Good Health

The creatures within

The importance of understanding our gut microbiome


We are raised to believe that our bodies are made up of trillions of cells. That would be a neat and tidy little story, but it’s not exactly true. 

While it’s true that your many cells contain the DNA and provide the body's structure, more than half of what makes up “you” is, technically, myriad communities of separate creatures. To be precise, while our bodies are made up of around 37 trillion human cells, we’re also made up of roughly 39 trillion microorganisms – bacteria, fungi, protozoa and other thing-ys – that have co-evolved with us over thousands of years. That is, most of “you” is technically… well… not you. Think about that…

The microscopic zoo inside us 

Coined by the Nobel prizewinning molecular biologist Joshua Lederberg, the microbiome is the word for the community of microorganisms that make up the more than half of us that is not exactly us. Some of them are just silent hitchhikers on our journey through life, serving no purpose and causing no harm. But other organisms are integral to the proper functioning of our bodies. This is especially the case with those that live inside our guts and make up our gut “flora” – a gastrointestinal jungle teeming with microscopic critters. Fun! Let’s meet our little inhabitants:  

  • Bacteria: single-celled organisms found pretty much everywhere. While we think of bacteria as “bad,” these little fellas help digest foods our bodies cannot, regulate our immune system, destroy the “bad” bacteria that cause disease, produce much-needed vitamins (e.g. B12, riboflavin, etc), and help break down complex sugars into simple glucose. 
  • Archaea: bacteria-sized organisms that help facilitate digestion by helping the aforementioned bacteria do their jobs.
  • Fungi: multicellular organisms such as yeasts and molds that can stimulate the body’s natural immune responses. However, they can also be hostile
  • Protozoa: a poorly understood group of single-celled organisms that feed on organic matter.

Each of these categories of organisms is incredibly diverse. They live on your skin and in your saliva, mouth, eyes, and, as mentioned above, in your gut. When you think about it, we are walking collections of symbiotic relationships. 

“They” are the foundation of our health

As a society, we’ve long believed that our health was determined by two things: genetics and diet/lifestyle. With the new scientific advancements in the understanding of the microbiome, it’s clear that BOTH genetics and lifestyle have a major downstream effect on the many communities of microorganisms that influence whether we become diseased. 

The exact composition of our gut flora can vary by age, region, health and diet, but there are between 500 and 2,172 distinct species of bacteria in the human gastrointestinal tract alone. This ecosystem is involved in many of our life-sustaining functions: 

  1. Harvesting energy
  2. Fighting off infections and boosting the immune systems. In fact, 70-80% of our immune system is located in the gut. 
  3. Communicating with our brains through our nerves and hormones to help us regulate moods and aid cognition, learning, memory and numerous physiological processes. Fun fact: dopamine and most of our serotonin is also generated from the gut microbiome.
  4. Digesting nutrients and absorbing vitamins
  5. Controlling blood sugar levels and cholesterol
  6. Helping to regulate weight, moods, and appetite
  7. Promoting “good” HDL cholesterol and triglycerides

The list of benefits of a balanced microbiome reads like the wish list of an average 55-year-old: better digestion, weight loss, improved sleep, healthier skin, mental clarity, mood stability, and more energy. Where do we sign up?!

Unfortunately, our microbiomes are often unbalanced

If you’re unaware of how to balance your microbiome, or perhaps even unaware that it needs to be, then it’s highly possible that your microbiome is, in fact, wonky. More specifically, it probably means that your microbiome lacks the species diversity that keeps it in balance. 

This is particularly true in decadent Western countries where we are all freaked out bundles of stress that sit too much, work too much, sleep too little, have shitty high-calorie/low-fiber diets, drink too many sugar-sweetened drinks, take too many antibiotics and don’t exercise nearly enough. As a result of our unbalanced, less diverse microbiome, we often tend to be overweight or obese, increasingly insulin-resistant and highly susceptible to diseases like diabetes, asthma, inflammatory bowel disease (IBD), and eczema. Let’s look at these bad habits one by one as they pertain to gut health: 

  • Stress: Stress hormones increase intestinal permeability (leaky gut), tipping the scales toward an imbalance of more bad than good bacteria in the gut.

  • Sedentary habits: Sitting around for long periods is thought to lessen the diversity of gut microbiota, which appears to be one precondition for chronic diseases.

  • Poor nutrition: Many of us overindulge on processed food and sugar, which can harm the beneficial bacteria in your gut and contribute to or cause inflammation throughout the body.

  • Antibiotics and antacids: There is a time and a place for these medications, but we westerners are famously over-reliant on them. Antibiotics are like a nuclear bomb to your gut - killing good and bad bacteria alike which obviously reduces gut diversity. Antacids tend to help bad bacteria grow by reducing the amount of acid in your stomach that would otherwise keep them in check.

  • Sugar over-consumption: Foods that are high in sugar tend to get digested too quickly and our microbial friends further down the digestive tract go hungry. They then eat the lining of our intestines instead. This allows inflammation-causing substances to enter the blood stream which can then contribute to disease.This can also lead to the reduction in the population of beneficial bacteria and an increase in harmful bacteria. No bueno. 
  • Sleep deprivation: Similar to stress, not getting enough sleep leads to hormonal imbalance which can cause the stress hormone cortisol to rise which can lead to intestinal permeability (leaky gut). And this leads to more bad bacteria in the gut. It’s worth noting that lack of sleep is also associated with making bad food choices. 

