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Gut Health - Introduction to the Microbiome

Did you know, you, can tell a lot about a person just from their poop along with their microbiome and gut bacteria. For example, a gut microbiologist could tell if you liked light or dark chocolate, if you eat a lot of carbs or fat and what drugs you take. From your microbes on your skin they could match you with your computer mouse or your pet. You may be wondering, if you can tell all of the above, shouldn't you be able to manipulate the gut and its bacteria to produce optimal health? We're not there yet, but it is something that researches are working on.

Here's an interesting fact, only 10% of our cells are human, the rest are microbes. That means that 90% of the cells in or on our body belong to microbes! Single celled organisms that are too small to be seen by the human eye. We're made up of 10 trillion human cells and 100 million microbial cells. It's been suggested that humans are super organisms which means we're dependent on other organisms to survive and that our inside environments may be a mirror of the ecosystem. These microbial cells collectively are called the human microbiota. For now, we will focus on the Gut Microbiota, the microbes in the human gut. But just so you know you also have microbiota communities on your skin, in your ears, mouth and just about any area exposed to the world. And remember this world is mostly microbial. Collectively the microbes in your gut weigh almost 5 pounds and this is what we refer to as the "forgotten organ".

"The forgotten organ" refers to a collection of microbes that function like an actual organ, which have evolved with us and provide many functions which are key to our survival. But this organ may be truly running the show when it comes to digestion and has been linked now to most major illnesses. The forgotten organ functions like an actual organ in a few key ways.

First as a group, gut bacteria influences almost every other organ and second, it uses energy similar to other organs. So, it has a metabolism worthy of its title and it’s just as heavy as the brain and the liver and maybe as smart too. There’s an evolutionary advantage to co-evolving with microbes. Of course, we’re out numbered so it’s smart for us to get along. But microbes also save us energy, it’s kind of like outsourcing, microbes evolve fast and can quickly turn on and off genes to provide all kinds of functions like when we quickly switch from eating a vegetarian diet for 10 years to biting into a hamburger. Microbes can turn on genes to help break the animal protein down.

If we were to rely on our own genetics for everything it might take us generations to make that transition. But with microbes we can adapt and carry the weight of extra genes without having to provide the energy to maintain them like we do for human genes. Microbes make us smarter and faster; they are great pals to have around.

So, what is the microbiota? The gut microbiota is made up of all different microbes, bacteria, viruses, fungi, archaea and protista. All small but mighty. We’ve known that there is bacteria in and on the body since around 1670 when Antoni Van Leeuwenhoek, the father of microbiology built his own microscope and caught the first glimpse of these little guys in his own poop. Remember microbes are too tiny to be detected by the human eye, hence the essential help of the microscope.

You might be asking if the first discovery was in the 1670’s then why all the hype now? How did the microbiota become forgotten? Well we started to study bacteria virus and yeasts that were thought to be the cause of disease but overall what we knew about the microbiota was limited to what could be cultured and grown in a lab. That meant that only organisms that survived when exposed to oxygen or air could be studied. And guess what, most of the organisms that find a happy home in your tummy are anaerobic meaning they thrive in environments with no air like inside your body.

In the mid 80’s an idea came about to map the entire human genome, the complete map of an organism's genes and it's DNA, which is the blueprint for how an organism is built and functions. A gene contains the information that instructs an organism on how to develop and carry out everyday functions. Your DNA is like a parent providing the rules, but like a rebellious teenager the body doesn’t always follow them.

In the 1990’s, the human genome project was funded and was underway. By mapping the human genome, it was thought this would unlock the key to disease, discover which genes were at the root cause and maybe even draw a map for how to turn genes on and off. The idea was if we could map those genes, we might know how to best manipulate our destiny. The hope was to discover what truly made us human and the complicated beings we are. Guesses were thrown around that humans might have over 100 thousand genes. An exciting blend of science and technology conspired as we took on a very expensive process.

Sequencing DNA, what cost 10,000 US dollars back then, to sequence DNA now costs 10 cents and can be done in a fraction of the time. In 2003, the human genome project was complete.

We mapped all 3 billion pairs and what did we find? That you and every other human is 99.9% identical in terms of genes, the person next to you, your neighbor, your best friend, someone across the globe and someone you’ve never met. Humans are 96% similar to our relative, the chimp, and back to our guess as to how many genes we actually have?

Whomever guessed 100 thousand would have lost, as it turns out we have about 20 to 22 thousand protein coding DNA, only a few more than a fruit fly.

