The Ultimate Guide To Understanding the Gut Microbiome

Why caring about our gut microbiome can revolutionize the future of our health

We have severed ties with one of our BFF’s for millions of years.

They are pissed that we would be so rude. We are now seeing the consequences of our actions…

Heart disease is the leading cause of death, autism rapidly turning into an epidemic, obesity rates rising, and nearly 14% of America with Irritable Bowel Syndrome.

Yes, we have a problem…

but the root of it isn’t getting the attention that it deserves.

One key component of our body that is the hub to all other functions in the gut. More importantly, the guys living inside the gut.

The gut microbiome.

The microbiome is amazing and powerful.

Just how powerful?

Let me show you.

Why the Microbiome is Important #1: Cardiovascular Disease

The big one.

610,000 people in the US die of it.

That’s roughly ¼ of every death is due to heart disease.

We have control over it too. 80% of it is preventable with proper diet.

But to have good heart health you need have good gut health.

Rhonda Patrick, Ph.D broke down why gut health is linked to cardiovascular disease with this wonderful explanation that I have paraphrased.

LDL-Cholesterol delivers cholesterol to your cells in your liver, cells in your muscles, cells throughout your body.

It does this because every cell in your body needs cholesterol.

Cholesterol is a part of the membrane of the cell which is essential for the cell to function.

Damaged cells?

They need cholesterol

Lifting session?

Need cholesterol.


When LDL cholesterol goes to your cell to repair damage, a small piece of it gets chopped off.

Now the LDL is a little bit smaller.

OK now we are going to link it to the microbiome.

Ready? 🙂

There are is over 100 trillion bacteria in your gut.

They are there because they are metabolizing the food you eat, making them into fatty acids, proteins, amino acids, vitamins, and minerals.

Pretty important stuff going on.

Some of these bacteria live around the gut barrier.

The gut barrier is what separates your immune cells from your bacteria.

When the gut barrier becomes compromised your immune cells start to kill bacteria in your gut. This releases a part of the bacterial membrane called endotoxin.

Endotoxin is then floating around in your bloodstream.

And guess what?

It attaches to LDL cholesterol.

LDL cholesterol soaks it up like a sponge…

…and when you are inflamed you make more LDL cholesterol.


Here’s the problem,

when the endotoxin attaches to that LDL cholesterol…

you know the one that was giving a piece of it to that cell…

…it binds on the same areas that the LDL cholesterol uses to go back to the liver and get out your circulation.

Now you’re really in trouble. -_-

That LDL cholesterol, which is smaller, has all this endotoxin stuck to it.


It can’t go back to the liver and it’s trapped in your circulation.

Endotoxin now becomes a target for your immune cells to go in like Tie Fighters after Rey and Finn.

Pew. Pew. Pew.


Now our immune cells come and try to kill the cholesterol but they can’t kill it, because it’s not a live bacteria.

It’s actually this cholesterol with endotoxin bound to it.

they secrete all these enzymes which begin to get stuck to the cholesterol creating the beginning of plaque.

Now the end product of this whole mess is the immune cells being stuck to this LDL particle.

A small dense particle has been created and is primed to stick to your arteries.

Fast track to cardiovascular disease.

It doesn’t have to be like this!

We can keep our gut barrier in tact.

The epithelial cells of the gut barrier need to produce mucin.

Mucin is this snotty like substance that covers your gut barrier.

Mucin is generated from short chain fatty acids (SCFA). SCFA are produced by commensal bacteria in our guts.

Mucin is good! (in the right amounts)


Mucin = √

SCFA = √

Guts = 🙂


The problem is….most guts don’t have enough good bacteria that make the SCFA.

This is because they were starved out.

The bacteria had to be fed the right foods (Fermentable fibers to be exact) to create SCFA. And the right bacteria need to be in our guts to eat those foods!

And when they are absent other bacteria comes in to take its place.

Freaking squatters!

In short…

…years and years of poor eating and lack of a healthy microbiome can bring on the many issues that we see today in our modern health crisis.

Why the Microbiome is Important #2:


No surprise’s here.

As a whole, the country is getting fatter.

