What is the microbiome?

02 February 2015

Interview with

Ed Yong, Science Writer

Do you consider yourself human? We hate to break it to you, but your human cells Microbiomeare outnumbered by the millions of microbes living in you and on you.

They're what are known as our microbiome, and recently researchers have started to realise that these multitudes may be having an effect on our health, weight and even mood.

To learn more about these microbial friends, how they get there and what they're doing, Kat Arney spoke to science writer Ed Yong to get the basics...

Ed - People think of themselves as individuals, as a single animal. But actually, every one of us is an ecosystem - inside our bodies and on our skins. We have trillions of bacteria and other microbes that live with us, that influence our lives. They aren't just mere hitchhikers or passengers. They are integral parts of our bodies. They do things like help us to digest our food. They protect us from other deadlier microbes that threatened to cause diseases. They help to shape our immune systems and perhaps even our behaviour. They're very much a part of us.

Kat - I guess that bacteria have a bit of a bad rap because we always think of them as causing diseases. How recently did we get this alternative view of them that actually, they may be a really important part of our lives?

Ed - I think people have known that for actually a very long time, but it's been quite a neglected concept. So, even people like Pasteur had some appreciation that microbes could play a beneficial role. But you're right that we've come to think of microbes generally as causes of diseases. So, you get endless news stories saying, "Your mobile phone or your keyboard has more bacteria on it then a toilet seat. The implication there is that bacteria are a sign of death and filth that there are bad things that you want to get rid of and destroy. Whereas that's just not true. There are obviously microbes that make us sick. But there are probably many more that actually help us or at worst, are completely neutral. Bacteria had the planet to themselves for billions of years before any human or any - even an animal came on the scene. So, we live in their world and we have evolved in their world.

Kat - If you say that bacteria are found all over me, my skin, in my gut. Where did they come from?

Ed - It's generally thought that people are born sterile so that the womb is a sterile bubble in which it's just the baby. Now, that may or may not be completely true, but the fact remains that most of a child's bacteria are seeded into it when it emerges from its mother. So, not to put too fine a point on it, when your born, your slathered with microbes which then become yours. They colonise the rest of you. They get in your mouth. So, you get them from your mum basically. A lot of animals do that. some inherit microbes while they're still an unfertilised egg. Some get them at the point where they're born. Others eat them from things that their mothers provide.

Kat - We see in the news there are good bacteria and bad bacteria. Is this a fair definition? I look at my hand. It must be covered in bacteria. How do I know which one's a good and bad?

Ed - So, I think some bacteria, you could reasonably classify as bad. So, Yersinia pestis which causes plague is probably bad, Bacillus anthracis which causes anthrax, again, I think you could call that bad. But in most cases, those definitions don't really work. Say, the bacteria that live in our gut, they play important roles in our lives, help to digest our food, but they can also revolt. If they get across the lining of the gut and enter the bloodstream, they can cause really strong debilitating immune reactions. so, the same bacteria can be good in one setting and if you translocate them by about a few millimetres, they can suddenly be bad and dangerous. So really, these concepts of good and bad, they are dependent on place and time, and context.

Kat - And recently, as we've heard a lot about gene sequencing and people reading the gene sequences, the DNA sequences of different bacteria, the microbiome, what sort of stuff is starting to emerge from these studies because we hear a lot about them and it's hard to know what do they mean?

Ed - It's clear and increasingly so that bacteria do play important parts of our lives and I don't think it's hype to say that and to emphasise it. we are used to thinking of ourselves as individuals that we live under our own steam, we behave under our own wills, we grow up from a single egg into this complicated organism under instructions from our own genomes. All of those things are complicated by the presence of bacteria. So, we know that bacteria shape our development, they shape our behaviour, they shape our physiology, but we also know that bacteria affect our health. So, lots of studies have compared healthy people and people with diseases or various health problems from obesity to diabetes to colon cancer, and compare to their microbiomes to those healthy people. And they found differences. Now, what this means is still unclear I think. In some cases, we've got better evidence that the bacteria are behind those conditions. But in others, it's not clear whether the changes in the microbiome are just going along for the ride, whether they're the results of the condition rather than the cause of that.

Kat - Are someone's gut bugs making them fat or because they're fat, they have different gut bugs?

Ed - Exactly or probably a cycle of both of things. I think that's where there's currently a bit of hype. Microbiome has been linked to virtually every health condition under the sun now. People have written reviews saying, maybe the microbiome is behind religious behaviour or all sorts of aspects of human culture and behaviour.

Kat - It's just the bug.

Ed - That's right. everything is to do with microbiome. why did I feel sad on Tuesday? Microbiome! why do I crave a coffee right now? Microbiome!

Kat - We're just a vehicle for our bacteria.

Ed - We are and I think - well obviously, we're not. I think this is where the hype around the science goes too far. We need to drain it back in. what we need now is some careful science that looks beyond just comparing patterns in different people and establishes things like causality. What is actually result of the bugs or vice versa and how did they affect our health? What is the mechanism behind these things?

'I Contain Multitudes' by Ed Yong is out in 2016.

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