Your microbiome exists symbiotically in your gut to enhance gut function, stabilize the gut environment, and even perform functions your gut can't do!A human body contains over 10,000 microbes — or more than ten times the number of human cells! The genome of the microbiome, as an entity, is 100 times larger than the human genome, implying that the majority of genetic material inside your body is not actually yours, but the microbes’. These microbes include viruses, fungi, and bacteria that use the body as a habitat to form a balanced ecosystem. This ecosystem is called the microbiome, which is found in and on the bodies of humans and living things—in the mouth, on the skin, inside the gut. The human microbiome includes both harmful and beneficial organisms. The balance is shifting constantly and can affect the human host’s health. For the most part, the bacteria found in your body are valuable to your health and well-being and play a vital role in your survival. These bacteria are not only depended on for survival, they assist in the daily functions of digestion, vitamin creation, and protection against infections, as well as in a plethora of other roles. This article primarily deals with the gut flora, those microorganisms that live in the digestive tract.

The NEM Stress Response

The neuroendometabolic (NEM) stress response is the body’s system of dealing with stress. There are six major components or circuits, each comprised of various organs and systems programmed to act on specific, targeted anti-stress responses. These components work synergistically to ensure that your body is well taken care of in the face of stressful situations. The neuroaffective and inflammatory responses are two circuits within NEM stress response that significantly alter mood, immune function, and cognition. These circuits involve three intricately interconnected components—the gut, brain, and microbiome—forming what is called the gut-brain axis. What happens to one component will affect the others. The neuroaffective circuit is made up of the autonomic nervous system, central nervous system, and gut. The inflammatory response circuit is composed of the gut, microbiome, and immune system. As you can see, the gut and its microbes are important to both circuits and link the two. The brain and gut seem so different and so far apart, so how does the connection work? Let’s take a look.

The Gut-Brain Axis

Gut flora influence various brain functions, affecting your thoughts, emotions, and memory. Three quarters of the body’s neurotransmitters are actually made in the gut. That is why the signals that go between the brain and the gastrointestinal (GI) tract are vital to establishing and maintaining homeostasis, immune health, and hormonal levels. This connection is regulated by the central nervous system and the enteric nervous system. When there is a disturbance in either of these systems, it affects your ability to respond to stress and influences your overall behavior. As can be seen in those with inflammatory bowel disorder (IBD) and irritable bowel disorder (IBS), there is a strong correlation between anxiety and gastrointestinal disorders that demonstrates the significance of the connection axis between the brain and GI tract.

There is also mounting evidence suggesting that the enteric microbiome (in the intestines) affects gut-brain communication, hence the naming of the microbiome-gut-brain axis.

Your gut flora - making up the gut microbiome - can heavily influence the signals the gut sends to the brain.An unbalanced collection of gut flora (dysbiosis), combined with stress, could lead to damage the gastrointestinal lining and increase the permeability of the blood-brain barrier. Thus, an unbalanced population of gut flora can contribute to the inflammation of the whole body in addition to affecting the neuron signaling from the gut to the brain.

How Microbiome Affects the Human Brain

There is a wealth of evidence that demonstrates complex interactions between host and microbe. There are three particularly important methods by which the microbes in your gut interact with the brain: directly, via the vagus nerve and a network of nerves that wrap around the gut and transfer signals to the brain; through the circulation of primed immune cells that exist in the gut and move towards the brain; and through metabolite molecules, produced by gut microbes, that enter first the bloodstream and then the brain and eventually affect behavior. These metabolites have been shown to cause abnormalities associated with anxiety and autism when injected into healthy functioning mice. This could lend further support to the possibility of microbial molecules connecting the brain, gut, and neuroaffective circuit of the NEM stress response system.


There is currently no perfect standard for a healthy intestinal microbiome. Due to environmental and genetic considerations, there are considerable differences in people’s “normal” gut flora. Generally, microbes that are healthy and diverse help to promote gut health and to maintain metabolic, structural, and signaling functionality. However, the gut can become imbalanced in a variety of ways; in particular, the term dysbiosis involves a change away from the normal diversity and stability found in the gut microbiome. This presents with an unstable gut that is unable to function normally and may eventually lead or contribute to neurological, metabolic, or autoimmune disorders. Causes of dysbiosis include environmental toxins, alcohol intake, excess stress, and overgrowth of yeast and bacteria.

