Biofilms (featuring Dr. Katrine Whiteson)

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Prices vary by event distance and participant age. Great news, Extraordinaries. Dr. Katrina Weitz in his back. This time she's here to talk to us about biofilms. We're going to talk about biofilms that are delicious, which she shares with the rest of her neighborhood. We're going to talk about biofilms that are adorable and you can find in the ocean. And we're going to talk about biofilms that are incredibly dangerous. And we're going to talk about how Katrina is using phages to do battle with these dangerous biofilms. And if you're dealing with an incredibly dangerous biofilm, obviously Katrina is someone that you want to have in your corner. Welcome to Daniel and Kelly's Microbial Universe. Hi, I'm Daniel. I study particles and aliens. Hello, I'm Kelly Weiner Smith. I study parasites and space and I love kombucha. You are just pandering, pandering, pandering, aren't you? I will pander to Katrina. I'm a big Katrina fangirl. I also like kefir. And if you had something growing on your countertop, would you like lean over and give it a lick? I have a child who licks just about everything and it hasn't killed that child yet. So probably I'd be fine. I'd rather not. But I've got pretty good evidence that that's not often lethal. Well, on today's episode, we're going to be taking an intellectual nibble of all sorts of gooey growths. And today's intellectual nibble is inspired by a wonderful question by listener Jen. Let's go ahead and listen to Jen's question now. Hi, Daniel and Kelly. I recently saw an Instagram post about someone who got Legionella from the water flosser. This got me thinking about biofilms. And I'd love a whole episode on the topic. What do you think? I don't know if there will be any aliens, but certainly poop will be involved. And it turns out we have the perfect person that we know to talk about biofilms. Who is it, Daniel? It's Katrina, of course. Yay! Any time we have an excuse to bring Katrina back on the show is a good day. Because you think she's going to side with you on all of our disagreements so you can outvote me. Just wait and see in the episode how that turns out for me. We've got this long running debate about what guest has been the most common guest on the show. And I'd just like to clarify that I don't really think of Katrina as a guest. I think of her as somewhere between guest and co-host. She's not on the show all the time, but she's closer to co-host than anything else. Anyway, so we wanted to ask the Extraordinaries, what is a biofilm to get a handle on how much folks know about biofilms? And so let's go ahead and hear what they had to say. My first thoughts were some thin layer of organic matter on top of a body of water. Then I thought, what would the weirder thing be? And then I thought, like, maybe it's some way of capturing video using biotechnology. I think that a biofilm is some sort of colony of microbes or bacteria or something that creates a film, much like a plastic film that embraces and protects some organic thing. A complete guess, maybe a biological film that goes round or protects bacteria, microbes, something like that. Biofilm is that thin, slimy, membranous, gooey-like film material that all my three daughters recovered with when they were born. Thanks, bye. It is a biological film that grows in water systems. So it's actually well-named. It is a thin layer of organic material, usually bacteria, I believe, maybe cyanobacteria and some other things as well, that forms over rocks, forms over sediment surfaces, and acts often as a preservative in the fossil record. An example of a biofilm might be the gunk on your teeth if you don't brush often, or maybe a movie about Abraham Lincoln or some such. I believe that biofilm is a natural sort of layer that some organisms have that protect them from outside invasions, I guess almost like humans have skin. Like a thin layer of biological material, such as bacteria or blue-green algae that forms a film on top of water. Eventually, if they become thick enough, they become what's called a mat. Biofilm, that sounds kind of like something that'd be on the surface of a lake, like algae or something. I don't know, it might be like a shell of a cell or something. A biofilm is not a 1970s documentary about childbirth. A biofilm is a layer of biological material, eg bacteria that coat surfaces like you have in a fish tank. Wow, these are some great answers. So our audience actually knows quite a bit about biofilms. Can I share a fun fact that one of our audience members shared with us? Yeah, OK, so Robin wrote and said, interestingly, biofilms can be important in paleontology as they can help stabilize sediment surfaces to make trace fossils more likely to preserve. Oh, wow. Anyway, long story short, biofilms are important for making fossils stick around longer. Robin, that's amazing. Thank you so much for sharing that. That's very cool. Yes. Ancient bacteria are helping preserve the fossil record. I know, so cool. And so anyway, I love when when listeners are like, oh, actually, I could have been a guest on your show because I know a ton of stuff. Another listener works on microscopes