As we learned last month, the connection between our gastrointestinal (gut) microbiome and our health is a very new area of scientific research. In the past, scientists were able to identify the totality of the human genome—the set of instructions that each cell in our body contains, to allow us to live and function. Like the human genome, the microbiome has been subject to intensive research to unravel all of its genetic information, i.e. the genes that are attached to all cells, bacteria etc.   The challenge with identifying and classifying the gut microbiota is that it contains over 3 million genes, making it 150 times more genetically varied than the human body. What science does know is that there is a link between the bacteria in our intestines and virtually every disease that ails us.

Due to the sheer numbers of gut microbiomes, there was an assumption that they must have an impact on our health. Why else would they exist in such large numbers in our body? However, until recently, scientists did not know much more than that. Of all the microbes, bacteria are the most abundant type in our intestines. Therefore, this has been the focus of most scientific studies—looking at the DNA of the bacteria in our intestines. Researchers are trying to determine whether specific bacteria cause particular diseases, and if there is a way to change the type of bacteria in our intestines to prevent disease.

A healthy gut is one that contains lots of different and diverse types of bacteria. When this occurs, the gut is in a better position to fight off and resist pathogens. For example, if one strain of bacteria is unable to do its job for whatever reason, then another similar type can step in and keep things running smoothly. What is still unknown is how to ensure or even to measure all the components of a healthy gut microbiome. For now the health of the gut is best measured by how well it is performing the totality of its very important jobs, rather than being able to determine the specific breakdown of all the types and amounts of bacteria in the gut.

There are certain lifestyle behaviours that have been identified that promote a healthy gut. These include eating a healthy diet, having adequate exercise and sleep, and reducing exposure to stress. Thus, each of our lifestyle choices influences and determines the content of our gut microbiome. We also live our day-to-day lives in different environments; we each have a different combination of habits and surroundings. Because of this, each of us has a gut microbiome that looks at least slightly different to that of even our parents and siblings, even between twins, and even more so to people that live far from us, especially in different countries and continents.

In fact, the microbiome that each of us have is so unique from anyone else’s that it can be called our bacterial fingerprint. For this reason also, it is difficult to say exactly what makes up a healthy gut microbiome. Because of the diversity of the gut microbiome from person to person, it is reasonable to conclude that there is no one healthy gut microbiome.

Even if science cannot yet identify the specifics of a healthy microbiome, a healthy microbiome is assumed if the following takes place: a healthy gut has a barrier that is effective at keeping the contents of the gut, such as its own microbiota, undigested food particles, and toxins, from escaping into the bloodstream. This barrier helps to fight off infections, while it is in the process of performing all of its usual digestive and regulatory functions, absorbing and synthesizing nutrients that are essential to keeping your body running at is best.

Last month we learned of the Human Microbiome Project. They were able to provide the initial characterization of the normal microbiota of healthy adults in a Western population. The goal of the project is to define all the microbial species that affect human and their relationship to health, thus providing large, publicly available databases from their genetic studies. Each individual hosts thousands of bacterial types, with different sites in the body having their own distinct communities. Because most of the microorganisms living in humans are located in the gastrointestinal system, this is where most new discoveries are being made.

In June 2012, five years after the start of the Project, researchers announced that more than 10,000 microbial species occupy the human “ecosystem” and they have identified between 81-99% of the genes contained in the microbiome. Because of the recognition of the close connection between our health and the microbes that live within us, the gut microbiome is becoming a cornerstone of preventive medicine. If we can develop a healthy gut, we can prevent diseases from developing.

Identifying variations in microbiomes between people can lead to an understanding of microbiome-based diseases by studying the differences in the microbiomes of healthy and unhealthy people. The Project developed ways to insert a new strain of organism into an existing microbiome without affecting the overall balance and function of the microbiome. This manipulation of bacterial colonies could potentially lead to treating disease by adding organisms to the microbiome that target specific health problems. It also opens up the potential for probiotic treatments and new methods of analyzing the makeup of the gut microbiota. Recent research has been done in knowing how potential germs/pathogens from outside the body invade the human body, and how this relates to the gut microbiota and its ability to function as a barrier. This will help to identify ways to limit the invasion of potentially harmful microbes and their disease-causing effects.

It has been determined that if the numbers of microbes grow beyond their typical ranges it compromises our immune system. Also, poor hygiene and injury can cause microbes to populate areas of the body where they normally do not colonize and contribute to illnesses such as urinary tract infections. Or, if microbes are introduced into areas of the body that are considered sterile, such as the blood, the lower respiratory tract, or the abdominal cavity, disease can result, such as bacteremia/sepsis of the blood, pneumonia, and peritonitis (infection of the abdominal cavity). Candida, which is the cause of yeast infections, occurs when certain microorganisms over-colonize (grow in number beyond what is considered normal).

“The indigenous microflora stimulates the host immune system to respond more quickly to pathogen challenge and, through bacterial antagonism, inhibits colonization of the GI tract by overt exogenous pathogens.” In other words, our gut microbiome stimulates our immune system to respond more quickly to the invasion of disease-causing micro-organisms, and prevents these micro-organisms from taking up residence in our intestines and causing disease.

The human microbiome has an influence on the following four broad areas of importance to health: Nutrition, Immunity, Behaviour, and Disease. We will learn about the first three in this month’s article. Next month we will learn more about the influence of our microbiome on specific diseases.


