Getting dirty with microbiology

At the British Science Festival in Brighton, Kat Arney was part of a panel discussion organised by the Biochemical Society focusing on DIY biology - the idea that anyone can get their hands dirty and do some science. And, as she found out from fellow panellist Laura Bowater from the University of East Anglia, some projects are taking that very literally.

Laura - The problem with antibiotic resistance is that we are getting more and more bacteria that are developing resistance to a wider and bigger number of antibiotics. And at the same time, the research into making new antibiotics is going down. So, it’s a two-pronged problem – bacteria getting more and more resistant, and we’re finding less and less antibiotics that we’re using in the clinic.

Kat - And why do you think that soil might be a source of new antibiotics?

Laura - Because we know that soil contains millions and millions of bacteria and we know in the past that some of those bacteria that we found in the soil are actually producing antibiotics. So we think that by going back to the soil and looking at the soil at the soil in new ways, and by searching harder, we might find some new bacteria that are producing new antibiotics that eventually might end up in the clinic.

Kat - This seems a little bit weird to me that you’ve got bacteria making antibiotics that kill other bacteria. Why are they doing that?

Laura - Well, they only do that in the concentrations that we use in the clinic or in the lab. So, we use really high concentrations of antibiotics and they do kill other bacteria. And what we’re realising now is that in nature, those antibiotics are not produced at those levels at all. They're produced at much smaller concentrations.

What we think is that actually, in reality, in nature, what these molecules are, are signalling molecules between different bacteria where they're passing messages between each other, perhaps about concentrations of food or the environment. So they're a way of communication and not the weapons that we think they might be, the way that we’re using them in the clinic.

Kat - So we’ve got these bacteria in the soil all over the place, some potentially unknown to science, potentially making exciting antibiotics – whether they're using them to kill each other or talk to each other – how are you trying to get the public to find these bugs? What are you trying to do?

Laura - What we’re trying to do is to encourage the members of the public to work with us. So, we want them to pick soil and they’ll come and bring the soil to us and we’ll put the soil in water, shake it, and actually, shake the bacteria off into the water. And then we get you to take little drops of the water and to spread that onto agar plates, and we’re using lots of different agar plates which are the plates that have nutrients in it that allowed the bacteria to grow.

Bacteria can be fussy so we would just want to give them the ingredients that they need and we’re hoping that when we take them back to the lab and grow them under different conditions that we can encourage new ones that perhaps haven’t been spotted before, because we weren’t able to grow them, to grow this time around and to produce these new drugs hopefully.

Kat - How do you spot if a bacteria is a new one?

Laura - Well, it’s difficult and you can't just do it by eye. So you can tell straight away by eye if it’s producing an antibiotic that might be killing another bacteria because you can see that on a plate because no other bacteria can grow near it. But we can tell some things about the bacteria so we can have an idea of roughly the kind of bacteria it is, but we don’t know. What we have to do is that we have to actually look at them in detail and perhaps even send them away for sequencing to absolutely find out whether this is a new one that hasn’t been found before.

Kat - So, if you found a new species of bacteria, you’ve got its DNA analysed, you know this is something new, how do you then work out what antibiotic it might be making?

Laura - Well, we do that by looking at the DNA and we know a lot about the kind of genes that make antibiotics now. So, what we have are really clever computer programs that will scan the genomes of the bacteria and they’ll find something that they’ll think, “Ooh! We think that’s a gene that might make an antibiotic.”

And when we know that, we can then go back and look at other antibiotics that might be similar and their genes and from that, we can kind of work out that that gene looks like something we found before that we know makes this. So perhaps, our one is making something similar but a little bit different.

Kat - So this all sounds very cool. We can find new antibiotics, we can find new species of bacteria. I've got a window box. Do you want some soil from my window box? How can people get involved in this project?

Laura - Yes, please. So, we will be running an event in Glasgow in the Botanic Gardens. We’ve also got another one coming up in the Norwich Science Festival. We’ve got a website called Antibiotics Unearthed. So, look us up there, Antibiotics Unearthed and you'll see our Facebook page and our Twitter tag, and you can contact us that way.

Kat - So, if people have got some interesting soil, they can just send it in. Do you want people’s soil samples basically?

Laura - Yes, we really like your soil samples, thank you.

Kat - Very few people might admit to that. And have you found any good candidates so far? And then, what happens if you do find a good one?

Laura - Well, what we’ve done is we found some bacteria that we know are producing something that looks like it’s killing two or three different potential pathogens that humans might have. So something called E. coli for example, which can cause nasty diseases. So we have two or three that we’re really interested in and that we need to follow up further.

And if we do find something eventually that we think has potential then it’s a start of probably a 10 to 20 year process where we have to look at that. We have to see if we can make it in sufficient quantities that we can use it, that when we give it to people or animals that it’s going to be safe. And that actually, when we take it and use it for us, that it does kill the bacteria in us and not just in the ground.

Kat - I'm going to go out and have a completely different view of looking at flower beds now and thinking, is there the new antibiotic superbug killer in there?

Laura - I hope there is!

Kat - UEA’s Professor Laura Bowater. The Antibiotics Unearthed project is being run by the Microbiology Society - just search online for ‘antibiotics unearthed’ to find out how to post in samples of your favourite soil, or to take part in a pop-up research event near you.