Over eons, the human immune system has evolved to keep us to keep us healthy. When harmful viruses,
bacteria, parasites or fungi enter our body, the immune system recognizes them as potentially dangerous invaders and then attacks to neutralize them. The immune system can also identify human cells that have gone awry, such as mutated pre-cancerous cells and is designed to disarm such cells before they start to grow and multiply out of control.
But, our immune system doesn’t do its job effectively on its own. It relies on training and support from about a hundred trillion microbes that live and on the human body. 90% of cells found in the human body are in fact non-human! And they are not simply passive squatters. The human-microbiome 
has co-evolved for many millennia and provides invaluable health benefits to us. In exchange for providing these friendly microbes (our commensal bacteria) with nourishment and a place to live, our microbes form an integrated and vital component of our body’s immune system.
Scientists are exploring the idea that the human genome itself does not contain all the genes required for optimal functioning but instead relies on genes found in our microbes to protect us from certain illnesses and chronic diseases, such as inflammatory bowel disease (IBD), for example. To the extent this is true, then disturbances to the healthy microbes that make up our microbiome can our harm health in direct and measurable ways.
Some microbiologists have gone so far to suggest that our immune system is in fact being regulated by our own microbial inhabitants!
Our Microbiome Supports our Immune System
The bacterial component of our immune system performs several different functions. It partners with our own immune cells to prevent disease caused by harmful microbes or mutant cells.
Starting at birth, our microbiome helps train the developing immune system in very young children. Disease fighting commensal microbes (the good guys) directly attack the disease-causing microbes (the bad guys), thereby signaling to the human immune system when to launch an attack against the threat. Healthy gut microbes line the digestive tract and prevent a “leaky gut” that would otherwise permit particles in the gut from entering the body and blood stream where they can cause ill health effects. Health-promoting microbes in the gut help to control inflammation, a component of many life-threatening chronic illness. Without these valuable services they provide, we would be much more vulnerable to disease.
Training the Immune System in Babies
The first few years of life are vital to the development of the immune system in infants. During the first year, the microbiome actually trains the human immune system how to perform its job.
A healthy microbiome helps to teach the infant’s immune system to identify and react to a wide range of disease causing pathogens – even those pathogens that the young infant has never before been exposed to. Training also includes teaching the immature immune system not to over-react to harmless stimuli such as the body’s own organs or innocuous microbes and particles in the environment.
Auto-immune Disease
Importantly, our commensal microbes teach the immune system’s fighter cells to identify “self” versus “non-self”. Without this preparation, the body’s immune system will sometimes attack its own healthy cells and tissues – incorrectly identifying them as a threat. When particular tissues are attacked by the immune system over time, it develops into an auto-immune disease. Chronic auto-immune diseases, such as rheumatoid arthritis, lupus, Type 1 diabetes, Inflammatory Bowel Disease and Multiple Sclerosis can lead to permanent organ damage and even death.
Allergies and the Over-reactive Immune System
Allergies are caused by an over-reactive immune response to otherwise harmless substances (allergens). An incorrectly trained immune system may have difficulty identifying which substances are harmful and which are innocuous. When the body raises an immune response against otherwise safe particles (such as dust, pet dander, or peanuts), treating them like a threat that the immune system needs to dispose of, causes an allergic response. Allergic reactions range from annoying seasonal sneezing or itching to life threating respiratory distress or shock.
Our gut microbiome teaches the immune system to identify which foreign particles that enter the body are harmful and worthy of immune response and which are not – thus reducing allergic reactions. We want our immune system to respond with vigor when it comes across a bacteria that can cause food poisoning. What we don’t want is for our body to feel the need to marshal all of its forces to “fight” tree pollen or dust mites.
Improving gut healthy and the mix of gut microbes has been shown to reduce allergy symptoms in some cases.
Immune-deficiency Diseases
An under-reactive immune reaction occurs when the immune system does not correctly identify harmful pathogens that threaten it and or does not launch an attack to neutralize the health risk that they pose. An immune deficiency disorder can also arise from inadequate training of the immune system by the gut microbiome.