For those with Adrenal Fatigue, high stress levels can often lead to dysbiosis. In addition, since your body is in a low energy state, the gut (and other bodily functions) often slows down in an effort to conserve energy. As your gut slows down, food stays in your stomach longer, resulting in reduced assimilation, longer transit times, and increased inflammation, as allergens have more time to seep into the body through the gut. If the food stays in the gut for a prolonged period of time, it can even start to rot in the stomach, releasing toxic compounds into the stomach. This may be another cause for gut dysbiosis.

Leaky Gut and Inflammation

Stress from the environment, relationships or other sources affect the balance of your microbiome causing dysbiosis and breakdown of normal gut functions.When the mucosal lining of the gut fails in its role as a barrier to protect against potentially damaging molecules that can enter the blood flow, the resulting condition is known as leaky gut. Lipopolysaccharides on the outer membrane of gram-negative bacteria can then be found entering the bloodstream, prompting an inflammatory response. Inflammation influences the brain in several ways and is thought to be a major contributing factor to depression. In fact, selective serotonin reuptake inhibitors (SSRIs)—one of the main classes of drugs used in depression treatment—has been found to reduce inflammation in the brain. This anti-inflammatory effect may be an important part of why the drugs are effective. Thus, it is easy to see how your gut can have a major affect on the neuroaffective circuit and your mood simply through an elevation or reduction of inflammation.

Increased permeability of the intestinal lining can also lead to food allergies, malabsorption, and toxic overload. There is a saying that a leaky gut leads to a leaky brain, as the buildup of toxins can cause changes in mood, depression, fatigue, poor memory, confusion, and anxiety.

Unfortunately, the details of these connections are difficult to study because every individual’s gut microbiome is unique, and the terms healthy and unhealthy are in reference to an individual’s specific state of normality.

Gut Flora and Neurological Disease

Disturbances in the gut — such as an alteration in the composition of the microbiome — have been linked to neurological disorders such as multiple sclerosis (MS), Parkinson’s disease, and autism spectrum disorders. A Parkinson’s patient’s first symptom is usually constipation; the second is often the loss of taste and smell. These gastrointestinal disturbances are present long before the symptoms of motor neuron dysfunction, such as tremors or a shuffling gait, appear.

Multiple environmental risk factors for neurological conditions have been found to promote an immuno-inflammatory response. In particular, improper folding and aggregation of proteins within the brain is a possible etiology for several neurodegenerative disorders. This could be caused by inflammation in the gut triggering inflammatory effects in the brain that cause misfolding of proteins and degeneration of neural cells.

Gut dysbiosis and inflammation have also been linked to autoimmune disorders. Western nations present with higher rates of multiple sclerosis and also tend to share similar dietary habits. These diets are thought to cause inflammation and disruptions in the optimal functioning of gut microbes. Patients with Parkinson’s disease and MS both have increased numbers of antibodies to a variety of antigens and lipopolysaccharides due to a more permeable intestinal lining. Taken together, the evidence indicates that a dysregulated inflammatory response circuit can be the result of prolonged stress, among other factors.

Alzheimer’s disease and general cognitive decline are marked by changes in the brain, disruptions in immune function, and increasing oxidative stress. These factors are all shaped by diet and gut flora in animal experimental models. One important link involves a neurotrophin, a type of protein that is responsible for the protection and the encouragement of healthy neurons. The production of this neurotrophin is dependent on the gut bacteria, and declines in individuals with Alzheimer’s. Changes to the microbiome occur with age and can be linked to neurodegeneration.

Gut Flora and Psychiatric Disorders

The connection between the gut and the brain mean that the microbiome has a strong influence.The connection between the gut and mental health has garnered increasing attention in recent years. Various psychological disorders, especially depression, may actually be disorders of inflammation, with the gut being a crucial mediator. Several animal studies have demonstrated that transplantation of microbes from anxious or depressed mice to germ-free mice could induce the same behaviors in the previously healthy mice.

Anxiety and depression are also common symptoms of Adrenal Fatigue. It is therefore vital for those suffering from Adrenal Fatigue Syndrome to keep the microbiome healthy. This will help to restore balance to the neuroaffective circuit, calming the body down and enabling a speedier recovery.

Read Part 2

© Copyright 2016 Michael Lam, M.D. All Rights Reserved.

Dr. Lam’s Key Question

When you feel bloated after eating cheese, it may be that your digestive system is missing the enzymes to digest lactose. Taking digestive enzyme may help or specifically lactase.

Microbiome are the make up of Gut flora