Gut health Health Weight Management

The Importance Of Gut Health And Microbiome Diversity

Written by Amy

Inside our intestines, also referred to as our gut, there are millions and millions of bacteria. In fact, there are more bacterial cells in your body that human cells. The most recent studies say 3 times more. That’s a bit freaky, right? Just don’t think too much about it and you’ll be ok. These bacteria are essential for us to be able to break down and digest our food properly. Not only that, though, but they play a huge role in our nutrition absorption, energy levels and hormone regulation. Our overall health is intrinsically linked to our gut health.

What Is The Gut?

what is the gut

When I talk about the gut, I'm referring to the small intestine and large intestines. It’s the part of the digestive tract where the nutrients are filtered out of our food and into our body. The rest that can’t be used is removed as waste products. If you were to take the membrane of this system and stretch it out, it would cover two tennis courts! However, it’s only one cell thick. If you know that your skin is around 50-100 cells thick, just imagine how thin and delicate your intestine walls are! The digestive tract is also a completely enclosed system. It has one opening at your mouth where things go in and one at the other end where things come out. That’s it. Other than these entrance and exit points, the digestive tract has no input from the rest of your body. So long as it’s healthy.

The Second Brain

The digestive tract also has its own set of neurones that control the functions that go on down there. In fact, there are 100 million gut neurones. That’s about as many as a cat’s brain has. For this reason, the gut is often called The Second Brain, a term first coined by Michael Gershon . While it’s not as sophisticated as the brain in our head, the gut neural system plays an important role in monitoring the feedback from the bacteria in the digestive tract as well as regulating the digestive functions, such as how quickly things move through, enzyme production and the volume and concentration of acid production in our stomach.

Gut brain connection

The neurones in your gut do communicate with the brain through the vagus nerve, which is the largest nerve connected to the brain, and passes through the throat and abdomen. There is also a complex system of chemical and hormonal signals that pass between the gut and the brain. These tell us that we’re hungry or stressed or we ate something we shouldn’t have. This is the brain-gut axis and is the reason why we feel emotions in our gut, so to speak. Just think about being nervous or anxious or stressed. Generally you feel sick or have “butterflies in your belly”. One common symptom of stress is a change in appetite. You’re having a physical, gut reaction to an emotional state.

The Gut Ecosystem

Within the digestive tract, there is an entire ecosystem separate from that of the rest of your body. It functions on its own and maintains itself independently. This is the gut flora; the bacteria that live in there. Everyone will have a slightly different array of bacteria in their gut. Our environment, our diets, genetics and medication have an effect on its makeup.

Even whether we were born by cesarean or not and what our mothers consumed while they were pregnant changes what bacteria we’re born with. A pregnant mother who needed antibiotics will reduce the diversity of the ecosystem in her baby’s gut. The same is true with a baby born by cesarean section as it won’t be exposed to the bacteria of the vaginal canal. Studies at the New York University School of Medicine are currently testing the effects of swabbing cesarean-birthed babies with bacteria from the vaginal tract as soon as they are born. Children are also more susceptible to environmental changes making changes in the gut flora.

The Importance of Gut Diversity

The environment within the gut plays a huge role in the diversity of bacteria that live there. For example, some bacteria are highly adapted to living in a mucous membrane, so if the gut lining reduces the mucous layer, these bacteria won’t fare so well. Broad spectrum antibiotics have a huge impact on gut diversity as the role of an antibiotic is to kill bacteria. After taking antibiotics, many of the gut bacteria will die out and the more resistant species will have a head start at re-colonising the empty space.

Gut diversity affects many functions within our bodies, from obesity to cognitive development and behavioural traits. To some extent, it’s responsible for a large part of who we are. What lives in our digestive tract dictates what nutrients we get, how well our body functions and how safe our tight junctions are from toxins. There have even been many correlations between the composition of the gut ecosystem and autism.

Mitochondria and Gut Health

When we eat food, it’s used to make energy. However, what you may not know is that this process is actually 3 times removed from your food. We eat the food, chewing it and breaking it down using enzymes in our saliva and acid in our stomachs. Then the bacteria in the gut break down the food further into micronutrients. These then move out into our body and fuel the chemical processes that happen in our cells. The nutrients are broken down further by the liver into fat or sugar and these are used by mitochondria to make ATP. ATP, or adenosine triphosphate, is the energy currency that our bodies use.

Mitochondria are passed on through the mother and they are essential in many processes even above making energy for our cells. The mitochondria produce redox molecules that are essentially antioxidants. They protect cells from free radical damage and are used to carry messages between the different parts of our immune system. They carry communications between the bacteria in the gut, the brain and the immune system. It also helps to maintain the tight junctions throughout the body. This communication is essential for our bodies to function well. The general idea is that more mitochondria is better. We lose mitochondria naturally as we age. However, some mitochondria loss is also due to toxins that come from by our unhealthy diets.

Gut Diversity and Obesity

microbiome effects weight

The makeup of the bacteria in your intestine can be an indicator for obesity. Obese Twin studies looked at microbiomes in pairs where only one twin was obese. They found that the diversity of bacteria in the gut of the obese twin was significantly less than in the leaner twin. When they took these microbiomes and inserted them into mice that had been raised sterile, the scientists saw that the mice who got the bacteria of the obese twin put on weight, despite being fed the same diet as the mice who got bacteria from the lean twin. These mice didn’t gain weight. Further experiments found that when enough bacteria from the lean mice were transferred to the obese mice, they began to lose weight on the same diet​.

