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The Importance of a Healthy Microbiome (And How to Achieve It)

"Make sure you take these steps to help protect your microbiome and keep it healthy."

We're getting microscopic with Dr. Keller Wortham, MD, today, as he explains the microbiome — the trillions of microorganisms that exist in our bodies — and the many roles the microbiome plays in our overall health.

Get ready for some truly fascinating facts. The body is even more amazing and complex than most of us realize! Plus, Dr. Keller will provide some tips for maintaining a good microbiome, and how to improve it when things go wrong.

Video Highlights

  • 00:49: What is the Microbiome?
  • 02:36: Functions of the Microbiome
  • 07:29: Where These Bacteria Come From
  • 09:47: What Happens When Things Go Wrong
  • 17:27: 10 Tips for a Healthy Microbiome
  • 26:07: Wrap-Up

Did you know that our bodies are home to a virtual universe of life referred to as the microbiome? As we learn more about how much we rely on these other life forms within us, we are coming to realize they are more a part of us than we ever thought. 

What is the Microbiome?  

The microbiome refers to the trillions of microorganisms that exist within our body.  There are literally thousands of species within us, including bacteria, viruses, and fungal cells. In fact, even though that may sound a little weird and gross to people, there are more than 40 trillion bacterial cells alone within our bodies. If you compare that to the fact that there are only 30 trillion human cells, it could be argued that we are in some ways more bacterial than human! If you added up all of the weight of all these bacterial cells within us, it would be roughly two to five pounds, which is about the weight of the human brain. And these bacterial cells are far more genetically complex than our own genome. 

So, most of the time these bugs exist peacefully within us, don't cause us any problems, and in fact, they cause such a plethora of benefits that some people refer to our microbiome as its own independent functioning organ system. So what does the microbiome do and why is it so important to our lives?

Functions of the Microbiome

The microbiome is with us from our very earliest days as an infant. The microbiome — specifically bifidobacteria — helps our guts to be able to break down the sugars in the milk we're getting from our mothers. So quite literally from the very earliest days, we are dependent on these bacteria to help us get our food source. In addition to that, as we grow and the microbiome diversifies, and we get more and more bacteria, they start to fill a bunch of very important functions in our body.

One of the first things that they do is help to break down thefiber in our diets. When they do that, they create something called a short chain fatty acid, which is vital to our health. They are a nutrient source from the foods that we get, and they help improve muscle function, and prevent diseases like inflammatory bowel disease. They help makeproper cholesterol for our body, thus reducing our risk ofcardiovascular disease. These bacteria are like our in-house doctors, creating this amazing short chain fatty acid which functions like a medicine for us in so many ways. 

They also have been shown to stabilize the immune system. It's thought that these microbes within us are actually communicating with our immune system all the time, helping control our responses, not only to things that might be coming along that we might need to defend against, but also controlling our response to our very own body. That’s right, it’s thought that the microbiome can help prevent autoimmune diseases, which are conditions in which the body’s immune response mistakenly attacks healthy cells.  

The microbiome it also breaks down potentialtoxins in our food source, protecting us from molecules in foods that might be unhealthy for us.  The microbiome is also critical in making very important vitamins. If you watched Dr. Keller’svideo on vitamins, you know that vitamins are substances that we have to get from our food, and can’t make on our own. But that was only part of the story. The actual truth of it is, not only do we have to get these vitamins from our food but we also rely on the microbes within us to finish making those vitamins. That includes very important vitamins like Vitamin K, and many of the B vitamins.  So, it'svery important to have these bacteria within us.

The microbiome also helps regulate our neural function, or the nervous system. Our gut is basically one big ball of nerves. Maybe you've felt that, if you've ever gotten nervous and felt it deep in your gut. There's actually something in your gut that's often referred to as the gut brain, and those nerves are constantly in communication with your actual brain. The messages that are getting sent back and forth are so important to regulating our mood, and we know that the microbiome creates neurotransmitters in the gut by taking the foods that we take in and then synthesizing these very important neurotransmitters like serotonin, that then can help communicate with our brain and set our mood. If you’ve ever experienced hunger-induced anger (sometimes referred to as being “hangry”), you've experienced the very critical communication between your gut brain and your actual brain. So, that microbiome helps synthesize neurotransmitters likeserotonin, that then go on to communicate with our entire nervous system and help control the way that we function.

In addition to that, the microbiome helps regulate our fat storage, as well as helping to protect us against pathogens. Pathogens are the bad bacteria that are always trying to assault us. The good bacteria inside us are constantly trying to battle off those bad ones. If you have ever had a parasite or a bad bacterial infection in the gut, you know how terrible it can feel if that microbiome lets one of those pathogens get through the cracks. So, as you can see, the microbiome is incredibly important to our bodies.

