Human Microbiome, Healthy Gut Bacteria, and Adrenal Fatigue Syndrome Part 1

By: Michael Lam, MD, MPH; Justin Lam, ABAAHP, FMNM

Healthy Gut Bacteria and Adrenal Fatigue Syndrome

The human microbiome in the gut is one of the most populous in our body, keeping a balanced population of healthy gut bacteria is key to good healthHuman microbiome is defined as the entire habitat, including the microorganisms, their genomes (i.e., genes) and their surrounding environmental conditions. The word itself is derived from the word biome which refers to the characteristics of an environment including abiotic (nonliving) as well is biotic (living) factors. Human microbiome can easily be mistaken from another commonly encountered term called microbiota, which is the composition of the microorganism population within a defined environment, such as the GI tract or oral cavity. An estimated 90 percent of cells found in the human body are not human after all but of mostly prokaryotic origin, derived from at least 40,000 bacterial strains in 1,800 genera. Though considerably smaller in size, these approximately 100 trillion cells weigh up to five pounds in an adult individual – approximately the weight of a full-grown human brain. They inhabit in all parts of the body that are exposed to the environment, such as the mouth, skin, and vagina. The biggest population resides in the gut where healthy gut bacteria have a constant supply of the nutrients necessary for their survival. Taken collectively, these organisms outnumber our human cells 10:1.

Human Microbiome Development

The fetal gut is sterile and is established at birth with microbes from the mother’s vaginal and fecal microbiome as well as with other environmental microbes confronted in the first days of life. Early colonization depends on the delivery mode, diet (breastfeeding vs. formula feeding), hygiene, and antibiotic treatment. The first colonizers are facultative anaerobes (e.g., Escherichia coli and Streptococcus spp.) and obligate anaerobic species, which colonize as oxygen levels in the gut decrease. A child’s microbiome stabilizes and becomes adult-like at three years of age. Throughout adulthood, our human microbiome is in a continuous process of self-balancing to help the body maintain homeostasis.

As we grow into old age, changes in our human microbiome occur, resulting in decreased microbial diversity, and with that, increased inflammation.

Most of the microbes in our body are not harmful at all, but help in maintaining processes that are necessary for a healthy body. They do not cause diseases under normal circumstances, and are deemed to be members of the normal flora or normal human microbiome. Our body needs healthy gut bacteria for a multitude of functions including the carrying out of various enzymatic reactions that otherwise we cannot do on our own, or synthesis of vitamins such as vitamin K necessary for good health.

Human Microbiome and Metabolism

The human gut has some functions it cannot perform such as digesting cellulose and needs a healthy human microbiome to help process food correctly.Metabolism is a term used to describe all chemical reactions involved in maintaining the living state of the cells and the organism. It is closely linked to nutrition and the availability of nutrients. Healthy gut bacteria are responsible for breaking down the complex molecules found in some foods such as vegetables and meats. They therefore assist in our metabolism. These microbes are not only responsible for harvesting energy for themselves from the plant fibers we consume, but also breaking down such plants into smaller molecules so our body can digest them easily. A simple study in mice showed that certain bacteria are associated with metabolic derangement such as obesity. When obese mice were injected with the gut microbiome of normal mice, the obese mice lost weight completely. The reverse was also true, i.e., when normal mice were injected with the microbiome of obese mice, the normal mice gained weight. Similar studies using human twins, different in weight, with similar upbringings and identical genomes, manifested the same association between obesity and human microbiome from the gut.

Research has also shown a direct relationship between diet and the thriving of certain gut microbial communities. This should be rather obvious. For instance, vegetarians have gut flora that is better equipped for breaking down plant roughage, making the otherwise indigestible molecules, such as cellulose, available for humans. During the bacterial metabolism of the complex molecules, chemical signals that are released end up in our brains and can affect behavior. It is not a great speculative leap to then consider that the microbes responsible for these chemical signals may be behind certain food cravings and have an effect on what we choose to eat. Clearly, the association between our human microbiome, healthy gut bacteria and metabolism is far greater than we envisioned.

It is interesting to note that at specific sites on the body, entirely different sets of microbes could perform identical functions for different people. For example, completely separate families of microorganisms existing on the tongues of different individuals will perform the same breakdown of sugars. So what are the functions of all of the microbes living in our bodies? The microbes benefit from a persistent, stable habitat, rich in energy from the food we ingest, and we in turn claim heat energy from the bacterial breakdown of compounds like cellulose that are indigestible by the human gut. The interaction between the human body and the microbes it plays host to is far reaching. The internal functions that go on in the body, which are essential for a healthy body, are dependent on specific microbiomes at various sites throughout the body. When human microbiome becomes imbalanced or altered, it is known as dysbiosis.


Dysbiosis can lead to systemic inflammation, which is associated with a wide array of diseases and conditions including heart disease, diabetes, obesity, asthma, and even autism. Dysbiosis is also being implicated in several inflammatory bowel related problems, notably those that are symptom-based such as ulcerative colitis and Crohn’s disease. There is also a strong association with the brain, triggering irritable bowel syndrome (IBS). Each of these debilitating conditions has strong links to shifts in healthy gut bacteria.

A common cause of dysbiosis is ingestion of antibiotics that destroy symbiotic and competing strains necessary for optimum balance. When our normal human microbiome is altered, our immune system can become negatively affected.

