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Gut Health and the Microbiome

· Health and Nutrition

Are we really 10% human and 90% bacteria?

Do we really have a "second brain?"

Should I be taking probiotics supplements?

I can actually remember the first time I became very intrigued with the concept of the microbiome. It was 2015 and I was listening to one of the early podcasts on the Tim Ferriss Show. Episode 54 featured a conversation between Tim, Jessica Richman, and Dr. Jonathan Eisen.

Jessica Richman is co-founder and CEO of uBiome, a startup backed by Y Combinator and Andreessen Horowitz, and Jonathan Eisen is a Professor at the UC Davis whose research focuses on the evolution, ecology and function of communities of microorganisms.

I don't remember the specifics of the podcast, but I remember thinking that bacteria and microorganisms were incredibly fascinating and maybe I should have studied bio-science in college instead of economics.

More recently, the topic of gut health keep popping up, in Nutrition School, books and articles I'm reading, and podcasts I'm listening to. In this post, my goal is to organize my brain and my Evernote around the topic of gut health and the microbiome, with hopes to further understand what it is, why it's important, and how to support it.

What is the microbiome?

As humans, we are made of trillions of human cells, but we have 10x the amount of microbes - single-celled organisms like bacteria, viruses, fungi, yeast - that live on us and within us. Single-celled microbes have been around almost as long as the planet itself. These microbes come from our mothers at birth, and continue to thrive inside us for the rest of our lives. They are like our roommates, working in harmony with our body.

Some of these microbes flourish on our skin, but the vast majority take up residence in our digestive tract, mostly in the large intestine, particularly the colon (bacteria can also be found in the esophagus, stomach, and small intestine). The gut is where food is digested, metabolized, and absorbed to be delivered into the cells and provide the body with energy. It is also essential in allowing for the removal of waste. The trillions of microbes in the gut play a big role in performing these functions, and this is why your diet has such a big impact on your gut and your health.

So it might be obvious that the gut microbiome plays a huge role in digestion and metabolism, and are probably linked to things like IBS and leaky gut. But what is less obvious, and incredibly interesting is that is also plays a critical role in shaping your appetite, allergies, mood, and neurological function. You gut actually talks to your brain! And scientists have begun referring to our microbiome - the term for the entire microbial being we each contain - as the "second brain."

The Second Brain

Your gut bacteria can have a huge impact on the way you feel. Certain species of gut bacteria produce chemicals that can affect immune function, and neurotransmitters such as serotonin, dopamine, and GABA, all of which play a key role in determining your mood.

Sarah Wilson, founder of the I Quit Sugar program, says that gut health is highly linked to anxiety, something she suffers from. "People used to think (and say) that anxiety and depression were caused by a deficit of serotonin in the brain. But although serotonin is a brain neurotransmitter, science now shows that 80-90 percent of the serotonin in our body is made in our digestive tract. So anxiety can be explained on a biochemical level by the health of our gut."

There was an article in the NY Times in Jan 28 2019, called Germs in Your Gut Are Talking to Your Brain. And Scientists Want to Know What They are Saying, which talked about how the body’s microbial community may influence the brain and behavior, perhaps even playing a role in Alzheimer’s disease, Parkinson’s disease, dementia, schizophrenia, autism, and depression.

It also works the other way around, our brain can influence our microbiome. On the Aubrey Marcus Podcast, gut health specialist Amy Meyers talks about how our stress and thoughts affect our microbiome. Stress, from overworking for example, can negatively affect the microbiome, but the way we perceive that stress is just as important. "What you think about your stress is just as important as the stress." So for example, being stressed about being stressed makes it worse, or if you eat something unhealthy, and then beat yourself up over it, the agony you are causing yourself only makes thing worse.

Cravings, Appetite, and Weight

Your microbiome can control your appetite, and play a role in weight and obesity. Studies have been done on mice, showing that when you do a fecal transplant between lean and obese mice, the lean mice have increased appetite and gain weight, while the obese mice lose weight. An article in the NY Times called "Unlocking the Secrets of the Microbiome" states that compared to lean mice, obese mice have a 50 percent reduction in organisms called Bacteroidetes and a proportional increase in Firmicutes, and lean mice get fat when given fecal transplants from obese mice.

