By Ruairi Robertson Ph.D.
Gut microbes, gut microbiota, gut microbiome, gut bacteria, gut bugs. These terms were once hidden in science and medical textbooks but now seem to be popping up on every cereal packet, bus stop, and Instagram account in your feed, as people become intriguingly keen to describe the in-depth details of their bowels. And if you’re reading this, it’s more than likely you’re trying to figure out what all the fuss is about. So here we have brought you a beginner’s guide to the gut microbiome.
What is the microbiome?
Let’s start with the basics; microorganisms (or microbes for short) are microscopic organisms, meaning we usually can’t see them with the naked eye. As we can’t see them, we’ve always underappreciated these little creatures, which are everywhere on earth, and I mean everywhere. Microbes have been found living in volcanos, 11km under the sea, under Arctic ice. They’ve even been found living in the Atacama Desert in Chile, the driest place on earth, which is essentially like the Moon.
Any community of microbes living together in one environment is called a ‘microbiota’. And all of the genes of these microbes are called a ‘microbiome’. But often these terms are used interchangeably. And you have your own microbiota/microbiome! Although you can’t see them, there are trillions and trillions of tiny living organisms living all over your skin, up your nose, in your mouth, in your lungs on your face and, you’ve guessed it, in your gut. In fact, there are so many of them in your body, they actually outnumber your human cells. Yep, there are roughly (very roughly) 40 trillion bacterial cells in your body and only 30 trillion human cells. And that doesn’t even include all the fungi, viruses and lots of other microbes. You are a walking, talking, microbial ecosystem.
Why is it a big deal?
But why is the microbiome suddenly a big deal? Well, we’ve known for a long time that there are microbes living on us, but we never really knew how many there were and how many different types. Previously, scientists were only able to study human microbes by growing them in the lab. But most of our bodily microbes can’t be easily grown in the lab using normal techniques. Suddenly, with better technology in the last 10-15 years, it’s become more accessible to study the DNA of these microbes instead of growing them. Using these new technologies, we’ve discovered that there are over 1000 different types of bacteria living in the human body and that they are extremely important for your gut, heart, brain and almost every other organ. But unfortunately, important microbes can be affected by overusing antibiotics, hand sanitizers, bad diets and general ‘Western’ lifestyles, which might be damaging our overall health. Not all microbes are bad, in fact, a lot have a beneficial impact on our health!
Most of your bodily microbes live in your gut. This is because it is warm, moist, has very little oxygen (which most gut bugs don’t like) and has a constant stream of nutrients passing down through it. Think of your gut microbiome like a dense jungle: there are thousands of different species living in this environment, each requiring different nutrients and conditions for growth and each carrying out different jobs in order to keep the ecosystem healthy. But instead of trees, monkeys, and spiders in your gut jungle, you’ve got fungi, viruses and bacteria, some with ridiculous names that have been called after the people who discovered them, like Salmonella (discovered by a guy called David Salmon) or Marvinbryantia (come on now Marvin, that’s a bit of a stretch). Like a jungle, it’s really important to have as many different types of species in your gut ecosystem, as they each have different jobs. If there weren’t trees in a jungle, who would produce oxygen; if there weren’t bees, who would pollinate the flowers; if there weren’t insects, who would keep the soil healthy? It’s the exact same for the different species of microbes in your gut. In general, healthier people have much more diverse gut microbiomes (in other words, many more different types of gut microbes) than unhealthier people.
How does the microbiome develop?
Now there’s a bit of debate about when we get our first microbes. For years, scientists thought the womb was sterile but some recent studies have shown that babies may even be exposed to microbes before they are born. Even still, you probably got your first proper splattering of microbes at birth. As you emerged into the world, you were covered in a microbial coating in the birth canal. Evolution has made sure that the microbes in a mother’s birth canal are the very first ones that her baby comes in contact with, as they are really important for helping to develop the immune system. But babies born by C-section instead get lots of different bacteria from the mother’s skin, which might be why they have higher rates of asthma and allergies (fortunately, it looks like these gut bacterial changes can be reversed if babies are breastfed). Some of these bacteria that appear first in a baby’s gut, like Bifidobacteria and Bacteroides, are really important for digesting all of the different sugars in breastmilk, which help a baby to grow.
As you grow up, your microbiome begins to expand all over your body, but most of them grow in your gut. These microbes like living in different parts of your gut. Most bacteria live lower down in your large intestine. Some prefer to live in the sticky mucus that lines your intestines, like Akkermansia (you’ve guessed it, discovered by a guy called Antoon Akkermans), which helps to keep this mucus layer thick and to prevent disease-causing bacteria and other things from passing through into your blood-stream. Other gut microbes prefer to chill out in the general space in your gut, tasting all of the different foods and chemicals that make their way down there to see if they should be allowed into the body or not.
What does it even do?
All of these microbes help to control your blood sugar and cholesterol, prevent you from getting infections, control the calories that you absorb and store, communicate with your nervous system and brain, influence your bone strength and hundreds of other functions that are too many to describe in one article. From a diet perspective though, one of their most important jobs is to digest fiber. In fact, you can’t even digest fiber on your own, as you don’t have the enzymes to do so. So fiber makes its way down to the large intestine where it is a feast for all of your gut microbes. When gut microbes eat fiber, they break it down into lots of chemicals such as short-chain fatty acids, which keep your gut healthy and can even regulate how hungry you feel.
So as you can see, it is important that we keep our gut jungles healthy and happy. We want as many different types of microbes in our gut to carry out all of these important jobs. This is why it is so important to eat as many different types of fruits, vegetables, nuts, seeds, whole grains and beans as possible as they are high in fiber and help your gut microbes to grow. Don’t just stick to the same old bowl of coco pops, ham sandwich and pasta each day. Mix it up, keep those gut microbes on their toes by feeding them artichokes, lentils, raspberries, spinach and as many different types of foods as you can imagine. And in exchange, they’ll make sure to look after you from belly to brain.
Dr. Ruairi Robertson is a postdoctoral researcher examining the role of the gut microbiota (all of the bacteria and other microbes in your gut) in many aspects of human health. He has a B.Sc in Human Nutrition from University College Dublin and a Ph.D. in Microbiology from University College Cork, where he conducted his research within the world-renowned APC Microbiome Institute. Ruairi also spent one year as a Fulbright Scholar working at Harvard University and Massachusetts General Hospital in Boston, USA. Ruairi is currently a Postdoctoral Research Fellow at Queen Mary University of London.
Ruairi’s research examines how the trillions of microbes that make up the gut microbiota can influence everything from weight to brain health, and most importantly how our diets influence this relationship.
Check out his TEDx talk here: https://www.youtube.com/watch?v=awtmTJW9ic8&t=110s