The results were underwhelming, but they are still being decoded. However, during this period of exploration, as I mentioned, the technology developed cut down the price and the time it took to sequence genes. What this meant was we could now look at all the bacteria we were previously unable to study because of their inability to grow in a lab and the new reduction of cost sequencing technology led to the next phase of the human genome project and a new project was proposed, the human microbiome project.

This is the study of all the genes of the microbes in our body. Our second genome. Now this project is impressive and still in progress but so far, we’ve discovered 20 million microbial genes. Most fascinating is that human microbiome is as unique as a fingerprint. There are 3.3 million non-redundant genes in the human gut microbiome alone. Microbial populations on different sights of one person’s body are more diverse than the difference between one human genome and another. And the difference between the microbial population of let’s say the desert to a lake. The implication is that we are more diverse inside than outside.

Besides the difference in sheer volume, the microbiota can easily change and are more valuable than the human genome. Rather than decades of incremental changes microbes can participate in what is known as horizontal gene transfer. Which means genes can essentially jump from one microbe to another and then can reproduce rapidly. Even though bacteria can swap genes the overall community of microbes in your gut remains pretty stable. For example, you will not acquire the microbiota profile of your significant other even if you share a few bacteria. But you do swap enough that with testing someone could identify your partner. Scientists in businesses have started large crowd funding projects to collect samples from a variety of people, locations, and cultures to compare their microbiota and microbiome.

So far we know the microbiome impacts:

· Disease

· Mood

· Immunity

· Inflammation

· Various other functions

The best insurance for a healthy microbiome seems to be diversity. The Hadza, a tribe in Tasmania who has been relatively untouched by Western Civilization culture carry around 1700 different species of gut microbes. The average person in the West has around 1000 to 1200 species. That may not seem like a big difference but when you lose large populations in an ecosystem there are less organisms to carry out essential functions. Think about animals and what happens when an entire species goes extinct.

So, remember the goal of the human genome project? Well it seems that the microbes in our body also have the ability to send signals to turn on and off the human genes, meaning the microbiome may be a large contributor to epigenetics.


The great news is that we’re finding that the microbiome can change quickly with diet and lifestyle alterations.

Part of the reason we’ve co-evolved with microbes is their ability to perform key functions with the smallest amount of metabolic output. As you can imagine in times where we have to adapt to climate or harsh conditions, we could rely on microbes to perform essential functions like extracting more nutrients from food or supporting immune function. These guys were the go-to for whatever was needed.

One of the most exciting parts about the human microbiome and the gut microbiome is that we are all learning together. The scientists, the doctors, you and I. No one has all the answers right now but as a collective we’re asking questions.

But information around the microbiome is coming out every day. We’re learning that the gut

Microbiota seems to respond to diet and also plays a role in how we digest and absorb medications, vitamins and supplements. As the science evolves its looking like the research around the microbiome supports the importance of lifestyle changes.

Within just 2-5 days of lifestyle changes the microbiome is noticeably altered. And it can just as quickly revert back to its prior population if those changes are ever abandoned.

We all know it can be very hard to stick to a program and doctors or practitioners may not have time to check in as often as you would like. As a health coach I am able to support and empower you to maintain your gut health which is the same way that your personal trainer at a gym sustains your fitness in between sessions.

The result of dietary and lifestyle changes make the difference in whether genes are turned on or off. Your environment including diet and lifestyle provide the trigger that can activate any genetic predisposition. If we look at the human genome project in genes as a map of our lineage and what we inherit perhaps our second genome, the microbiome might be more reflective on the influence of our environment. Due to its ability to adapt daily changes we make to improve our health can have a ripple effect. Perhaps rather than being a victim to our heritage and trying to outsmart our DNA we may be able to collaborate with a group of malleable microbes that exist not only in and on our body but also all over the world.

To recap, the forgotten organ is a collection of microbes that have evolved with us providing many key functions for our survival. We always knew germs and microbes were important, but we’ve forgotten that there is an entire world beyond what we can see with the naked eye. Our health and our fate will rely on our ability to create balanced ecosystems that include microbe.

The microbiome also serves as a mirror for the health of our external ecosystems. The sooner we embrace the fact that we are super organism’s dependent on one another for survival, the sooner we can co-create a better environment for all.

So, what was your take before reading this blog post? Did you know your microbiomes had so much influence over your health or did you subscribe to the idea that your health is ultimately dictated by your genes? How can you use this knowledge to empower yourself to take control of your health through diet and lifestyle modifications?

Next Monday we'll continue with our Introduction to the Microbiome and discuss:

The Microbiome and Digestion


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