Where These Bacteria Come From

You may be wondering where these bacteria come from. How do we get these 40 trillion cells within us? Well, again, it starts during the very early stages of life, primarily when we are born and passing through the birth canal. As you pass through the birth canal your mother has a lot of bacteria from her own microbiome in the vaginal canal and on the skin. As babies are born, they get a lot of that bacteria from the birth canal them on their skin and in their eyes and mouths. As gross as that sounds, it is super critical to life. So much so that children who are born via C-section, and therefore don't pass through the birth canal, are often swabbed with bacteria, to make up for what they missed by not passing through the birth canal. 

So initially we get some of those bacteria from passing through the birth canal, and then we get more from the world around us — the objects that we touch, and coming in contact with our mother’s skin. There's bacteria in breast milk, in the foods that we eat, and the place that we live. There can be more or less, depending on  what area of the world we live in, and how cleanly our environment is. Medications we take, like antibiotics, also directly affect the microbiome, and other medications that don’t have a direct impact, can still have a big influence on it. So, as we grow and develop and have all of these influences coming in — where we live, what we eat, whether we were breastfed, whether we we're born by C-section — our microbiome becomes very unique to us. The genetics of the bacteria and other microorganisms within us are so specific to us that they could almost be used to identify us.  

What Happens When Things Go Wrong

It's also been shown that the more genetic diversity you have within your microbiome the healthier you are. We're going to talk about ways that you can improve and increase the genetic diversity of your microbiome, but first let’s talk about what it looks like when things go wrong. 

In the microbiome world, that is calleddysbiosis and it’s a fancy way of saying we have somehow thrown off the proper function of the microbiome.  So, what happens when we get dysbiosis? It can result in a number of different symptoms, such as the following.

Weight Gain

The bacteria inside us are influence how wedigest foods and how we absorb calories. Therefore if that bacteria get altered, it can directly affect our weight gain. In fact, they've even done some very fascinating studies on this, such as one that looked at identical twins, where one twin is overweight and the other is a normal weight. They looked at the microbiomes of those twins and observed that the overweight twin had a bad bacteria balance, or a dysbiosis in their microbiome, when compared to the normal weight twin.  What's even more fascinating is that after taking the gut bacteria from those identical twins and implanting them in identical twin mice, who are fed the exact same diet, researchers could see that the mouse that received the dysbiotic microbiome started to gain weight compared to the mouse that got the microbiome from the healthy human twin. So, that's one way that dysbiosis can cause health problems.

Inflammatory Conditions

A dysbiotic gut can cause inflammatory conditions, primarily of the gut, like inflammatory bowel disease and inflammatory bowel syndrome. There's an interaction of our gut and our immune system with the bacteria within us that helps keep everything in balance.  And if that gets thrown off, not only can you start getting inflammatory conditions within your gut, but in the rest of your body as well. This could includeskin inflammation andjoint inflammation and otherinflammatory issues in the body.

Heart Conditions

A third way that dysbiosis or a bad microbiome can affect us is related toheart disease.  It has been shown that people with a dysbiotic microbiome are at an increased risk for heart attack and stroke. It’s thought that this is because these gut bacteria are very involved in regulatingcholesterol. The better our microbiome, the better the balance of good and bad cholesterol in our bodies. Also, if you have a bad microbiome and you're making bad cholesterol, you're increasing inflammation, which is also bad for the heart. So your microbiome is tied directly to your heart health.  

Mood Problems

We have seen that people with dysbiosis, or with bad combinations of bacteria in the gut, can have mood disorders such asdepression and other psychiatric issues. Researchers have looked at people with depression and actually seen that their microbiomes are off kilter.  That’s why you can sometimes use aprobiotic, which helps improve the microbiome, to actually treat depression. There’s a fascinating relationship between the gut brain, with its nerves and neurotransmitters, and our actual brain, and this relationship really affects our moods.

Allergies, Diabetes, and Immune Issues

Another way that dysbiosis can cause health problems has to do with allergies and immune responses. Allergies occur due to our body’s overreaction to things it really shouldn't be reacting severely to. In some cases, that can become a grave situation — if you've ever known someone who's deathly allergic to peanuts or bee stings, for example, you know this can be quite serious. In other cases, it might just be the sniffles and other things that just pester your immune system. It is thought that people who have less of a diversified microbiome are more prone to allergies. Part of this is something calledThe Hygiene Hypothesis which states that if you grew up in a really sterile environment (like hospitals, or even just an extremely germ-conscious home where everything is spotless all the time) you might have been done an actual disservice. It's been shown that people who grow up in very hygienic environments get less exposure at an early age to those other microbes and therefore the immune system doesn't really learn how to adapt to all the different things around us. That can actually lead our immune systems to be hypervigilant as we get older, so they attack everything that comes our way. 

Interestingly, this has been documented in kids who are born via C-section. Babies born via C-section are at a much higher risk of developing allergies and eczema as they grow to adulthood, because they didn't get that initial bacterial dosing when they came through the birth canal. For the same reason, they are also at a higher risk of diabetes. Diabetes is an autoimmune disorder, meaning a condition in which the immune system attacks itself. 


Another way that dysbiosis can affect the body is through conditions like autism. It's been demonstrated that people with dysbiosis have a higher risk of developing conditions like autism. Researchers examining Autistic children observed that their microbiomes had less variety in their genome. We’re not sure if this is an association or a cause, but there definitely seems to be some correlation.