A similar shift has been observed in people. Previous studies have found differences in the gut microbiota of lean and obese adults.

In the book SuperLife: The 5 Simple Fixes That Will Make You Healthy, Fit, and Eternally Awesome, author Darin Olien has a chapter called "Feeding Our Other Body" in which he talks all about the gut microbiome.

He writes, "There is an estimated 500 different species of bacteria in the gut, each having specific functions and nutritional needs. Our gut flora makeup is directly influenced by the dietary choices we make. We decide which microbes to feed and which ones to starve. We create the ecosystem for them. Even a brief dietary change has been shown to alter the gut microbiota.

"Our microbes don't just sit around waiting for us to eat the things they need. They are capable of sending signals, actual cravings for specific kinds of food. Then we get the sudden urge for a sweet snack, and we think it's our lack of willpower that makes us give in. Microbes also send us signals telling us we are full. We think it's our own bodies, our own metabolisms talking to us, but we could be wrong.

"If we feed ourselves sugary, processed food, then the microbes that thrive on them proliferate and dominate our digestive system. And we will suffer. If we eat healthy foods, then the microbes that consume them will flourish. And so will we. That is a healthy symbiosis between us and them."

So my takeaway from this is that when you eat bad food - junk, processed, sugar - you crave more bad food. And when you eat healthy food, you crave less bad food. And even one meal can change the microbiome composition in 24 hours.

There is also evidence that the typical high-calorie American diet rich in sugar, meats and processed foods may adversely affect the balance of microbes in the gut and foster the extraction and absorption of excess calories from food. A diet more heavily based on plants — that is, fruits and vegetables — may result in a microbiome containing a wider range of healthful organisms. (Unlocking the Secrets of the Microbiome)

So eating more plants is not just about the micronutrients that the body needs, it's also about feeding the good organisms in the gut.

Tips for a Happy Gut

Vincent Pedre, author of Happy Gut, says that "Your gut is basically your internal garden, and requires tending to just like a garden does. A "Happy Gut" is one where a diverse world of friendly bacteria live, creating a harmonious symbiosis to help us digest, produce vitamins, stimulate a vibrant gut lining, and keep unfriendly organisms in check."

Here are his 5 tips for a happy gut:

  1. Diversify your diet - this is the key to a vibrant healthy gut
  2. Eat prebiotic rich foods like greens, onions, garlic, artichokes
  3. Eat probiotic rich foods like Kombucha and kefir, sauerkraut kimchi and fermented veggies
  4. Don’t graze between meals - give your gut a break
  5. Eat 3 hours before bed - you’ll sleep better if you’re not digesting

I've heard from multiple experts that there are benefits from intermittent fasting. Taking prolonged breaks in between meals, and/or not grazing between meals, gives your digestive system a break and time to heal.

Probiotics and Prebiotics

Amy Meyers says, "Prebiotics are compounds that are fermented by beneficial bacteria in your gut in order to enhance your gut health. Probiotics, on the other hand, are live microorganisms that keep your gut flora balanced and provide you with health benefits including improved immunity, digestion, and brain function. Basically, prebiotics feed your probiotics and the two work together to enhance your digestion and boost your overall health."

She gave this analogy on the Aubrey Marcus Podcast that helped me make sense of it: "Probiotics are increasing the ranks of the army of healthy microbes, while preboitics serve to feed that army."

A list of probiotic foods include yogurt, fermented drinks like kefir and kombucha, and fermented veggies like sauerkraut and kimchi.

Here are Amy Meyer's Top 10 Prebiotic Foods: dandelion greens, asparagus, bananas, apples, onions, garlic, leeks, Jerusalem artichoke, chicory root, and jicama root. Many of these foods are very high in antioxidants, and have anti-cancer properties.

There are some other specific foods that I have recently read that support gut health -

What Your Microbiome Really Needs is Fiber, Not Kombucha

Probiotics have become trendy. Kombucha bars have popped up all over Orange County where I live, that serve kombucha flavors on draft. And supplement companies are making fortunes from selling probiotic supplements in pill form.

Katherine Harmon Courage is the author of Cultured: How Ancient Foods Can Feed Our Microbiome, and wrote this Medium post earlier this month titled, What Your Microbiome Really Needs is Fiber, Not Kombucha.

