivities. Stomach viruses, bacteria, environmental toxins, and food can all disrupt this mucous and cellular barrier, causing pathogenic microbiota to multiply. One cohabitant in our gut that many people suffer from is an overgrowth of Candida, or yeast. Candida does not overgrow in a healthy gut. The gut has to be damaged first; then, Candida sets up housekeeping.

The next-to-last part of the intestines is the colon or large intestine. The majority of the bacteria in our gut are found here. Many of these germs turn on and turn off our immune system. They are critical to our health. This is where Bacteroides predominate, or where Firmacutes can take over. Again, balance is the key.
Harmful Offenders

With a healthy microbiome (and in an idyllic environment), everything works together beautifully, just as described above. Unfortunately, there are other external offenders that muck up the system. Consuming genetically modified foods, Bacillus thuringiensis (Bt) toxin foods (foods containing a bacterial pesticide… discussed in more detail later on), and glyphosate (an herbicide in produce that damages bacteria), gives greater advantage to the pathogenic organisms by destroying the “good” bacteria that were designed to keep the “bad” bacteria under population control. When this imbalance occurs, many adverse events ensue.

Glyphosate, the chemical in Roundup®, is sprayed in large amounts on our crops to kill weeds. Not surprisingly, the weeds are becoming more resistant to this chemical, so larger and larger amounts must be utilized to accomplish the same feat. Glyphosate is not only used as an herbicide – it also is sprayed on many nonorganic grains, beans, peas, lentils and cane sugar to dry out the crop just prior to harvest. Monsanto recommends specific timing to control weeds for the next year and to ensure even ripening and easier harvesting.[1] How widely this practice is utilized by wheat and other farmers is a source of debate. This chemical (and all pesticides and herbicides) also kills the fungi and bacteria that are part of the soil microbiome. These friendly fungi and bacteria in the soil and on the plant roots are responsible for bringing the nutrients from the soil to the plant. When chemicals are used, they wipe out these friendly bacteria and fungi, rendering the plant anemic.

Roundup also has surfactants, which open up the pores of the plant and drive 80-85% of the glyphosate into the plant (and into our bodies), so washing the fruit or vegetable or grain doesn’t help. The surfactants combined with the glyphosate are 1000 times more toxic than glyphosate itself.

Glyphosate also binds trace minerals both in the plants and, once consumed, in the human body, rendering minerals incapable of absorption. Because it depletes our bodies of nutrients in multiple ways, our immune system is imbalanced and our ability to replicate DNA is compromised. It takes nutrients to make healthy DNA (cell replication). It takes nutrients to detoxify. It takes nutrients to make energy. It takes nutrients to have a healthy immune system.

Glyphosate is a potent antibiotic that damages our good gut bacteria and causes an overgrowth of bad bacteria. This causes a huge shift in the gut flora that has profound effects on our health. 80-90% of people with chronic gut symptoms get better over several days-to-weeks when they stop eating processed food and eliminate GMO food from their diet. It even affects our ability to manufacture of L-tryptophan, which is the building block to make serotonin and melatonin. By doing so, it causes problems with mood, behavior, sleep, overeating, and insulin regulation. Glyphosate also knocks out portions of the p450 enzyme pathway, which is responsible for the first phase of detoxification. This results in a bottleneck that slows down detoxification of many other toxins in the body.

Bt toxin is also a huge problem. Companies like Monsanto have taken the Bt bacteria and genetically changed it. They have inserted the Bt toxin DNA into corn, soybean, and cotton cells using viruses, bacteria and a “gun” as a vehicle. The plants themselves then produce the insecticide, and are thusly categorized as a pesticide. Farm animals and humans fed this corn have shown increased gut permeability. When consumed by animals and humans, this toxin first punctures the gut (just like it does in insects), causing gastritis and irritable bowel-type symptoms. The toxin doesn’t just stay local; it leaks across the damaged intestinal walls into the rest of the body. It has been found in the blood of 93% of pregnant women tested, and in 80% of umbilical blood in their babies, according to Dr. Joseph Mercola in a Canadian study. Bt toxin is a “gift that keeps on giving”; it also infects our healthy gut bacteria, turning them into pesticide factories.

