July 29

The Gut Microbiome: Do We Have Free Will or Are We Ruled By Microbes?

If the title of this article makes you feel like you've landed in the biology section of the science fair, I empathize with you. There's a good reason I pivot this week to discuss the gut microbiome instead of my usual pondering about abstract philosophical subjects such as how to cultivate eulogy values.

Strange as it sounds, there is a connection between the two: the gut microbiome has much to do with whether you feel motivated to even contemplate self-improvement. Who'd have thunk?

But first, some disclaimers. I'm not a qualified medical professional, or a nutritionist, or a dietitian—never been and will never be (too much work, for starters). That said, after reading and listening to much material on the subject of microbiomes, I have, to put it mildly, been blown away by just how impactful and influential these tiny little organisms are to our health and well-being. To the point where I feel it would be remiss of me not to touch upon this subject.

But this article is merely an introduction to the subject of microbes. I hope it motivates you to do your own research on how you can help your gut microbiome help you.

The Beginning. And the End.

Evolutionary biologist Stephen Jay Gould, named by the Library of Congress in 2000 as a "Living Legend," wrote a popular article in the Washington Post in 1996 in which he referred to Earth as the "Planet of the Bacteria."

Before humans evolved on the planet, and even before dinosaurs roamed, the very first organisms on Earth were the microbes—tiny organisms that can only be seen under a microscope. These microbes continued to thrive when the dinosaurs went extinct and, according to scientists, will continue to do so after our species is gone too. In short, they will be the last surviving organisms when our planet ceases to exist.

Gould, referring to the microbes as the stayers and keepers of life's history, said

Our shenanigans, nuclear and otherwise, might easily lead to our own destruction in the foreseeable future. We might take most of the large terrestrial vertebrates with us -- a few thousand species at most. I doubt that we could ever substantially touch bacterial (microbial) diversity.

Translation: The microbes own this place. We merely rent it.

So, let's understand a little bit more about our owners. Starting with who they are and where they live.

Intro to microbes

Microbes are tiny organisms, too small to be seen without a microscope, and include things like bacteria, archaea, eukaryotes, and viruses. And the word microbiome simply refers to a collection of different microbes coexisting in a habitat.

Where do they live?

The short answer? Everywhere on the planet. Including on us. Literally. Trillions of microbes cover our skins, mouths, lungs, and of course, the largest number of them line our guts (the small and large intestine).

And the fascinating thing is that no two people have the same microbiome—not even identical twins. Like unique fingerprints, our unique microbiomes are a testament to the depth and diversity of the microbiota surrounding us.

The gut microbiome: What we know

The gut microbiome is essentially a collection of all the genetic material from the microbes in the small and large intestines, containing roughly 3 million genes.

Why should we care about the gut microbiome?

The gut microbiome is the most important scientific discovery for human healthcare in recent decades—James Kinross, a microbiome scientist, and surgeon at Imperial College London.

The gut microbiome has risen to fame because it performs functions other organs can't. The microbes digest our food, convert food into vitamins, and help develop our immune systems by fighting and destroying any harmful bacteria we ingest through water and food.

They determine our health and our cravings, and in some ways, you can say they even shape our personalities.

That said, our collective understanding of the subject is still very rudimentary. Science is only beginning to scratch the surface of this complex subject.

But here are some key things we do know about the gut microbiome.

They are beneficial (for the most part)

To reiterate, microbes were there before us and will remain after we're gone. We're simply vehicles they use to grow up and develop. Having said that, most of the microbes in our gut are symbiotic: meaning we have a mutually beneficial relationship. They help keep our bodies running smoothly. We, in turn, help them thrive by feeding them the foods they need and keeping them alive: a win-win relationship.

They have a direct correlation with disease

But sometimes, things get a little out of control. Every disease and health condition—diabetes, obesity, cancer, depression, etc.—is associated with poor gut health. Though, we're still finding out exactly how.

Diversity is key

Not just in the workplace, but in the gut too, it seems like diversity is a big plus. The more diverse (containing different types of bacterial species) our gut microbiomes are, the healthier we tend to be.

Diversity is important because each species of bacteria has a specific skill. Think of it as if you're planning for a social event. You need multiple parties—caterers, florists, musicians, etc.—to come together to make the event a success. If the caterer, for instance, is missing at your event, good luck getting your DJ to fix the missing appetizer.