This means that infections become more frequent when they are not identified early by the body’s first responders and become more dangerous than they otherwise would be because of a slow and or inadequate response to the infection. When they occur, these conditions pose an extreme threat to human health.
In the laboratory, scientists raised germ-free mice – meaning that they were delivered by cesarean section (thereby preventing transmission of microbes from mother to pup) and were kept in a sterile environment thereafter. The researchers then exposed these specially raised pups to disease-causing bacteria. The germ-free mice, which had never received immunity training by their microbiome, showed decreased immune response to the infection and increased rates of death than the normally-raised control group of mice showed.
Identifies and Fights off Invaders
Bacteria in our microbiome recognize potentially harmful invaders and signal to the body to launch an immune attack. Many of the microbes actually produce neuro-chemicals that communicate directly with our brains and our immune cells, signaling to our body to launch an attack against the threat and also tell it to produce more disease fighting cells. Because we have microbes living on our skin, in our mouths and noses and in large numbers in our digestive tracts, often our commensal bacteria are in a position to identify a threat before our body does.
Not only do our microbes help by training our own immune systems to fend off health threats, they also actively engage in the fight themselves. Some bacteria actually attack and overpower other harmful bacteria that enter to the body. Gut bacteria, for example, have been shown to attack and fight off rotaviruses – the viruses that cause stomach flu.
When our digestive tract is full of health-promoting microbes, it makes it harder for harmful bacteria to establish themselves in the guts, where they can cause disease. The commensal bacteria can outcompete the invaders, taking up available real estate and using up available food.
The ability of certain microbes to fight off disease can be harnessed in medicine. Russian doctors, who did not have access to antibiotics, actually used bacteriophages (viruses that kill specific bacteria, but do not harm humans) to successfully treat disease-causing bacteria during World War II, using them to treat dysentery and gangrene. Phages are targeted and only attack certain types of bacteria, leaving the health-promoting ones unharmed. This is unlike antibiotics that kill a broad swath of bacteria, both disease-causing and health-promoting one. This type of treatment is having a resurgence due to the increase in antibiotic resistant infections.
Microbes Calm Inflammation
The microbes that support our immune system play a critically important role in calming inflammation in the body. Doctors suspect that disruptions to the healthy human microbiome may be what is behind the ever-increasing rates of inflammatory diseases. Chronic inflammation is harmful and can lead to tissue damage.
When it is working properly, an inflammatory response is triggered by the body in an attempt to destroy infectious organisms, to heal damaged cells in the body, or to isolate damaged or diseased tissue from healthy tissue. This self-protective response can morph into inflammatory disease when inflammation in the body becomes uncontrolled and continues in the absence of any health-threat. For some reason the body does not turn of the inflammatory response. When this happens, the immune reaction damages healthy tissues.
Some microbes in the gut have been shown to calm inflammation in the body while others have been shown to trigger it in some instances. Certain microbes that inhabit a healthy gut have been shown to reduce the chance of developing diseases caused by inflammation. A well-functioning microbiome will communicate with our specialized immune cells (T Cells) promote inflammation when needed to fight disease or injury. At the same time, the microbiome simultaneously works with our immune system to reduce disease-causing inflammation when it is not helpful. How exactly this works, is not well yet understood. Nonetheless, having a healthy balances of microbes can influence how much inflammation is in the body and when and how it gets triggered.
Diseases associated with chronic inflammation are increasing in frequency. Common ones include:
- Asthma
- Cancer
- Celiac Disease
- Crohn’s Disease
- Fibromyalgia
- Graves Disease
- Lupus
- Psoriasis
- Rheumatoid Arthritis
- Type-1 Diabetes
- Ulcerative Colitis
Evaluations of the gut microbiome in patients with chronic inflammatory conditions show that they have alterations to the compositions of microbes in their digestive tracts as compared to their healthy peers. At first, doctors were not sure which came first – the changes to the microbiome or the inflammatory condition. However, large, long-term monitoring of the microbiomes of study subjects showed that the changes to the microbiome seem to predate the onset of the inflammatory condition. It is becoming commonly accepted that microbial dysbiosis underlies many of these inflammatory diseases.
Thus, developing and preserving a healthy microbiome may assist the body in maintain appropriate levels of inflammation and reduce the likelihood of developing a disease of chronic inflammation.
