An x-ray image of the gut

The Ecosystem Inside Your Gut

Your gut is home to a complex ecosystem of microbes that influence your health. So who are they, and where did they come from?

We provide microbes with a place to live, and in turn they help to keep us healthy. Though our discovery of them is relatively new, they’ve lived with us, around us, on us and IN us since the beginning of evolution. As Ed Yong (author of ‘I contain Multitudes’) describes, if we were to put the whole of the earth’s history into one calendar year, then life emerged in March, microbes in October and humans in late December, right around the New Year’s Eve party. 

In short; microbes have always been with us, and we need them to continue life as we know it. Without them, our entire food system would collapse, but that’s a story for another day. 

The microbes inside you

Microbes include bacteria, yeasts, fungi and protozoa and they’re a varied bunch. Some thrive in extreme heat, others bloom in sub-zero temperatures and thus you can find microbes everywhere on Earth. Microbes are resident in the bottom of the ocean, the clouds above your head and the soil beneath your feet. They’re present on the keyboard I’m tapping away on and they’re inhabitants of just about every nook and cranny of my body (and yours too). Microbes are nestled in your nose, they munch the sweat in your armpits and support the barrier on your skin, but the vast majority of body dwelling microbes are found in the depths of your gut, more specifically - your colon, or large intestine. 

That’s because your colon offers the kind of environment that is attractive to a large number of microbes that prefer more easy-going environments - it’s warm, low on oxygen and much less acidic than the rest of the gut. Plus, there’s a pretty consistent buffet available in the form of your digestion’s leftovers. By comparison, the stomach contains virtually no microbes because it’s too acidic and fast flowing to be a viable nesting place.

Bacteria by numbers

Bacteria make up ~99% of the microbes in your gut and they’re also the ones we know the most about. That’s not to say that the other 1% of microbes (which include fungi and viruses) aren’t important or influential, there's just not enough research into them yet.

It’s hard to describe the sheer enormity of bacteria that call your gut home. Scientists estimate that the Milky Way (the galaxy, not the fluffy nougat bar) contains 100-400 billion stars. 100 billion is roughly the number of people who have ever lived on Earth. Your gut houses more bacteria than there are stars in the Milky Way; 10-100 trillion. A trillion is a thousand billion. Are you still with me? It’s a lot I know. But hopefully you’re getting the message that the bacteria inside your gut are a pretty significant community. 

Your gut bacteria possess some seriously influential genes too. Data from the ground-breaking Human Genome Project (which set out with the hefty goal of mapping all of our genetic material) taught us that humans have around 23,000 genes - about the same as… um, a mouse. And less than a houseplant. By comparison your gut microbiota contains around 3.3 million genes. So genetically speaking, you're about 99% microbe and 1% human. This genetic superpower living inside you is your gut microbiome, and it’s one of the reasons that microbes are so important to your health, because their genes offer more diversity and flexibility than your own, allowing them to carry out functions that your own body can’t.  Let’s look at some of the jobs your genetically gifted gut bacteria do for you.

1. They’re Digesting Superheroes

Many gut microbes harbour genes that can break down and extract energy from the parts of foods we can’t digest, like fibre, found in foods like beans, wholemeal bread, fruits and veggies. When gut microbes break down (ferment) fibre, they churn out compounds known as short chain fatty acids (or SCFAs for short) which have positive effects both in the gut and around the body.

For example, SCFAs make the colon more acidic, which favours the growth of beneficial bacteria and prevents pathogenic (disease causing) bacteria from gaining a foothold. SFCAs also play an important role in strengthening the gut barrier, by ramping up production of special proteins that keep gut cells tightly linked together, preventing unwanted invaders from crossing the gut wall. Outside of the gut there’s evidence that SCFAs have anti-inflammatory effects throughout the body and can influence our appetite, glucose and cholesterol levels.

2. They Support Immune Function

From birth and for the first year of life, gut microbes play a crucial role in training the immune system how to respond appropriately to unknown substances, which means that your body is able to correctly recognise allies and enemies without triggering a false alarm. Bacteria lining the gut also behave like doorkeepers, screening all the microbes that pass through the gut for pathogens that could make you sick. But that’s not their only line of defence - beneficial gut microbes compete for the same food as pathogens (and they’re often better competitors) which effectively starve off the bad guys before they can take hold.

3. They Influence Brain and Behaviour

Gut bacteria are also capable of communicating with your brain via various compounds that they produce, which send signals to the brain. Animal studies have shown that early life exposure to gut microbes is essential for developing a normal stress response, and that some types of beneficial microbes (known as psychobiotics) may have positive effects on our mental health. This is an emerging but exciting area of research.

Where did I get my microbes from?

Your first big dose of microbes would have been transferred to you during birth. If you made your way earthside via vaginal delivery, you would have been seeded with microbes from your mum’s birth canal. If you were born via Caesarean section, the first microbes to colonise your gut would have been those found on the skin’s surface. 

During the first few weeks and months of life, your microbiome would have undergone rapid change, shaped by feeding (formula milk or breastmilk), skin to skin contact (hugs and kisses) and your home environment (location, siblings and furry friends). In breastfed babies, nearly 40% of gut bacteria in early life comes directly from breast milk. Yep, even breast milk contains microbes!

What about pets? Well, it turns out that growing up alongside a furry friend can enhance your microbiome. Canadian researchers found babies living with a family pet had more diversity in their gut microbiomes than those without. In addition, they also found that babies in homes with pets had higher levels of a microbe linked with a lower risk of allergic disease. It seems that pets (particularly dogs) transfer a protective effect when a baby’s microbiome (and immune system) is forming. If you’re looking for more reasons to get a dog, well…. You’re welcome. Once our labrador George stopped sulking about us bringing home a teeny tiny person, he spent a lot of time licking my son’s newborn head and now my son takes great joy in throwing bits of lunch to George from his highchair. 

Ok back to your developing microbiome. After those early weeks, the next major milestone to influence your microbiome comes at around 6 months, when you graduate from milk to smooshed broccoli and banana. Yep, it's weaning time. This transitional period to solids results in a shift from milk loving microbes to those which break down more complex carbohydrates found in foods like fruit, vegetables and bread. Pretty clever huh?

From 6 months onwards, your gut microbiome begins to stabilise and by the time you reach your third birthday, your microbiome looks similar to an adult. From this point onwards your gut microbiome remains pretty stable and resilient, but it can be reshaped with changes in diet, antibiotic use, sleep deprivation and stress.