When considering the relationship between nutrition and the human microbiome, without a healthy gut microbiome, we would not be able to absorb nutrients and we would die. It helps us break down the complex molecules contained in proteins and vegetables, which our stomach and small intestine are not able to digest. However, what we eat also impacts the health of the gut microbiome. The capacity of diet to modify the gastrointestinal microbiome of humans and other mammals has been extensively studied. Results indicate that the composition of the diet, habitual dietary intake, and acute dietary changes all impact the microbial communities within the gut

A diet that is deficient in key ingredients, including fibre and prebiotics, can negatively impact the composition and the function of the gut microbiome. This is turn affects its ability to absorb nutrients. Therefore, it is crucial to the health of the microbiome and to the health of the entire human body to eat foods that our microbiome and our body need to function at its optimum level. Studies of human populations across the globe show that greater dietary fibre and whole grain intake is associated with a more diverse gut microbiome. Low-fibre diets cause depletion in the diversity of the human gut microbiome, and subsequent increases in chronic diseases such as obesity, cardiovascular disease, diabetes and colon cancer. For example, significant changes in bacterial diversity in the gut can occur in as little as 24 hours when someone switches between a meat-based diet that is lacking fibre, to a plant diet high in fibre (more than 30 g/day). Next month we will discuss fibre and prebiotics in more detail.

A healthy gut microbiome reduces food cravings and promotes feelings of being full, thus helping to prevent overeating. The more diverse one’s diet is, the more diverse the microbiota. Adults trying out a wide variety of foods display a more varied gut microbiota than adults who follow a set dietary pattern. As we have learned, good health is directly connected to the diversity of the gut microbiota.


Humans acquire their first microbes from the entrance of their mother’s cervix on their arrival into the world. Without this early introduction of microbes from the mother, adaptive immunity would not exist. Adaptive immunity refers to a vital defensive mechanism that our body uses when it encounters disease-causing organisms for the first time. Our immune system learns how to “adapt” to these organisms. With repeated exposures it allows for a quicker and more effective immune response to disease-causing organisms, preventing them from causing illness. Testing done in mice that are completely lacking gut microorganisms shows an underdeveloped immune system. Autoimmune conditions and allergies are more likely to develop when exposure to maternal microbes is disturbed early on in life, such as in infants born via Caesarean section.

A significant proportion of our immune system is in our gastro-intestinal system (gut). More than 70% of all the white blood cells in the body live in the gut. White blood cells consist of all the germ-fighting cells in the body. Immune system bacteria in the gut line the walls of the inside surface of the intestine, preventing harmful bacteria from entering into the body. Bacteria also line the outside walls of the intestine. The total bacterial composition of the human gut plays a role in the healthy functioning of the immune system. The gut is also the second largest site of exposure of the body to the outside world after the skin, which is a largely impermeable barrier. In most people, a delicate homeostasis (balance) develops, with the immune system ignoring commensal (normal) bacteria and food proteins, but actively eliminating pathogens which cause disease. When an imbalance develops, it can lead to inflammatory bowel diseases like Crohn’s disease and ulcerative colitis. These imbalances can play a role in illnesses throughout the body as well.

Research has shown that there is significant interaction between the body’s immune system and the bacteria in the gut. However, the implications of this interaction are not yet fully understood. How exactly the immune system interacts with gut bacteria and how that relationship functions in the prevention of disease is unknown. Most recently, research is looking into the way the composition of the gut changes in the presence of different diseases. Scientists are only beginning to understand the microbiome, and they don’t necessarily know what a “healthy” bacterial composition might be yet.


The composition of our gut microbiome affects the brain. And, in fact, the gut microbiome is often referred to as a “second brain”. It influences neural (nerve cell) development, brain chemistry, and a wide range of behaviours, including emotional behaviour, pain perception and how the stress system responds. Links have been identified between the gut microbiome and psychological disorders such as depression, anxiety and autistic spectrum disorder (ASD).

As with nutrition, not only does the gut microbiome influence various brain functions, the brain can also exert a powerful influence on gut bacteria. Even mild stress can affect the microbial balance in the gut, making the person more vulnerable to infectious disease and triggering a cascade of reactions that feed back to the central nervous system (brain and spinal cord).

Part of the nervous system is located in your gut, and is considered a part of the total nervous system in our body which comprises our brain, spinal cord, and the nerves that go from the spinal cord to all the parts of the body. The nervous system in our gut is able to perform some tasks on its own, independent of the brain, such as coordinating reflexes and secreting certain enzymes, one of which is serotonin. Even though serotonin is known as a brain chemical, 95% of serotonin is made in the intestines. Altered levels of gut serotonin can cause irritable bowel syndrome (IBS), which affects 20% of North Americans. IBS symptoms occur when food moves through our intestines either too fast or too slow; low levels of serotonin causes constipation whereas high levels causes diarrhea. Flare-ups of IBS can also be caused by stress or anxiety, which come from the brain. Nerve pathways connect your gut nervous system and your brain, and each affects the other—think of butterflies in your stomach when you are nervous, or having to use the bathroom when you are anxious. Some gut nerve receptors are responsible for sending messages to your brain that signal nausea, bloating, and pain. Others change your sensitivity to or intensity of how distended or full your intestines feel.


Dysbiosis is a state that occurs when the gut microbiome becomes imbalanced or disrupted. Some causes that have been identified include stress, illness, being overweight, overuse of antibiotics, or eating a poor quality diet. Continuous activation of the immune system because of lifestyle choices and the inflammation that goes along with these choices puts us at risk for a range of diseases and can compromise both our physical and mental health. Next month we will learn more about the diseases that are linked to an imbalanced gut microbiome.

“Over many graves might be written. . . . Died of an abused stomach.” –Child Guidance, p. 374

“Never cheat the stomach out of that which health demands, and never abuse it by placing upon it a load which it should not bear.” –Christian Temperance and Bible Hygiene, p. 58