Discover biofilm and learn about potential benefits of harvesting ocean bacteria
Discover biofilm and learn about potential benefits of harvesting ocean bacteria
An overview of biofilm and bacterial potential.
University College Cork, Ireland (A Britannica Publishing Partner)
Transcript
One of the major problems with chronic infections is this idea of a biofilm. Now a biofilm is something that we may or may not have come across, but believe it or not, every morning when you get up and brush your teeth, you're actually fighting a bacteria biofilm.
And we call it plaque. But it is effectively begins as a bacterial biofilm. And when you want to think about a biofilm, or to understand what a biofilm is, normally anybody has heard of bacteria, if you see them in a picture, or if you see them in a lab or you see them on television.
You see this picture of a cell, sometimes with a tail or flagella, and it's swimming around on its own, or you pick up a test tube and it's cloudy. And we're told that's bacteria. They are bacteria, and there are planktonic bacteria. They're, in effect, in an acute phase, each cell fighting its own battle. But when you give bacteria a surface to attach to, and that can be any surface. It can be a medical implant, or can be the lining of your lung. It could be the pipe in a water processing plant.
They start to aggregate on that surface. And when they aggregate on the surface, they begin to change. And by changing, they form a complex community and we call that a biofilm. Now in that acute phase, we can generally treat those with antibiotics in a lot of cases, but once they switch to a biofilm, they're almost impossible to eradicate. And it's estimated that about 80% of all infections occur as a biofilm.
So when you hear of somebody who's come out of hospital with a medical implant or that has an infection, chances are it's a biofilm. Now they're in here and again, you always have to think outside the box, but the key part here is that, in order for bacteria to form a biofilm, they have to communicate with each other. The same way that we're speaking here, bacteria communicate.
They just don't use words, they have their own language. And that's the in, because if you can understand that language, you can begin to disrupt it. And that's part of the work that we do as well, and it's something as simple as this. I mean that just looks like a structure. It's almost something that a child would make, but effectively, that's a signal molecule. To a bacterium, that is an instruction.
And for this particular structure, it says form a biofilm. So when the bacteria attach to the surface, they'll send a Pseudomonas aeruginosa for instance, with this particular signal, it will secrete this out, it will send it out like a message, to tell all the other cells around, let's form up this biofilm. And that's when you're in trouble. But we're looking to get to a stage where almost-- we can do the same with a sentence.
I mean the sentence says, or this instruction says, don't form a biofilm. But if I put-- or form a biofilm, but if I said, do not. I just changed the sentence slightly. I've kept most of the sentence, but by changing it, I've completely altered what happens. So why not do the same with a structure?
So if we take this, and we take part of it off, and stick something else on, we can change this instruction from form a biofilm, to the not form a biofilm. And that's where we come in with our collaborations with synthetic chemistry. Where we begin to modulate or we begin to decorate this signal and we look for anti-biofilm compounds. Compounds that we can feed in that will stop bacteria forming biofilms.
That's a very exciting area of research. But you're limited by that. Because there's only so many ways you can decorate this. And you're limited with what you can do with synthetic chemistry. So we've got to think again, we've got to look for alternatives. And that's where our marine bio discovery programs come in. So we have marine bio discovery, which is effectively where you're going out into the ocean and you're trying to harvest the natural ecosystem that's in the ocean.
From our perspective, we focus on the bacteria that are there, and many years ago, people thought there were no bacteria in the ocean. I mean, how could there be? What would they be doing there, but-- we find actually, most of the sponges that you see in the ocean or most of the sponges that exist in there, have rich reservoirs of bacterial systems.
And those bacteria are producing lots and lots of metabolites, lots and lots of compounds or instructions that we can begin to harvest. And it's not just instructions. They actually produce lots of anti-cancer compounds. They produce lots of enzymes that we can use in the pharmaceutical industry.
So the range and the extent to which these things can be used is vast and largely unexplored. But there's a catch, as there always is. So when you go and you undertake these marine bio discovery, one of the big limitations to that is that when you try to take the bacteria out of the ocean, onto an artificial system like a petri dish that we would use in the lab, it doesn't like it.