The effects are beyond what is shown on the outside.

The root of the problem begins with the microbiome.

As we were talking earlier about when the diet is lacking the fermentable fibers, we end up with broken down gut barriers aka leaky gut.

A normal Western diet might get you around 15 grams of fermentable fibers.

We should be looking more around 25-30 grams.

And that is being generous. That is just the beginning of the issues.

Due to obesity being more than just over eating, it comes down to poor eating.

A diet of simple sugars is a sure way to make sure you starve out the commensal bacteria.

Lean healthy guts have been compared with fat sick guts.

What was found isn’t surprising.

Fat sick guts have a dysbiotic microbiome.

A microbiome that couldn’t care less about the host (you)

It’s doing its own thing, making the host sick and nasty.

The result is added on pounds, poor digestion, and leaky gut.

Why the Microbiome is Important #3:


15% of Americans are suffering from IBS.

150 million of Americans suffered from IBS symptoms each year.

The most common symptoms (taken from NHS.UK) of IBS are:

  • abdominal (stomach) pain and cramping, which may be relieved by having a poo
  • a change in your bowel habits – such as diarrhea, constipation, or sometimes both
  • bloating and swelling of your stomach
  • excessive wind (flatulence)
  • occasionally experiencing an urgent need to go to the toilet
  • a feeling that you have not fully emptied your bowels after going to the toilet
  • passing mucus from your bottom

In addition to the main symptoms described above, some people with IBS experience a number of other problems. These can include:

  • a lack of energy (lethargy)
  • feeling sick
  • backache
  • bladder problems (such as needing to wake up to urinate at night, experiencing an urgent need to urinate and difficulty fully emptying the bladder)
  • pain during sex (dyspareunia)
  • incontinence

What happens when you go to a gastrologist?

You are told you have neuropathy, given pills, and shooed out of the office.

Come back to us when you get ulcers or when your appendix bursts, k thnx bye.

We are a country that is experiencing gut issues.

Why can’t we get the help that we really need?!

It just isn’t getting the attention it truly deserves.

It is mostly laughed off and taken as part of life.

Cramping leaving you in tears is no joke.

Big pharma knows American guts are broken, that’s why they are making BILLIONS on PPI’s.

You know those purple pills that make heartburn disappear?

5.5 BILLION dollars for Nexium.

830 MILLION for Dexiant

They aren’t so harmless either.

They can cause SIBO or small intestinal bacterial overgrowth.

It is time to take this condition seriously.

There needs to be immense healing going on.

Our health is largely stemming from the gut. Source:

Creating a Healthier Microbiome

The human gut wants to function and perform the way it was intended. The point is to give it the microbiome it needs to provide you with the health for a long lasting life.

The epidemic of Americans having a sick gut needs to be solved.

Luckily, it is within our own grasp.

On a smaller scale, I was able to heal my own gut.

A more incredible story, Dr. Terry Wahls, was able to recover from her debilitating condition of having MS or multiple sclerosis.

Within 7 years of her initial diagnosis, she went from good health to being wheelchair bound.

Now she is free to walk underneath her own two legs!

All with the power of healing her gut and integrative medicine.

By paying attention to our guts we can have an impact beyond digestive issues. Better mental health, prevention from the onset of diseases, improved happiness.

How can we make sure that our guts are in the best possible condition as possible?


Testing reveals what is living inside of us.

If we have certain pathogens we must seek professional health of a functional medicine doctor.

If you have a basic gut and have been on a Western diet with no signs of beneficial bacteria it may be time to take these steps to help rebuild.


How to retool and rebuild a stronger microbiome: Part 1

It’s all about giving the gut the ingredients to heal and recover after years of turmoil. The process can be long, but by taking it each step at a time, you too can begin to feel the full benefits of restored gut function.

  • Bone Broth

Why is Bone Broth such a super food?

Inside those bones is this substance called marrow. When slow cooked, it is softened and the vitamins and minerals are released into the broth.

These vitamins and minerals include




and phosphorus.

Pair that with the amino acids glycine and proline and you have a powerhouse drink ready to reconstruct your new and improved gut.

