Looking for a healthy microbiome? Start here!

The microbiome is a hot topic in the health world these days. As is the case with most things, the initial hype has been met with a bit of disappointment. But, I think this is more of a pendulum swinging back to sanity type of thing.

One of the fundamental problems with looking at probiotics as a cure-all is that they don’t even appear to colonize our gut. They’re there when we take them and when we stop they go away. I’ve tried numerous probiotics, but to be honest, I’ve never experienced anything remotely amazing.

In fact, I think probiotic foods have a lot more potential due to the biogenic compounds they make in the food. In pill form, you just get several million(or billion) dead bacteria and possibly some of their enzymes.

But one of the fundamental problems with thinking probiotics are a panacea is that we need them to colonize the microbiome for long term benefit. And for that to happen, we need to provide an environment where they can do just that.

If you do that, the pills probably aren’t even necessary.

The microbiome: Planting a seed

One of the first series I did on this blog is the Hacking Your Gut series. You can check out part 1 and follow through the series by clicking here. My goal was to show how a soil-based probiotic and cleaner eating could prevent the negative effects of antibiotic use. Before taking antibiotics/probiotics my diversity was terrible: 3%.

I didn’t see any of the results I expected, so I had to change course. Rather than playing around with probiotics, I decided to manipulate the environment in the gut. I got the idea from a book called The Hidden Half of Nature.

In the book, the authors make the case that a garden is a perfect analogy for the microbiome. Planting a seed in your garden will only grow a plant if the environmental conditions allow it. In the same way, your microbiome will only support microbes that the environmental conditions allow.

So, in essence, thinking I could take a pill and significantly change my microbiome was foolish. It’s the garden equivalent of thinking I could toss tomato seeds in to sand, water them, and grow a tomato plant.

The microbiome and time restricted eating

Throughout my little N=1 experiment, I saw major movement. My microbiome went from the 3rd percentile to the 42nd percentile. It happened over a long period of time, because it also coincided with my dive in to circadian rhythms.

The first step was time-restricted eating. Time restricted eating works by creating a need for microbial diversity. It creates periods of feeding and fasting that require different strains of bacteria for each purpose. During feeding periods, microbes snack on the nutrients and glycans found in food.

But during the fasting period, there’s no food to snack on. So microbes turn their attention to the glycans in your mucus layer. The problem is, this requires a separate set of bacteria, most of the bacteria snacking on your food can’t do it.

Our colon secretes mucus that forms 2 separate layers. The loose outer layer is where most bacteria hang out. The dense inner layer keeps bacteria away from the intestinal lining.

When we eat, a group snacks on the fiber that makes it to the colon and blooms. During our fasting period, when food becomes scarce, these guys retreat and the new gals come in.

Time restricted eating was great and really got me moving in the right direction. But over the course of months, I tweaked other variables that moved the needle further. As a result:

  • My sleep improved
  • Energy improved
  • Digestion improved
  • I had tons of energy
  • I also dramatically increased the diversity in my diet.

Overall, this was a much more effective approach at improving my gut health. Shifting the focus from what I take to what I do completely transformed my gut.

How it all works

Humans have evolved with their commensal pals for millenia. As such, we help support each other. We give them food we can’t digest and safe harbor. They help keep our gut healthy and inflammation-free by crowding out pathogens and modulating our immune system.

We secrete bile to help break down fats in our diet and this sets us up with a microbial community that can survive bile. High levels of physical activity and a preference for butyrate metabolism by the cells in our colon keeps oxygen low. This shuts the door on aerobic pathogens our microbes compete with.

In essence, our physiology helps select our microbes and they select us. But if we don’t live up to our end of the bargain, our microbiome can’t help us out. A major key to this process is circadian rhythms, which was covered nicely in this recent review.

If we eat non-stop, the microbes that thin out our mucus layer can’t do their job. As a result, it can get crowded down there. Nearly every function in our gut is circadian, so ignoring circadian rhythms pretty much makes it carte blanche for whatever can grow there.

Another problem is that the microbes snacking on the fiber we eat create the short chain fatty acids such as butyrate. Butyrate feeds the cells of our colon and tweaks our circadian rhythm.

But microbes snacking on our mucus layer create propionate, which goes to the liver and creates glucose. This sets us up great for our cortisol awakening response, which should help elevate glucose when we wake up.

So, we’re working as a team. But to have a good team, you have to do your job. Most people don’t, and have the microbiome to prove it.


What matters?

So what matters? In a word: everything.

  • Light exposure
  • Food timing, frequency, quantity, and quality
  • Macronutrient profile/fiber intake
  • Select nutrient requirements
  • Metabolism
  • Sleep
  • Stress
  • Alcohol intake
  • Habitual schedule

Most of these are covered in the above review. Many people are doing 3 or more of these things wrong. They work a desk job, are stressed to the 9s, have a nutrient poor diet, and get improper light exposure. And if they’re diabetic or prediabetic, that needs to be corrected first.

Another review on aging indicates that changes in behavior are the primary drivers of the change in the microbiome as we age. This includes the influential life factors on the left of the above image.

It’s possible that probiotics may play a role, but it will only be secondary to changing your lifestyle. Believing otherwise is like believing you can grow tomatoes in sand, much like I did 3 years ago.


The microbiome holds a lot of promise for improving our health. But, in order to have a health-promoting microbiome, there are certain things we need to do to cultivate their existence.

By cultivating a healthy gut environment with a healthy lifestyle, we create a healthy microbiome. In return, the microbiome helps our digestion and prevents food intolerance. This is how we lived as a potent tag team together for millenia, and may hold the key to preventing chronic diseases of the gut.

Interested in learning about how our evolutionary past weighs on our current health? I created a free class on the topic. It’s called the Human’s Guide to Being Human and you can enroll by clicking here.

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