Prevents Leaky Gut
A strong gut microbiome is lined with microbes that prevent invaders from leaking into the body and causing inflammation and disease.
When a healthy microbiome is present, the microbes in the digestive tract form a protective film that covers the digestive tract, which decreases intestinal permeability. This serves an important function by acting as a barrier, preventing microbes, bits of food and other particles from entering into the body where they can cause harm and stimulate a chronic inflammatory response, ultimately leading to disease. With a permeable gut, certain proteins can leak into the body where they can trigger allergies. Leaky gut is a common cause for the chronic inflammation that can lead to auto-immune disease.
Several disease, from mildly annoying to serious are associated with leaky gut. These include:
- Acne and Rosacea
- Asthma
- Celiac disease
- Inflammatory bowel disease,
- Multiple sclerosis
- Type 1 diabetes
Keeping the intestines from leaking their contents into the rest of the body is a very important function our symbiotic microbes provide, which supports the body in preventing disease.
It has been shown that improving microbial balance in the digestive tract can heal a leaky gut and improve diseases associated with the condition. Maintaining intestinal integrity is one more compelling reason to achieve or maintain a healthy gut microbiome.
Conclusion
Without a microbiome made up of a variety of species of bacteria, yeasts and fungi that work without immune system, it is not possible to achieve optimal health. Our human immune system does not work well without its microbial partners.
In Infancy
Without a healthy microbiome, that supports well-being by training the infant’s immune system to identify and respond to threats, to distinguish between self and other, and to know what particles pose a threat versus being harmless, a young person’s immune system will not develop properly. This can lead to lifelong healthy challenges and diseases and underscores the importance of gut health from birth.
One theory, which is gaining a lot of support from the medical community, holds that modern changes in lifestyle are causing early-life imbalances to the infant’s microbiomes during critical developmental windows and leading to the increased rates of immune disorders in the developed world.
The microbiome is formed during the first few months of life, arising from exposure to healthy microbes from the mother and from the early environment. Unfortunately, common modern birth and parenting interventions can interrupt colonization of a baby’s microbiome by harming some species of bacteria required for the proper development and training of the immune system. Potential threats to healthy colonization and development of an infant’s microbiome include: birth by caesarian section, exclusive formula feeding, increased cleanliness with reduced exposure to dirt and germs, vaccination, and use of antibiotics early in life.
Parents can and should take steps to promote healthy development of their children’s microbiome.
Later in Life
Even if a healthy microbiome was established in early childhood, later disruptions to the gut microbiome can alter the ability of the immune system to prevent and fight disease.
Without sufficient numbers or varieties of friendly microbes in the gut to signal to the immune system that there is a threat, our body’s response to disease-causing threats may be delayed. What response there is may be inadequate without these microbes signaling to the body to create more specialized immune cells. Finally, our own microbial soldiers may no longer be present to help fight off other bacteria and viruses.
Gut dysbiosis, caused by insufficient microbial lining to the digestive tract, can lead to a leaky gut. Leaky gut, among other triggers, can then trigger inflammation. Chronic inflammation leads to inflammatory and auto-immune diseases.
This underscores the importance of maintaining and improve gut health, for without it, we are much likelier to develop disease.
There are many factors in our modern lifestyle that can harm our microbiome. Antibiotics is a common and significant culprit leading to gut microbiome disturbances. Alcohol, stress, food preservatives and other chemicals in the food supply and environment such as herbicides like Roundup (active ingredient glyphosate) can also harm our friendly microbes.
Eating a high fiber, low starch, low sugar diet will feed our commensal microbes and reduce growth of those microbes that are less desirable, such as yeast (Candida). Eating fermented foods, which contain naturally high levels of probiotics can also help supplement our own heathy gut bugs.
Our immune system is not fully human. It includes the trillions of microbes that call our bodies “home”. Modern medicine is just now starting to understand how vital these commensal bacteria are for our well-being and to develop treatments for disease that take them into account. When we take steps to promote our own health, this must also include taking steps to take care of our microbial inhabitants, without whom our immune system cannot fully protect us.
Awesome article. Very few get it right. This is dead on.