Clearly it’s extremely important to protect our microbiome. So we’re going to go through 10 very critical things that you can do to increase your microbiome’s diversity, keep it healthy, and prevent dysbiosis.  

10 Tips for a Healthy Microbiome

Eat Diverse Foods

Diverse foods help increase the diversity of the bacteria inside us. Basically, those foods need to be whole and healthy foods, not processed, and not containing a lot of chemicals. This means we should eat things like whole fruits, which have the fiber that we need to get those short chain fatty acids that we talked about, as well as legumes, like lentils, and otherfiber-rich foods. That will increase a species of bacteria calledbifidobacteria, which is so important to ourgut health.  

Eat Fermented Foods

Fermented foods are great for our lactobacilli — that's another class of bacteria. This includes foods like kefir, a fermented milk product. Other fermented foods include yogurts, especially if they are live culture yogurts, sauerkraut, and kimchi. is a fermented food.  These are all things that you can eat to help increase the diversity of your very important microbiome.

Limit Artificial Sweeteners

Artificial sweeteners are terrible for your microbiome. That includes Equal, Splenda, and Sweet'n Low. Studies have shown that when you take artificial sweeteners, you drastically change the kinds of bacteria in your gut, and not in a good way. That might be a reason why a lot of people who consume artificial sweeteners end up gaining weight.

Eat Prebiotic Foods

A prebiotic is something that helps give nutrients to the bacteria in your gut. Bananas, asparagus, and oats are all really good prebiotic foods. Again, these are going to give nutrients to the bacteria themselves to help keep them alive, healthy, and happy.  


You can’t really control whether this happened to you, but it can influence your decisions for your children. This is one of the reasons it's thought that breastfeeding is so important for babies, ideally at least for six months. When you breastfeed, that baby is not only going to get healthy amounts of bacteria, but he or she will also get immune stimulation. Ingesting breast milk in the very early ages is one way to set the microbiome on the right path and help start to mold the immune system. So, in a way, it can continue to benefit your children throughout their whole lives.

Eat Whole Grains

Whole grains great for your microbiome. A lot of that has to do with fiber — as bacteria digest whole grains and release that fiber in those short chain fatty acids, they're basically helping your body in multiple ways. It's helping with cholesterol levels, with heart health, and it may even help reduce different kinds of cancer.  So, get those whole grains in to keep the microbiome — and in turn the rest of the body — happy and healthy.

Eat a Plant-Based Diet

We’ve talked in the past aboutvegetarianism and why it can be such a healthy option.  One of the reasons is that meat products, especially red meat, tend to increase the amount of bad bacteria in your body. Eating a plant-based diet doesn't mean you have to become a strict vegetarian. Just really ask yourself, “Do I need to be eating meat at every meal?” or “Do I need to be eating it every day?” And if you can reduce your intake of meat, especially red meat, you're going to reduce the bad bacteria in your microbiome. 

Eat Foods Rich in Polyphenols

Polyphenols function like a prebiotic. Prebiotics or polyphenols are important because they help protect the lining of the gut, and they also help give nutrients to the microbiome,  and the good bacteria in it. In fact, it's thought that some of those polyphenols are actually toxic to bad bacteria. It’s believed that the good bacteria in our guts have learned to handle the polyphenols and even thrive on them, whereas the bacteria become weakened, and shrivel and die because of these polyphenols. So, where do you get your polyphenols? One of the best sources of polyphenols is dark chocolate! You can  also get polyphenols from red wine, olive oil, and green tea. These are all great sources of polyphenols, and some of them are really delicious too!

Take a Probiotic

If you think you're having some disruption in your microbiome, or you just to be proactive about maintaining it, take a probiotic.  There are different kinds of probiotics out there — make sure you're getting a probiotic from a trusted source. TheSmarter Nutrition probiotic ensures you’re getting bacteria that can withstand the acid environment of the stomach, and includes prebiotics, so not only are you getting the good bacteria, you're also getting the foods that help fertilize them. Taking a probiotic is a great way to make sure you're replenishing and balancing your microbiome.

Avoid Antibiotics Whenever You Can

We know that sometimes you don't have a choice. You may have a bad infection and need to take an antibiotic. But according to Dr. Keller, doctors do prescribe antibiotics for things that you don't need an antibiotic for. Sometimes a doctor will write you a prescription for an antibiotic just because you demand one. So, don't put pressure on your doctor to give you an antibiotic if you don't really need it — it's going to be terrible for your body.  Again, there are times where you absolutely need an antibiotic. But when it comes especially to a lot of respiratory stuff you might be dealing with, like a common cold, you might not need one and you may be able totake other measures instead to get it under control. Talk to your doctor about those options, instead of defaulting to antibiotics.


We hope you learned a lot about the fascinating world within us that is the microbiome. The microbiome is so important for so many aspects of our health. Make sure you take these steps to help protect your microbiome and keep it healthy.

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