You're taking it from its natural environment, into something completely artificial, in many cases, they won't grow. And the estimates range from about 1% to 10% at best, you can actually culture or grow. And until recently enough, if you couldn't culture it, then how are you going to get-- how are you going to harvest it? How are you going to get these metabolites or these compounds, or these enzymes or new drugs out of the bacteria?
And that's where metagenomics comes in. So metagenomics is effectively a way of getting at that other 90%. And again, that comes all down to understanding. Everything has a code, everything has a sequence. I mean a lot of people would have heard of computer code, 1-0-1-0 and everything is a binary from that. Well bacteria are the same. And we're the same. All our cells are the same. So DNA, the way it works with the four bases, it's simply the organization of those four bases.
By understanding that, we can effectively take a blueprint, and turn that into an active product. So we don't need to grow the bacteria. We don't even need to see the bacteria. We can take its genetic blueprint, we can put it into a shuttle, like an adaptor system, like a translator if you want, a genetic translator, and that will turn that genetic blueprint into a molecule or the compound that we are looking for.
And that's when you've got to be a small bit ingenious, because that's where the screening comes in. You can imagine, if you can take all the genetic information from the ocean, most of it's just going to be clutter. The same as if you watch television, you might get one good program in a week. You're looking for that killer program. So you've got to get in there and you've got to fish for specifics.
And that's where things like gene traps, where we put colors or chromophores, and we get color changes that will light up when a particular compound you're looking for comes out. That's where the screening comes in. And it's a very exciting space to be in, because I mean it's an untapped reservoir. And the potential is massive.
And again, true collaboration, I mean a lot of the work is being done in the Biomerit Research Centre, but we will have strong collaboration throughout Europe. And we're actually involved in a European program at the moment, which is looking to improve the culturability of the organisms, purely for that reason, because in tandem with fishing out all this genetic information, if you can find a way to let these things grow or to maybe culture 50%, again you're increasing your capacity to harness the potential from the ocean.
And all of this will translate, and is translating into clinical drugs, pharmaceutical solutions, anti-biofilm compounds. So it's an exciting place to be.
And we call it plaque. But it is effectively begins as a bacterial biofilm. And when you want to think about a biofilm, or to understand what a biofilm is, normally anybody has heard of bacteria, if you see them in a picture, or if you see them in a lab or you see them on television.
You see this picture of a cell, sometimes with a tail or flagella, and it's swimming around on its own, or you pick up a test tube and it's cloudy. And we're told that's bacteria. They are bacteria, and there are planktonic bacteria. They're, in effect, in an acute phase, each cell fighting its own battle. But when you give bacteria a surface to attach to, and that can be any surface. It can be a medical implant, or can be the lining of your lung. It could be the pipe in a water processing plant.
They start to aggregate on that surface. And when they aggregate on the surface, they begin to change. And by changing, they form a complex community and we call that a biofilm. Now in that acute phase, we can generally treat those with antibiotics in a lot of cases, but once they switch to a biofilm, they're almost impossible to eradicate. And it's estimated that about 80% of all infections occur as a biofilm.
So when you hear of somebody who's come out of hospital with a medical implant or that has an infection, chances are it's a biofilm. Now they're in here and again, you always have to think outside the box, but the key part here is that, in order for bacteria to form a biofilm, they have to communicate with each other. The same way that we're speaking here, bacteria communicate.
They just don't use words, they have their own language. And that's the in, because if you can understand that language, you can begin to disrupt it. And that's part of the work that we do as well, and it's something as simple as this. I mean that just looks like a structure. It's almost something that a child would make, but effectively, that's a signal molecule. To a bacterium, that is an instruction.
And for this particular structure, it says form a biofilm. So when the bacteria attach to the surface, they'll send a Pseudomonas aeruginosa for instance, with this particular signal, it will secrete this out, it will send it out like a message, to tell all the other cells around, let's form up this biofilm. And that's when you're in trouble. But we're looking to get to a stage where almost-- we can do the same with a sentence.