for visualizing biofilms. And I was like, oh, my gosh, you all are amazing. So anyway, people made me laugh. People taught me stuff. What a great setup for this episode. Well, these are my favorite kind of episodes we need to discover. There's a whole topic with like a deep well of science that you never heard anything about. And so there's a lot to learn here and it can really change your perspective on like disease and how we study it and how things work inside the body. Yes. And unsurprisingly, with a topic like that, you and I had a ton of fun talking to Katrina. I maybe had even more fun because she did side with me a lot. And so maybe we should go ahead and just jump into the episode. It's my great pleasure to once again introduce Professor Katrina Weitzin. She's the most frequently requested guest on the pod. She's co-director of the Weitzin Research Institute and recently self-appointed chair of in-house fermentation. Colloquially known as Queen of Kombucha, potential poisoner of neighborhood children. Katrina, welcome back to the podcast. Wow. That is not the benign feeling that I have towards most microbes and our kombucha. It was a really mixed bag of an intro there, Daniel. Well, you know, we tell like it is on this podcast, you know, we don't sugarcoat anything, including the fact that we may be poisoning neighborhood children. Wait, wait, have have the parents of neighborhood children been contacting you all to get a bit of additional information about what they're imbibing at your household? I think Daniel is the only one who's worried about the safety of this kombucha, but he did ask me to make a waiver. And why is that? Why is that? So we do now have a waiver if you drink the kombucha at our house or like if we bring it to someone's house, because the neighborhood kids were just enjoying it and saying it tasted like apple cider. And Daniel viewed this beautiful activity with suspicion. Wait, what? Why do they sign a waiver? Because we have this thing bubbling away in the corner of our kitchen. Who knows what's growing in there? Nobody's testing it. Nobody's doing any safety protocols. Now we're just feeding it to any child who wanders into the house, sending them home. You know, who knows what happens? I don't want to be responsible. The kombucha waiver is mostly a sarcastic document just to be clear. I feel like I have so many questions, like how many children are wandering into your house and do you just like leave the door open? How did this start? Oh, man. It's one of these old fables, you know, there's a house in the forest that children wander in and then, you know, the old lady who makes kombucha in the forest. Oh, my goodness. Oh, Daniel, whoa. Let me try that one again. Oh, my gosh. And then, you know, the beautiful young scientist who makes kombucha in the forest, you know, draws them in with her poison. I need Daniel to survive so that we can't continue recording together. So I am cutting off this guest introduction right here. And we are moving on to the meat of the interview. Katrina, we are so excited to have you back. We are. Daniel aside. And and today we're talking about biofilms, which is another one of the many amazing things that you work on. And so let's start with what is a biofilm. And I'd like to mention since you didn't hear the intro because we're recording this before even Daniel gets to hear what our extraordinary has had to say about biofilms. We got a lot of great answers. Our audience is excited about biofilms. So let's start there. Katrina, what is a biofilm? Well, a biofilm is a structured community of microbes that are living together in a sticky matrix that they produce themselves so that they can face the world together as opposed to facing the world alone. And so they are unicellular organisms, but they choose to live in these communities. It can be just one kind of microbes. It can be lots of different kinds of microbes. And they live in these structured communities surrounded by a goo of their own making. And as a result, they can stick to surfaces. They can float together in clumps. And they can be protected from all kinds of evils that might change the course of their lives in the world. What a joy to live in the goo secreted by those around you. It's not for everyone. It's like a little HOA, right? Exactly. We live in a gated community. So this is really fascinating because it sounds like it's sort of in between the usual way we think about organisms, like either you got individual cells on their own, facing the world and all the dangers of, you know, people offering them kombucha versus like multicellular organisms, you know, like lions and tigers and whatever, where every cell has its own role and they're specialized and they all work together. So this is something sort of in between, right? There's still, as you say, unicellular, which I guess means they're all basically the same. But now they're forming like a macroscopic blob so they can work together somehow. Yeah, exactly. So I mean, it doesn't have to be that they're all the same to be in a biofilm. It can be very different types of microbes that come together to form a biofilm. But but yeah, they could also be identical sister cells and they are