Science is slowly shedding light on what is now being called the Microbiome: the 100 trillion microbes that live on and within us. And contrary to popular opinion, it seems these microbes don’t threaten us but instead, offer vital help with our basic physiological processes.

As new data is being collected, we now know that our Body’s ecosystem includes several delicate and complex symbiotic relationships with over a 100 trillion microbes.

Recent research suggests that this small universe of microbes consists of what is called commensals (harmless freeloaders), mutualists (favor traders), and only in the tiniest amount, pathogens. It appears that this microbial community does far more good than harm and the ‘services rendered’ are proving to be somewhat remarkable and shocking.

This microbial ecosystem also referred to as the microbiome is essential to maintaining the complex coordination of health and homeostasis in the body. As we dive deeper, we are afforded a more expansive view of what health really means.

Take our mood for example, the ‘source’ of one’s mood has long been a mystery to science. Why are some people more uptight than others? Why do we feel grumpy and low sometimes? Although it would be nice if we could blame our foul mood on our partner’s shortcomings, recent discoveries suggest otherwise (1). Our gut bacteria play key roles in the manufacturing of some neurotransmitters such as serotonin (contributes to feelings of well-being and happiness), some enzymes, vitamins, and some signaling molecules that influence the immune and metabolic systems. Some of which play a role in regulating stress levels and, surprisingly enough, even temperament. When the microbes from easy-going, adventurous mice were transplanted into the guts of anxious, timid mice, they became more adventurous (1). Who knew the tiny critters that take up shelter in our gut are the answer to our mood.

The last few years have seen a major paradigm shift in our understanding of the role of microbes in our health. This change is akin to the shock when watching the last few minutes of a movie, when it hits you that the villain is really the good guy, and the protagonist you have been rooting for is the evil schemer.

From the time we were infants, we were warned about the dangers of “germs”, things that would make us sick. We may have been vaccinated to protect us against terrible viruses. We may have suffered with colds and flus caused by these germs. We may have grown up with antibacterial wipes and other products to scrub our homes clean from these invisible but deadly bugs. We may have learned in school about even deadlier diseases of the past – the bubonic plague in the Middle Ages.

Then, fast forward to 2012 when the Human Microbiome Project findings usher in a new paradigm of symbiosis between humans and microbes (the bugs are NOT the bad guys!). The work of the Human Microbiome Project has revealed that the human body is actually a superorganism or complex ecosystem of human cells living in a symbiotic relationship with 100 trillion bacteria and other microorganisms, collectively called the human microbiome.

The vast majority of microbes that reside in different habitats on our skin, eyes, oral and nasal passages, and within our digestive and reproductive systems, are essential for our health. They provide key functions and proteins that our bodies require. Microbes have moved from their longstanding position as evil pathogens, invading our bodies and making us sick to “friends with benefits” or mutualists – organisms that live symbiotically together with us. We provide them with a nice, warm home. They reciprocate by providing essential services that our bodies need for healthy digestion, brain function and a proactive, but not overzealous, immune system.

In contrast to our resident 100 trillion mutualist microbes covering 1000 or so different species, there are only about 50-100 pathological bacterial strains known. So while the focus in medicine and BodyTalk has been on the tiny part of the puzzle – the pathogens – it is time to consider the mutualists and the treatment strategies afforded by this new era of cooperation.

Here is a sneak peek at the GUT Microbiome.

The Gut Microbiome

The GI tract is the most exposed organ system to the outside environment and has an overall surface area of 200 square meters, about 100 times larger than the surface area of the skin! The most extensive and complex microbiome in the body is located in this environment.

The intestine lining is a multi-layered system with distinct functions. The outside layer is a physical mucus layer that prevents pathogenic bacterial adhesion and blocks access of infectious pathogens to the inner tissues. The deeper functional barrier amazingly can distinguish the good bugs from the pathogens. The mutualist microbes are tolerated while the pathogens are recognized and eliminated.

Meet a mutualist ….


Stained pus from a mixed anaerobic infection. At least three different clostridia are apparent.

Stained pus from a mixed anaerobic infection. At least three different clostridia are apparent.

While there are a few dangerous Clostridial pathogens, most of the species in this group are mutualists.

They are involved in the care and feeding of colonocytes, providing the colon cell’s food of choice, butyrate, as the end product of their fermentation process. Butyrate has anti-inflammatory properties in the colon and has been implicated in protection against colitis and colorectal cancer.

Clostridial species have evidence for converting inactive forms of dopamine and norepinephrine neurotransmitters made in the gut to their active forms. These neurotransmitters can then be used for communication between the enteric nervous system and the brain. These organisms therefore are a key part of the gut-brain communication pathway and hence, can influence mood.

It is being proved that our complex immune system engages in a constant intricate symbiotic dance with our under-appreciated and previously vilified microbial residents. It also gives us a pause to consider other perspectives, before we opt for the mainstream options of antibiotics, antimicrobials, anti-fungals or anti-inflammatories to stifle, inhibit or suppress what our natural immune system attempts to do to help balance us back into health.

While antibiotics certainly have their place to address life-threatening illness, it may not always need to be the first responder on the scene as a solution for all infections. The recent surge in drug resistant infections (e.g. – MRSA) is rampant and provides evidence for a shift in current mainstream approaches. An imbalance in our microbiome has also shown to cause depression and other symptoms related to hormonal imbalances.

As many of us enter into the cold and flu season its encouraging to know that there are other options available. If you are experiencing recurring infections, sluggish digestion, food cravings or related gut issues including skin rashes, foggy brain, exhaustion, chronic respiratory or digestive issues, hormonal imbalances etc. it may be possible that your microbiome is out of balance.

Contact me today to learn how you can boost your immune system and stay healthy this Winter season as we get busy with the holidays.