In a similar vein, for our bodies to chug along nicely, we need different types of microbes to act collaboratively. That way, the right microbes are available within the gut to handle crises.

Finally, someone to blame.

The gut microbes aren't always quiet workers. They can be demanding too. And sometimes in selfish ways.

If you struggle to give up sugar and feel guilty, you don't have to blame your willpower (or lack of). Instead, blame your gut microbiome because that's probably where those sugar cravings may have originated.

Let's say you've always enjoyed sugary treats, which means you have developed within you a colony of bacteria that are used to gorging on sugar. When you suddenly decide to swap your bowl of multicolored boxed cereal for turnip greens, you essentially withhold sugar from these impish organisms. Unhappy at the sudden change, the sugar-hungry microbes protest by sending messages to your brain demanding to be fed. Next thing you know, you're polishing off a doughnut.

This is why getting good workers, i.e., setting up a good-for-you microbiome, is essential.

Why me and not her?

Does it drive you insane that eating one cookie immediately causes a 2-lb spike in your weight, but your friend can seemingly gorge on an entire pack of muffins and still look and feel like she chewed on celery sticks?

We tend to blame our genes in such cases, but the culprit may be your microbiome. Not for nothing do we say, you are what you eat.

It is said that your gut microbiome influences your health and well-being more than your genes do.

Given what we know about our gut microbiome, what can we do to care for our precious friends?

The gut microbiome: Do's and don'ts

Like most things, the microbiome is influenced both by nature (what you're born with) and nurture (your environment and what you eat.)

As I alluded to earlier, the science on how the gut microbiome works and how to influence it is still nascent and developing. But there are a few things we know now that we can incorporate into our lifestyles.

Eliminate unnecessary antibiotic use

Antibiotics, of course, are one of science's most significant accomplishments. But we, as a society, are over-exposed to antibiotics; a classic case of taking a good thing too far. And that has broad repercussions.

A study showed that one course of broad-spectrum antibiotic use reduces gut bacteria and diversity by 30%.  

Using antibiotics on an as-needed instead of a may-as-well basis can help keep our bacterial friends happy in our gut.

Up the fiber

Without getting into the weeds too much, let's just say dietary fiber is crucial to wellness. The gut microbiome uses the fiber and converts it into short-chain fatty acids, which promote weight loss, and plays a crucial role in keeping us healthy and well.

Another research study showed that mice put on a continued low-fiber diet (such as the Standard American diet – SAD) showed a 60% loss of gut microbial diversity.

Enough said. Fiber is crucial.

Eliminate ultra-processed foods

Preservatives, chemicals, additives, emulsifiers, etc., are added to food to make them shelf-stable. Your stomach is not a shelf for things to sit on forever.

We know that the gut microbiome has a hard time dealing with these added chemicals in food, but current research seems to point to the fact that the consequences may be much worse than we currently know.

We could be kinder to our digestive process by feeding it stuff that's easy to break down. Replacing ultra-processed foods with fermented, living foods is the first step in that process.

Make friends with dirt

Science has proven that we kept losing gut microbial diversity as mammals were domesticated. Here's an excerpt from a research study titled Does Soil Contribute to the Human Gut Microbiome?

Soil and the human gut contain approximately the same number of active microorganisms, while human gut microbiome diversity is only 10% that of soil biodiversity and has decreased dramatically with the modern lifestyle.

Simple changes such as not reaching for the hand sanitizer or the mouthwash every hour, letting kids play in the dirt, etc., may help salvage some of the losses we've incurred and continue to incur as we lead highly sterilized lives.


It's beside the point whether it was the Roman poet Virgil or someone else who said, "The greatest wealth is health." But the underlying message is true and has stood the test of time.

It's hard to get motivated and focus on esoteric self-improvement efforts when you feel lousy physically and mentally—something that is bound to happen when you have poor gut health.

Knowing what we do about the gut microbiome today, it's in our best interest to keep the trillions of microbes in our bodies happy and healthy.

As Prof. Tim Spector said in an interview with the Guardian,

It's (the gut microbiome) a vital organ in your body, and you need to look after it. If you do that, it will look after you.



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