For more research and recipes I recommend checking out this and this.

Feeling lazy, here is a delicious option to get bone broth shipped right to your home!


  • Eliminate Potential Allergens

The gut is stressed and has become permeable.

That only means one thing: stop eating the trigger foods.

If your gut is all out of whack, give your gut a break from the inflammatory trigger foods for 30 days.

These trigger foods include dairy, sugar, nuts, eggs, alcohol, coffee, and grains.

A Tall order, I know, but depending on how vigilant you are in wanting to heal the gut, certain steps have to be taken.

This doesn’t mean that you have to eliminate these foods forever, once the 30 days have passed, slowly introduce these foods back.

Have an over-easy egg, and give it two days to see if you have any symptoms.

Then you add another from the list.

High five for gut healing!

  • Stop Stressin’

Feeling like you have zero control of your symptoms can take a toll on you.

Added stress can slow the healing process.

Don’t forget…

The gut brain axis is a two-way street.


If you can keep positive mentally, you can at least have one part of the street in good working order while the other is repairing.

Piling on more stress will only hamper the healing, thus continuing the cycle of poor gut health.

Accept the place that you are in right now presently. Know that you will be undergoing the healing process and don’t get discouraged by lack of results.

This process takes time and patience.

Practicing mindfulness during this turbulent period will give the gut the needed break from the onslaught stress inside and outside our own body.

  • Sleep

What adds to the stress on the human body?

Lack of sleep.

Sleep restores our minds and gives the body the time needed to repair itself after the daily rigors of every day.

Add on daily inflammation

and sleep becomes even more important!

Getting 7+ hours of sleep is essential to the healing process.

Helpful tip: Bring a book to bed, instead of your tablet, and steer clear of all blue light.

  • Probiotics

There is a lot of buzz going around about probiotics.

With everyone looking to find an edge for their health, probiotics have been catching on quickly.

While taking probiotics can be extremely helpful to your digestive system and realigning your flora, it can help you in much more ways than just digestion.

Knowing the basics is key to balancing your flora quickly.


How to retool and rebuild a stronger microbiome: Part 2


Probiotics can help realign the gut back to more of a homeostasis, making the balance between the good and the bad more equal.

Once this occurs, healthy foods will be broken down properly, and all the nutrients will be allowed to go to its destination.

Your flora is back!

Unfortunately, it’s not so cut and dry.

Probiotics don’t usually take up residence in your gut.

They are more like support troops that come on in and help force out the enemy.

Once that cycle of probiotic is gone, they are off to the wonderful lands of sewers and septic systems.

We need to keep the good guys there, this way we don’t always have to continually buy these pills.

This is where pre-biotics come into play.

Prebiotics give the food needed for the good bacteria (and sometimes bad) needed to flourish in our guts.

But back to probiotics.

Many questions arise when choosing which probiotic to buy.

Some are contained in a refrigerator;

others are just on the store shelves.

8 Strains

100 Bazillion





It can all be a bit over whelming, and in the end, you might just pass by the counter with a befuddled look, and have nothing in your basket.

Maybe next time.

Here’s how I choose and buy my probiotics:

Know what strains are in the bottle

The probiotic must have the strains listed on the box.

The number of billion doesn’t matter.

Effective bacteria MATTERS.

You want a diverse amount of strains 8 or more, each specifically named.

Numbers aren’t everything

Quality usually comes at a premium, and QUANTITY is just a marketing tactic to have you buy their shitty (no pun) probiotic.

Yes, it might have had 100 billion before packaging, but due to lack of quality control, you’re most likely left with a capsule full of dead bacteria.

Price isn’t always a good indicator, but in this case, it usually tells you how well a product is cared for.

I usually try to purchase a probiotic that is at least 25$.

Show me the tests

Sometimes the company will have the test results of their probiotics on their website. Other times they will have on their box the strains that have been shown to have benefited the flora.

The best type of test is a double blind placebo study.

Although those are rare, if you happen to find a probiotic with positive results in the double blind placebo study, you most likely have yourself a good strain.




Refrigeration required?

Not necessarily.