independent cells, the same type of cell, but they all live together and they do form structured communities where that's driven by the gradients of nutrients around them. What do you mean when you say structured communities, like some guys are on the outside and some are in the inside or what do you mean by structure? Exactly. Yeah. I mean, the way that when the biofilm gets started, somebody's got to produce something sticky and then that will help the first cell. That's the way a lot of fun projects start. Yes. Who's the sticky guy in the group? Gross. All right. Somebody makes something sticky. All right. Walk us through a Katrina. Yeah. Somebody has to make something sticky and then either that helps the first cell stick to a surface, then either it can multiply. You know, they're sitting and replicating in the middle of all this too, or other cells can come by and stick and become part of the community. And then they have really interesting molecular communication going on. And since most bacteria live in biofilms, probably 80 percent, there's a crazy diversity of how this happens. But, you know, a classic example in a textbook would show a couple of microbes sitting on a surface and then as they get bigger and denser, they start to communicate with molecules to shout out about their density. And then that helps other processes happen. You know, they're used to living in these communities. So the molecules they're able to produce have all been selected for an evolution to be able to to do things in biofilms. And that communication, I think I remember, is it is it called quorum sensing? And and if it is called quorum sensing, does that mean that we get to talk about the squid? Because every chance I get, I want to talk about the squid. That is a great example. And yes, that's a perfect example of quorum sensing. What's a quorum and why do we want to sense it? A quorum is just like a count, you know, like a number of people in the room. Like, do we have a quorum? Like, are there enough people here that we can call it a thing? And then sensing just means that they are sensing their own quorum. I see. And how does this work on the squid? Well, the squid is such a cool example. So there are these beautiful Bobtail squid that the whole system was discovered in. And this was discovered by Margaret McFall Nye, who's now up at Caltech. And her husband, Ned Ruby, who's a microbiologist, the two of them together have been working on this for decades. And it's really it'll blow your mind. Are they like a little mini science biofilm? Well, you know what? They actually created a science biofilm because every person they trained fell in love with the squid and went off in the world to start their own lab to study the squid. And now there's these photographs of the 60 or 100 labs that are all working on squid, Vibrio, the microbe that causes this phenomenon around the world. So that is actually a good way to look at it. But now I'm wondering who the sticky guy is out of that group. But let's move on. We don't need to know who the sticky guy is. All right, let's talk about the amazing squid and their amazing microbes. Yeah. Well, these squid have evolved a relationship with a microbe called Vibrio. Just as a big picture level, the Vibrio inhabit a light organ that the squid have. And when this Vibrio, the bacteria in this light organ get dense enough, they quorum sense and actually produce light. Wow. And that light in the light organ will help the squid by canceling out their own shadow. So cool. And so then they're safer in the world because prenders can't detect them as easily because they don't have a shadow. Wait, so there's a squid floating around and it's casting a shadow because there's a source of light behind it. But then the bacteria in the squid produce the light to cancel out that squid's shadow. Exactly. So that's the big picture thing going on. But there is a real biofilm story here. And so basically when a squid is born in the first six hours of its life, a single Vibrio has to get into its light organ. And this is this happens. I mean, there's tons of Vibrio bacteria floating in the ocean. So the chances are very good that it'll work. But wherever squid live, this works that a Vibrio cell that gets into the light organ and starts multiplying. And this is critical for its survival. So it's like really interesting to think about the co-evolution of the squid always needing to be in a place where there's a Vibrio that can get in there in the first six hours. Why does it have to be in the first six hours? That's a really good question that Margaret McFall and I has answered in front of me multiple times. So let's see if I can come up with a good answer. But I mean, it's it's early enough in the squid's life that the Vibrio gets in there. And I think that the light organ won't develop properly without the Vibrio being in there. But I don't know. Dr. McFall and I can answer that question for real. So yeah, you need the Vibrio in there and it's it starts multiplying. And I don't know at what age this daily cycle begins, but I think it's pretty early on that the Vibrio will copy make copies of themselves inside the light organ. And once they hit a certain density, a