Human Microbiome and Immune System

The populations of our internal human microbiome, like healthy gut bacteria, to teach the immune system what bacteria is good so it only attacks the bad.Early in life, human microbiome from the gut plays an integral role in the formation of a very strong immune system in humans, especially during our early childhood as the adaptive immune system develops. During this time, our immune system becomes accustomed to the foreign antigens in our body and develops a tolerance for such foreign antigen. Once a homeostasis is built, non-pathogenic microbes and the other harmless antigens will not provoke an inflammatory response. This is a good adaptive response to keep our body in a steady state. Over exposure to allergens, when combined with a weakened or underdeveloped immune system, can trigger inflammatory responses that are pathological, such as acute allergies, food sensitivities, chemical sensitivities, and autoimmune diseases. This concept is principally illustrated in germ-free mice (i.e., mice kept sterile throughout their life). These sterile mice are exceptionally unhealthy and have drastically underdeveloped immune systems. They exhibit undesirable traits and suffer from autoimmune diseases.

It is clear that the human microbiome that is first developed in the gut of an infant, can have a perpetual effect on his or her health. Scientists have compared babies delivered through C-section, where the newborn is colonizing its mother’s skin biome, and babies vaginally delivered, where the infant is colonizing its mother’s vaginal and gut biomes. Babies delivered through C-section have a greater likelihood of developing obesity and allergies than their vaginally delivered counterparts.

Human microbiome and leaky gutWhen dysbiosis occurs at the GI tract, resulting inflammation can lead to damaged mucosa. The tight junction between mucosal cells is compromised and triggers further immune system responses. Unwanted proteins, toxins, and bacteria can more easily pass through the damaged lining of the gut and enter our systemic circulation. This is often referred to as a leaky gut. This can result in brain fog, depression, pain of unknown origin, fatigue, anxiety, insomnia, just to mention a few.

On the other hand, having healthy gut bacteria and diverse human microbiome in the gut, and therefore no gut inflammation and leakiness, supports a person’s immune system. Those with healthy human microbiome in the gut tend to be physically strong and less prone to infections and recurrent illnesses. Their defense system is simply stronger.

Human Microbiome and The Brain

The human microbiome in the intestinal track hasa strong connection to the brain. A bi-directional communication channel connecting the gastrointestinal and neural systems, also known as the gut-brain axis, coordinates the behavior of healthy gut bacteria with brain activity. This axis has a significant impact on brain development and behavior. It is evidenced that this extended communication system affects a broad spectrum of diseases, including psychiatric disorders, irritable bowel syndrome, and demyelinating conditions such as multiple sclerosis.

The brain can directly affect human microbiome in the gut, via signaling molecules discharged into the gut lumen from the cells in the enterochromaffin cells, neurons, and immune cells. The brain can also influence the enteric human microbiome directly or indirectly, via changes in gastrointestinal secretion, motility, and permeability of the intestine.
The reverse is also true in this bi-directional gut-brain highway. Communication from human microbiome ni the gut to the brain can occur via epithelial-cell, receptor-mediated signaling, and – when the intestinal permeability is improved – through direct stimulation of the immune cells. The disruption of these bi-directional interactions between human microbiome in the gut and the nervous system may be involved in the pathophysiology of chronic and acute gastrointestinal disease states, including the functional and inflammatory bowel disorders.

The gut has so many nerves that it is sometimes called the second brain. It's important to keep a healthy human microbiome to keep both brains happy.The gut is therefore, called our “second brain” for good reasons. In addition, many neurotransmitters, including serotonin, are made in the GI tract. Microbes normally present in the gut stimulate host intestinal cells to produce up to 90 percent of the body’s serotonin. Peripheral serotonin is produced in the digestive tract by enterochromaffin (EC) cells and also by particular types of immune cells and neurons. Microbes are needed by the EC cells to make serotonin. EC cells are therefore rich sources of serotonin in the gut. Without proper healthy gut bacteria, serotonin, also called our “feel-good neurotransmitter” is severely compromised. Changes in levels of peripheral serotonin have been linked to conditions such as IBS, cardiovascular disease, depression, and osteoporosis.

Human microbiome also has an important influence on the behavior of its host. Many nerve endings are positioned around the gut, which transmits signals straight to the brain via the vagus nerve. Metabolites and other minute molecules that are released from healthy gut bacteria can influence everything from taste to mood. In fact, in a study, scientists swapped the microbiome of risk-taking mice with that of cowardly mice and their risk-aversion interchanged as well. Other studies have hypothesized that the types of food we crave, as well as what tastes good to us, can also be commanded by the human microbiome population in our guts. It may even be related to the human microbiome population’s ability to make use of particular foods for energy.

Human Microbiome and The Liver

The liver is the body’s major metabolic clearing house. It is responsible for breaking down food, toxins, nutrients, medications, etc into smaller component parts called metabolites and prepare them for excretion as part of the body’s overall detoxification process to keep us clean internally. The interaction between the innate immune system and the intestinal microbiota during obesity or autoimmunity promotes chronic liver disease progression. There is a central relationship between the immune system, human microbiome, and liver disease initiation and progression.

Liver disease has long been associated with qualitative and quantitative (overgrowth) dysbiotic changes in normally healthy gut bacteria of the intestinal microbiota. Unhealthy external factors, such as high sugar, a fatty Western diet, and alcohol, can alter the homeostasis. Dysbiosis results in intestinal inflammation, a breakdown of the intestinal barrier, and translocation of microbial toxic products across the intestinal wall into the liver, which can promote liver injury and inflammation. It is clear that human microbiome–immunologic–liver interaction plays an important role in overall health.

Read Part 2

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

Dr. Lam’s Key Questions

Eating a diet high in refined carbohydrates, sugar, and alcohol can cause the candida population to grow out of control.

Fat cells have 4x more cortisol receptors than peripheral tissues.

human microbiome