Your microbiome is a big part of the system of systems that is “you,” so any imbalances there can reverberate throughout your body. Unbalanced, unhealthy gut microbiome can cause or contribute to myriad gastrointestinal problems such as constipation, gallstones, acid reflux, infections, hemorrhoids, IBS/IBD, and ulcers as well as other kinds of diseases like liver disease, diabetes, pancreatitis, and hepatitis. It can also interfere with your serotonin and therefore your ability to control moods as well as your cognition, learning, memory, and numerous physiological processes.

How do you know if your microbiome is unbalanced? 

For around $200 you can take an at-home test that analyzes your mRNA, measures microbial and human gene expression and gives you recommendations for how to improve your gut flora. Alternatively, your doctor can perform a test for you. You can also simply notice the various patterns going on in your body. Here are some signs your microbiome is off kilter: 

  1. Autoimmune problems, such as thyroid issues, rheumatoid arthritis and type 1 diabetes
  2. Digestive issues, such as irritable bowel syndrome, constipation, diarrhea, heartburn or bloating
  3. Sleep issues
  4. Skin rashes and allergies
  5. Sugar cravings
  6. Unexplained fatigue or sluggishness
  7. Unexplained mood disorders, such as depression or anxiety
  8. Unexplained weight gain or weight loss

What can you do about it? 

Now that we understand our bodies to be a delicate balance of mutually beneficial (usually) relationships, how should that impact how we live our lives? Or what we eat? To what degree should we change our lifestyles to ensure internal harmony and wellbeing? 

Lots of behaviors, habits and preferences can impact your gut health, but none more than your eating habits. A little dash of patience helps too, because it can take up to six months to rehabilitate an unbalanced microbiome. All of these suggestions will sound familiar to you, as we’ve all read them a thousand and one times.

1. Vegetables are fiber-lous 

Our guts dig fiber - especially the kind that can't be digested without their help. Green leafy veggies especially – leeks, onions, asparagus, broccoli, spinach, artichokes and so on. But also whole grains. The fiber passes through the small intestine to the colon where microbes break it down and convert it to energy. One study found that “Adding fiber to the diet can trigger a shift from a microbial profile linked to obesity to one correlated with a leaner physique.”  It can also help ensure those microbes are well fed and don’t start munching on the protective mucus lining of the gut, which possibly triggers inflammation and disease.

2. Sugar, the hidden inflamer

Sugar is in a ton of different foods, and it’s not an altogether bad thing. But a lot of food we eat is laced with sugar without our knowledge. The bread on a Subway sandwich, for example, has so much extra sugar that a court in Ireland officially declared it a dessert - like a pastry. In fact, many restaurant dishes and a good number of processed foods contain hidden sugar. Given that it’s almost unavoidable, it’s a good idea to cut the sugar you do know about. That will help the “good” bacteria thrive which improves diversity which improves digestion, improves your skin, decreases your brain fog and improves your mood. It's all connected, you see. 

3. Probiotics are living medicine

Though historically a complacent and largely ineffectual product category, probiotics have recently started to make a big comeback. Much of the progress is thanks to high-resolution, long-read DNA sequencing, which helps scientists target specific imbalances in the microbiome that lead to diseases like diabetes, IBS, and more. One 2018 study of 22 types of probiotics found that 68% of them had “strong-moderate” evidence for efficacy for at least one type of disease. By leveraging this technology and applying pharma-like manufacturing processes, it is possible that probiotics advance to become another branch of medicine.

4. Spicy food lovers rejoice

As counter-intuitive as it is, that hot sauce threatening to eviscerate your bowels might just improve the health of your microbiome. It’s too soon to say for sure, but according to early studies out of the Harvard School of Public Health, spicy food (specifically the capsaicin in hot peppers) might lower inflammation, improve metabolic health and have a positive effect on gut bacteria and weight.

5. Fermented foods are fabulous

Break out the yogurt, sauerkraut, pickles, and kimchi (not all at once, that’s gross). They all contain healthy bacteria, mainly the strain Lactobacilli, which help the body break down food, absorb nutrients, and fight off disease-causing organisms in the gut.

6. Get your polyphenols

You’ve probably heard of these things before. Found in things like red wine, dark chocolate, olives, and green tea, polyphenols are a particular type of organic compound that gets broken down by the microbiome and then stimulates healthy bacterial growth.

It’s hard to overstate the shift in our understanding on the microbiome. We used to believe that it didn't have much impact on our overall health. Now we believe it's absolutely central. We used to believe that our eating habits, medicines, and lifestyles had very little effect on it. Now we believe that it's highly sensitive to what we put in our mouths and how we live our lives. We used to believe that it wasn't terribly relevant to disease. Now we believe that an unhealthy gut flora can cause or contribute to a whole host of chronic conditions. The study of the microbiome used to be a backwater science. Now, thanks to DNA sequencing, it's hit the big time, baby. We’re on the cusp of a revolution in microbiome science, so expect to learn a lot more in the years to come.

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