Gut Microbiome - Part 1

Gut Microbiome - Part 1

Hey friend!

This week, I wanted to talk about a topic I haven’t really mentioned before – the gut microbiome. Now, this is an absolutely monster of a topic. I could spend a lifetime writing about it and still come no where close to scratching the surface. However, the topic is thrown around so much these days with all the probiotic and prebiotic supplements that I really felt the need to make sure you know what the science actually says about it. And let’s please remember that marketing claims are not science.

I’m going to do a two-part series talking about what the gut microbiome is, why you should care about it, and how you can influence it with your diet.

What is the gut microbiome?

It might be weird to think about, but there is a huge population of bacteria living on you and in you. The biggest population lives inside your gut (specifically your large intestine).

These bacteria are GOOD for us. We co-exist in a nice symbiotic relationship.

Fun fact: There are more bacterial cells living with us than there are actual cells of ‘us’. You are more bacteria than you!

What does it do for us?

The gut microbiome has its hands in many important functions:

  • Helps harvest energy from food
  • Manufactures neurotransmitters
  • Manufactures enzymes and vitamins
  • Aids the immune system
  • Directly impacts and helps regulate our metabolism
  • Provides structural support to our intestine
  • And much more…

How do we first get it?

Our first exposure to bacteria comes as we pass through the vaginal canal during the birthing process (Note: C-section babies miss out on this first exposure). From here, it takes several years for our colony to become well-established. These first few years are critical for the development of a healthy gut microbiome. Different factors can severely impact its development:

  • Early antibiotic use (avoid unless absolutely necessary!)
  • Feeding type (breast feed please)
  • Less exposure to soil, animals, and environmental microbes (no babies in bubbles)

How do these gut bugs stay alive?

They eat what you don’t eat. Your body gets first dibs at the nutrients in food. We’ll extract everything we can, and then hand the remainder over to our friendly neighborhood gut bugs. The stuff they end up getting is mostly fiber. They love fiber.

If you eat a no fiber diet, you are starving all of your gut bugs. They’ll start looking for food nearby to eat and survive. One food source is neighboring bacteria. If forced, they’ll turn cannibalistic and eat each other (creating loads of LPS, see below section). They can also eat the mucus layer separating your intestinal wall from them. And if they eat through the entire mucus layer, they’ll start eating your intestinal wall. This leads to chronic inflammation and things like leaky gut (allowing more LPS to get in).

Not good.

What happens when your gut microbiome is unhealthy?

Unhealthy gut microbiomes are associated with nearly every disease we have looked at. The ones with the strongest links are Type 2 Diabetes, atherosclerosis, IBS, obesity, and various psychiatric conditions.

To put it in perspective, we have done research studies where we transplant different types of microbiomes into sterile mice (no gut microbiome). When you give a sterile mouse the gut microbiome of an obese person, they will spontaneously gain weight and become obese!

Pretty crazy, right?

But how is it linked to the brain?

Second fun fact: The gut microbiome makes about 95% of the body’s supply of serotonin (a neurotransmitter associated with the brain).

Not only does the gut microbiome help with production of neurotransmitters, but the GI system has what is commonly called our ‘second brain’ – an entire second nervous system that can operate independently of our brain and spinal cord.

Given this, it makes sense that we see huge disturbances in cognitive/emotional processes whenever there are issues with our gut.

What is endotoxin and how does it relate?

There are various endotoxins, but most people are referring to lipopolysaccharides (LPS). LPS is a cell wall component of bacteria, with our gut microbiome being the biggest source of LPS.

LPS is pro-inflammatory if it gets inside your system and is associated with all the above problems we mentioned. LPS shouldn’t be getting inside to any meaningful degree if your intestinal walls are strong and your gut microbiome is healthy.

However, once it does get inside, it starts a vicious cycle. The LPS triggers your brain to start a stress response that releases cortisol. Cortisol increases intestinal permeability – it’s trying to suck up more nutrients for a fight or flight response – which allows more LPS to sneak in. The more LPS that gets in, the stronger the stress response, which keeps perpetuating the cycle.

Now that you have a good handle on what the gut microbiome is and why it’s important, we’ll dive into some practical strategies next week.

As always, thanks for reading. Please shoot me a message with any feedback you may have, or if you simply want to say ‘Hello’. My email is and I’d love to hear from you.

Take care.