How Your Diet Affects Diversity and Obesity

A high carbohydrate diet creates an environment in the gut that facilitates the grown of fermenting bacteria. Fermentation creates an excess of sugar, which is stored as fat by insulin in case of a future energy shortage. Although we can’t say for sure which outcome is the cause and which is the effect, it seems that once started, this situation creates a circular process whereby the obese person has a microbiome of a certain makeup, which then causes them to store fat It also causes carbohydrate cravings, because the bacteria that they have are sending signals that this is what they want to eat. This causes more fermenting bacteria to grow, making more sugar and so storing more fat. They therefore become more obese, creating an unhealthy gut microbiome, which then causes them to store more fat…

Sharing A Microbiome

We also know that mice who shared a the same cage can transfer microbiomes between them. Obese mice picked up some of the bacteria from lean mice and vice versa. During the studies, the mice that received the lean twins’ bacteria were kept separate from those that received the obese twins’ bacteria.

This poses an interesting topic on sharing microbiome. Dr Zach Bush uses methods such as intermittent fasting  and diet changes to improve the gut flora diversity as treatment for multiple issues such as obesity and Type-II diabetes. He said that often he’ll find that his patients reach a plateau in their treatment and weight loss. This happens despite them doing everything they should be. When he digs deeper into their lives, he has almost always found that there is someone else in the home who is unwilling to make the same changes. This person is then spreading their “obese” microbiome into the environment and affecting their spouse.
kissing for gut health

We can share microbiome with the people around us simply by breathing the same air. We also share ecosystem through saliva and skin contact. If you’re trying your best to be healthy and your partner isn’t, tell them that until they change their diet, you’re gonna have to go around kissing all the slim, healthy guys / girls that you meet to share their gut flora! Once Dr Bush manages to convince the other person to make the healthier changes in their life, he usually sees that his patients’ progress continues.

Changing Your Gut Health

Now, before you go and throw your hands up announcing that you have fat bacteria and are doomed forever, there is some good news. You can change your gut flora.

Improve Your Diet

The best way to do so is through your diet. The food that you eat feeds the bacteria inside you so when you change what you feed them, you’ll change which ones grow. By reducing sugar, you’ll reduce the amount of fermenting bacteria present. If you increase your fiber intake, you’ll feed more of the lean bacteria like Akkermansia muciniphila, which is found in the lean gut ecosystem. You should also be aware that, just like how the bacteria and mitochondria are eating what you eat, you are also eating what your food eats. If you then eat GM-grain fed beef pumped full of hormones and antibiotics, you’re also eating GM grain and hormones you don’t need.

Prebiotics And Probiotics

Along with food, prebiotic and probiotic supplements can be helpful. Prebiotics are usually a fibre source that feed the bacteria you want in your ecosystem. There is a concern that the prebiotic will only feed a small number of bacteria and so you end up encouraging overgrowth of one or a few species. Even if those species are helpful to our health, we still want as much diversity as possible.

Probiotics are also a bit controversial. Often, they are full of millions of copies of just a few species. While this is helpful when your microbiome is lacking diversity, you’re still only adding in a few species to an environment that should have tens of thousands. Imagine that you want your gut to look like a rainforest. If it's already a reasonably diverse forest, then adding loads of one kind of tree won't help it much. A good time to take a probiotic is after antibiotics, a viral infection or chemotherapy. Basically after anything that will damage your ecosystem. At this point, your gut is more like a back yard, or sometimes even a desert. So any trees at all will make a difference.

It’s worth noting that there’s no regulations on supplements, like probiotics. The means that no-one checks if it is what it says it is. If you’re interested in finding a good probiotic then check out Labdoor to find a probiotic that’s been tested to make sure it is what it claims to be.

Get Some New Bacteria To Move In

Exposing yourself to a new ecosystem is a great way to improve your gut microbiome diversity. Too many people live in essentially sterile environments. They get up and shower straight away, drive to work with the windows up. They spend the day in an air conditioned office before driving home again to their house that’s been bleached and scrubbed, killing as many good bacteria as bad. Of course, things should be clean. We want to avoid disease and infection, but we do also need exposure to some bacteria. So how do we do that?

Go Outside And Go To New Places

If you want new bacteria to get into your system, you have to go meet them. If you have  a balcony or a garden, do your morning yoga or have your coffee out there. Get into the garden and pull up some weeds. Breathe in the bacteria from the soil as you work. From the respiratory tract, they’ll make their way to your digestive tract and colonise some space in there.

Make an effort to go to new places and expose yourself to new environments. Each new place has a different bacterial ecosystems. Go for a walk in the woods and smell the trees; hang out at the beach and dip your feet in the sea; find a botanical garden to visit. Even just go to a new city for a couple of days. All of these places will have different bacteria than your home. Once you breathe them in, they'll find their way to your digestive system and hopefully find a space to set up home.

Steal Bacteria From Other People

hug for gut health

As we mentioned earlier, different people also have different ecosystems and we can share these. Instead of catching up with a friend online, go have coffee with them. Give them a hug and a kiss on the cheek and share the bacteria on their skin. The same is true with our pets. People who have cats and dogs at home tend to live longer. For a while we thought this was because of the the anti-stress factor of having a companion. While that may still play a role, we now know that it’s also because of the different ecosystem that lives on their skin and in their fur that we can absorb. Cats and dogs also pick up new ecosystem from their adventures outside, so when they come home give them a fuss and a cuddle to get the benefits of wherever they went.


Your gut health could be the most important aspect of your overall health. Not only does it control your weight, and therefore all of the health issues that come with an unhealthy weight, it also contributes to your immune system and mental health as well. Taking care of the bacteria in your gut could be the most fundamentally important thing you do for your body. 

P.S. I’m currently designing a programme that will take you through improving your gut health. It's all about healing your ecosystem through your diet. The first Beta test ran in April and after some improvements, I'm going to be doing another one. Spaces are limited, so if you want to be part of the next test group, just click here to find out more and get on the waiting list!

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