She says, "But in many cases, our focus on which foods to eat to benefit the microbiome has been misplaced...

we get distracted by the most inventive new kombucha flavor, the best kale kimchi, or the most local goat milk kefir. And who can blame us? These are interesting, live, effervescent cultured foods. But the microbes in our probiotic foods don’t actually take up residence in our guts. They can be valuable for health, but they are not, generally speaking, replenishing an anemic microbiome. By focusing solely on these trendy products, we are neglecting the upkeep of our full-time microbes. And what our native microbes need is fiber. Complex, rustic, now-elusive fiber."

She draws an important distinction between our gut microbes. "When it comes to our biomes, we can break microbes into two key categories: those that live permanently in the human gut and those that are just passing through." She goes on to say, "The microbes that reside more permanently in our guts, day in and day out, did not come from yogurt or kimchi. They are our native microbes. These microbes are acquired at birth, throughout infancy, and in early childhood — with a few picked up here and there later in life... I do hate to burst your highly cultured bubble, but with a spoonful (or crate-full) of yogurt, you have not actually reestablished your native gut bacteria, restoring you to peak ancestral intestinal health, no matter what the marketing will have you believe — and no matter how many live and active bacteria or strains are included."

So what is the best way to feed our microbiomes? She say, fiber.

She says that the Average American consumes about 15g of fiber per day, while the US government recommends 30g, which is still only about a third of what she thinks we should be eating. What happens when we don't eat enough fiber? "When our resident microbes go hungry for too long, they start to eat through the better part of that barrier, opening up holes for all kinds of material to escape into the bloodstream, a condition known, unappealingly, as leaky gut."

But here is what she says happens when we do get enough fiber:

  • "When we do eat food that contains prebiotic fibers, gut microbes in turn repay us by making compounds that can help quell inflammation or defend us against infection. These compounds, known as metabolites, are microbial byproducts, expelled during microbes’ metabolic process of digesting food that comes their way. Fortunately, these byproducts just happen to be beneficial for us."
  • "Adding in more prebiotic food also means, simply, more helpful microbes. Some research has suggested that for every 10 grams of prebiotic carbohydrates that reach the gut microbiota, about three grams of additional bacteria blossom into life. That’s roughly 3 trillion new organisms for just adding those 10 grams of microbe fodder each day. Not a bad tradeoff for eating some extra whole grains — and cold potato salad."
  • "So, when it comes to prebiotics, instead of “build it and they will come,” think “eat it and they will multiply” — and possibly even help protect you from a myriad of increasingly common health concerns. All it takes is paying a little more attention to what you’re feeding your microbes."

Top Takeaways

It seems like I see a new article about gut health and microbiome research every week. In the above, I cited many authors, podcasts, articles, and books. Here are my top takeaways when it comes to gut health:

  • It's crazy that we have trillions of microorganisms living within us, and that they outnumber even our human cells. It's even crazier that our microbiome has such a big impact on our health, and the way we think and feel.
  • Since most of our microbes live in the gut, the food we eat highly affects them. We are either feeding the good microbes, with whole foods and fiber-rich foods, or we are negatively impacting our gut by eating processed foods (sugar, refined carbs, artificial ingredients) and pro-inflammatory foods (high sugar, meat, alcohol, toxins). Even one meal can rapidly affect the microbiome. Either way, the microbes that are fed will be the ones that control our cravings, appetite, weight, and mood.
  • Who would have thought that 80-90% of serotonin (the happy chemical) is produced in the gut, not the brain? That shocked me. Studies show a relationship between gut health and anxiety and depression. And I'd bet that there is a correlation rate between rising rates of anxiety and depression in America and the Standard American Diet. 
  • Having a diverse diet of whole foods is highly beneficial to gut health. Eating probiotic and fermented foods is beneficial. Not grazing in between meals gives your gut much needed break time. And de-stressing is also beneficial for the gut.
  • As with anything, beware of the marketing and overhype of probiotic foods. Kombucha is very trendy right now. It's far more important for gut health to eat foods high in prebiotic fibers, or basically most vegetables, fruits, whole grains, legumes, nuts, and seeds.
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