It’s not just environmental chemicals and Bt toxic food that damage the gut. Dr. David Perlmutter, author of Grain Brain, reported on a study that showed that gut biopsy specimens from patients with and without Celiac disease both released zonulin (a protein that increases gut permeability) when exposed to gliadin (a protein in wheat, and a component of gluten). This damage was most pronounced in samples from Celiac disease patients, but it was also present in specimens from patients without Celiac disease. This means that whether or not you have a genetic predisposition for autoimmunity, eating wheat will cause the release of zonulin, which in turn may cause a leaky gut and may lead to autoimmunity.

Zonulin levels were measured to indicate the degree of gut “leakiness “ from these toxins or other insults. Zonulin, secreted by the gut lining, causes brush border cells (the tight junctures between the gut cells in the small intestines) to open, allowing food particles, bacteria, and toxins to eventually pass into the blood stream. The damage to the tight junctures and the gut cells – whether from stress, repeated courses of antibiotics, NSAIDS, toxins, Bt toxin, glyphosate or GMOs – may result in increased gut permeability (also referred to as “leaky gut”), leading to the occurrence of food sensitivities, autoimmunity, malabsorption and chronic disease.

Brain-Gut Connection
There is also a clear brain-gut connection when it comes to zonulin and wheat. Zonulin causes the blood-brain barrier to become leaky just like the gut. Bacterial, viral, and fungal toxins can do the same thing. Aristo Vojdani, PhD, owner of Cyrex Labs, published a comprehensive review of the causes of a leaky blood-brain barrier. Similar to the gut tight junctions, cells that line the blood vessels and feed every single nerve cell can also be damaged and then bridged by many toxins and infections. Ergo, if the gut is leaky, the brain may not be far behind. Leaky Gut = Leaky Brain = Chronic Diseases and Food Sensitivities.

The digestive system contains half of the body’s nerve cells. The system that connects the gut to the brain is called the enteric nervous system (ENS). Its neurons are embedded in the walls of the gut, from the esophagus to the anus. The ENS has 100 million neurons, more than in either the spinal cord or the peripheral nervous system. Every class of neurotransmitter is made in the ENS. These neurotransmitters and the nerves that produce them have an intimate connection to the brain.

It’s not just the gut giving feedback to the brain via the ENS. The brain also directly communicates with the gut. Mental stress can alter the body’s environment chemically, thus affecting the microbiome, which in turn affects the ENS.

Malabsorption of nutrients necessary for brain function also affects our mental state. The gut bacteria make vitamins B-7 (biotin), B-12, and others. If there is not a healthy gut flora, there will be a deficiency in these vitamins. This may contribute to depression, fatigue, memory problems, neuropathies, diabetes, hair loss, gray hair, and anemia, just to name a few.

85% of Serotonin and Dopamine neurotransmitters are made in the large intestines. Disruption in the gut’s health and these neurotransmitters has a huge impact on mental health. In last month’s article “The Chemistry of Sex”, we showed the connection between certain neurotransmitters and sexual health. Who would have thought there was also a direct link between the gut health and sexual health?

Restoring Balance
The reestablishment of a healthier microbiome is critically important and necessary for optimal health. Next month’s article will discuss probiotics, more information on how certain bacteria influence our health, and what we can do to manipulate those bacteria in our favor through diet, rest, supplements, and reduction of exposure to toxins and drugs that damage our gut microbiome.

This article is part one of a two-part series. Make sure to check back with us to read part 2!


[1] http://roundup.ca/_uploads/documents/MON-Preharvest Staging Guide.pdf

Content created by Elizabeth R. Vaughan, MD, and Tina Arey, BSN, RN

3 comments:

robbie said...

great article

Elizabeth Vaughan said...

Thank you, Robbie!

Anonymous said...

What would be considered a healthy gut microbiome of a hunter gatherer would be considered an unhealthy gut of a westerner and vice versa.