While refrigeration might keep the shelf life of the probiotics live longer through the travel process of the plant to your home, it’s not necessary to specifically seek out refrigerated probiotics.

Soil Based Probiotics

You might see SBO (soil based organisms) or HSO (homeostatic soil organisms) labeled on the box or bottle of probiotics.

Which totally makes sense, considering our ancestors weren’t living in a sanitized environment like we are today.

Bacteria from the soil would be very close to the food, thus being a normal part of our flora.

There is some skepticism about these organisms, due to the fact that they are spore forming organisms. The fear is that if your immune system is so depleted, these organisms will act as opportunistic bacteria, take hold of the immune system and become problematic.

For those of us not battling an extreme long term illness, these SBO’s are extremely powerful in helping restore the flora. SBO’s get my thumbs up approval.

Consume with Fat

Heisenbug brought this to the forefront saying that consuming probiotics with fat gives the probiotics a better chance of survival and higher success rate.

This study shows that fats especially helped the probiotics in their effectiveness to help replenish the flora.

Just remember when taking probiotics, don’t be afraid to have it with your meals, or better yet sprinkle it on your guacamole.

Now that we have the basics down with our probiotics, time to use another hack to help form a healthy microbiome.

How to retool and rebuild a stronger microbiome: Part 3


Sitting is the new smoking.

Humans are meant to be squatting, running, or climbing.

Only recently have we become accustom to the soft cushy feeling of a sofa or a rolling chair.

Most of us are on our asses for over 10 hours a day.

I am no different.

Staring at a computer screen hours on end, I can just be glued to that thing and forget to get into motion.

I believe Newton said it best:

“an object at rest, stays at rest.”

Exercise does more than just make us lose weight or release endorphins.

It stimulates our gut microbiome.

Moving can also get you some awesome views!

Exercise promotes microbial diversity.

Check this out:

“Our findings indicate that exercise is another important factor in the relationship between the microbiota, host immunity and host metabolism, with diet playing an important role…”

Diversity is king.

Without it, we can expect ourselves to be in a world of hurt.

This is the exact reason why antibiotics are so harmful.

They destroy diversity.

Looking for ways to grow a diverse microbiome is vital in harboring optimal health.

Eating whole foods + movement =  SUPER DIVERSITY.

I’m not one for gyms.

Getting out in nature is more of my style.

Not to mention it’s free and refreshing.

You might even pick up some ancestral microbes along the way!


Here are a few of my favorite activities that can be done just about anywhere to promote movement

Get Outside

Grab yourself a bike (and helmet) and start exploring your town and city

Head out to a local park and take a walk or run (even if it’s just for a mile)

Live next to a forest or open outdoors? Take a hike! I use and for all my hikes.

While doing this alone is fine, having awesome fun people to join in on your adventures makes it even better. Use Meetup and Gociety to meet new friends and active people in the outdoors!

Throughout the Work Day

For those of us who sit during work here are few of the things I do to get around and about. I’m looking for your microbiome 😉

On those bathroom breaks, go to one that is a few floors above or below you. This gets you away from the screen and in motion just a little bit longer.

Stretch! Every hour, get out of the chair and outstretch to the sky, elongating the body. A backbend here and there is never a bad thing. Throw in a few sitting squats and you are a superstar!

Lunch time is a perfect time to get a quick walk around the building even around the block. Walking after eating is actually beneficial for digestion

At Home

Pick up a pull up bar to throw in your door way.

If you can’t do a pull up yet, just set a chair underneath to assist you.

Or slide yourself under a table and lift yourself off the ground by grabbing onto the table.

Body weight exercises: wall squats, pushups, burpees

Mark Sisson has a neat Prison Workout you can do at home.

You’re now armed with a starter kit to give you the motion needed to jump start your body and microbiome. Start building that diversity!

Well, what are you waiting for, get moving!


The target is to keep the microbiome healthy and thriving. Once it becomes compromised we can expect to see problems pop up and bigger issues down the road.

Luckily, the human body is incredibly resilient.

By making a few changes to diet, exercise, and mental health, the microbiome can be healthier and more robust. A Super Biome! 🙂


…how good is your microbiome?