I mean the sentence says, or this instruction says, don't form a biofilm. But if I put-- or form a biofilm, but if I said, do not. I just changed the sentence slightly. I've kept most of the sentence, but by changing it, I've completely altered what happens. So why not do the same with a structure?
So if we take this, and we take part of it off, and stick something else on, we can change this instruction from form a biofilm, to the not form a biofilm. And that's where we come in with our collaborations with synthetic chemistry. Where we begin to modulate or we begin to decorate this signal and we look for anti-biofilm compounds. Compounds that we can feed in that will stop bacteria forming biofilms.
That's a very exciting area of research. But you're limited by that. Because there's only so many ways you can decorate this. And you're limited with what you can do with synthetic chemistry. So we've got to think again, we've got to look for alternatives. And that's where our marine bio discovery programs come in. So we have marine bio discovery, which is effectively where you're going out into the ocean and you're trying to harvest the natural ecosystem that's in the ocean.
From our perspective, we focus on the bacteria that are there, and many years ago, people thought there were no bacteria in the ocean. I mean, how could there be? What would they be doing there, but-- we find actually, most of the sponges that you see in the ocean or most of the sponges that exist in there, have rich reservoirs of bacterial systems.
And those bacteria are producing lots and lots of metabolites, lots and lots of compounds or instructions that we can begin to harvest. And it's not just instructions. They actually produce lots of anti-cancer compounds. They produce lots of enzymes that we can use in the pharmaceutical industry.
So the range and the extent to which these things can be used is vast and largely unexplored. But there's a catch, as there always is. So when you go and you undertake these marine bio discovery, one of the big limitations to that is that when you try to take the bacteria out of the ocean, onto an artificial system like a petri dish that we would use in the lab, it doesn't like it.
You're taking it from its natural environment, into something completely artificial, in many cases, they won't grow. And the estimates range from about 1% to 10% at best, you can actually culture or grow. And until recently enough, if you couldn't culture it, then how are you going to get-- how are you going to harvest it? How are you going to get these metabolites or these compounds, or these enzymes or new drugs out of the bacteria?
And that's where metagenomics comes in. So metagenomics is effectively a way of getting at that other 90%. And again, that comes all down to understanding. Everything has a code, everything has a sequence. I mean a lot of people would have heard of computer code, 1-0-1-0 and everything is a binary from that. Well bacteria are the same. And we're the same. All our cells are the same. So DNA, the way it works with the four bases, it's simply the organization of those four bases.
By understanding that, we can effectively take a blueprint, and turn that into an active product. So we don't need to grow the bacteria. We don't even need to see the bacteria. We can take its genetic blueprint, we can put it into a shuttle, like an adaptor system, like a translator if you want, a genetic translator, and that will turn that genetic blueprint into a molecule or the compound that we are looking for.
And that's when you've got to be a small bit ingenious, because that's where the screening comes in. You can imagine, if you can take all the genetic information from the ocean, most of it's just going to be clutter. The same as if you watch television, you might get one good program in a week. You're looking for that killer program. So you've got to get in there and you've got to fish for specifics.
And that's where things like gene traps, where we put colors or chromophores, and we get color changes that will light up when a particular compound you're looking for comes out. That's where the screening comes in. And it's a very exciting space to be in, because I mean it's an untapped reservoir. And the potential is massive.
And again, true collaboration, I mean a lot of the work is being done in the Biomerit Research Centre, but we will have strong collaboration throughout Europe. And we're actually involved in a European program at the moment, which is looking to improve the culturability of the organisms, purely for that reason, because in tandem with fishing out all this genetic information, if you can find a way to let these things grow or to maybe culture 50%, again you're increasing your capacity to harness the potential from the ocean.
And all of this will translate, and is translating into clinical drugs, pharmaceutical solutions, anti-biofilm compounds. So it's an exciting place to be.