quorum, then the Vibrio are capable of communicating within themselves to produce this molecule, which causes light. And then every morning, the light organ ejects 95 percent of the bacteria and the cycle starts all over again. So then they build up the density of microbes and it's actually at night that they are dense enough to do this light producing phenomenon with the quorum sensing. And that always confuses me because I think of the shadow as being more important during the day, but these squid are nocturnal and it's actually the shadow of the moon that's being canceled out by the light organ. It is such a cool system. It is. It's amazing. So the bacteria don't know if it's day or night. They're just producing light, but the squid's light organ ejects them when it doesn't want light and then they grow back when it needs light again. Exactly. So it's it's timed so that they eject them in the morning, then the density is low again, then they have all day to build that density back up. And at night, there's enough of them to do the quorum sensing and produce light. And I think it's also because you need a fresh crop of healthy young bacteria to be making light. I think if you left them in there for too long, they wouldn't really be in good shape for that job anymore. And presumably the bacteria need to get back out into the environment if they can hope to infect a new light organ and keep the cycle going. And so is is getting out into the environment part of, I don't know, the site, does it help the bacteria in that way? Or is it just they get booted? Yeah, actually, Vibrio are kind of famous for being good at living independently in water and then also inside animals. And so probably the most famous Vibrio that people on this podcast have heard of is Vibrio cholera. And cholera also can live in water and it's perfectly happy living its life without a host. But if it if it does come into contact with a host in the case of the diarrhea, we've all heard about the cholera syndrome. That is when the cholera gets into the gut and has a totally different lifestyle. Similarly, the Vibrio in the squid can live independently in the ocean or they can go into the light organ. OK, cool. So it's got like this safe little home that it can reproduce inside of. And then every morning after it's made a load of babies, it just releases the bacteria babies out into the world. And then it gets to start the cycle again. Exactly. Cool. So it benefits from the squid not getting eaten too, because it gets to make babies every day. Yeah. Yeah, it has like a little protected zone to live in for a day. Exactly. Yeah. And why does it have to be a biofilm? Why can't it just be like a bunch of these guys floating around inside the light organ? I think we talk about that particular system as a biofilm because of the communication going on that they have to be at a certain density for that communication to work. So I guess that's kind of a circular definition. But I mean, basically, you're not going to get light if they aren't at a density that allows them to communicate like, hey, we're all here. And that's when they decide to produce the light. So that definition has to do with density. And they're all they're all living inside that light organ. So they're corralled together. In other cases, the biofilm forms even without any kind of physical, you know, sack that they're living in like this light organ. So biofilms can form in all different kinds of environments. They can be more out in the wild and just decide to clump together too. I see. So it's like the collective action here. That's crucial. Yeah. And I think the question in my mind was, you know, why would these vibrium make light? But the answer is then they're useful for the squid and it's a co evolution, right? They've done this thing which for themselves is irrelevant, but is helpful for their host and it's good for them if their host lives. That's pretty incredible. Yeah, it really is. It's amazing. So we've talked about the most delicious biofilm, which is kombucha. We've talked about at your own risk. I take that. I love that risk. It's a delicious risk. We are not endorsing kombucha on this podcast, by the way. Well, yes, we are. Oh, that might not be a joint decision. All right, let's hands up. Who's endorsing kombucha? Wait, no, no procedural objection. Oh, my God. OK, the podcast has gone down in flames. You know, we used to be that podcast that didn't just like push supplements and, you know, unstudied at home, brewed randomness, you know, but hey, now that's who we are. You know, my objection to supplements does not include kombucha. Kombucha is the epitome of like non-processed, you know, there's no. I'm not making any claims. I'm not saying you should like put kombucha to cure all your ills. I'm just saying it's delicious. Yeah, right. And Daniel, you're like anti-white chocolate without any science. So I feel like Katrina and I get to be pro kombucha just because it's delicious. Well, when we all go to prison, you know, I guess you guys will enjoy the, you know, toilet brewed prune or whatever they make there, the equivalent. What's totally different, totally different. Really? We're moving on. We've talked about the most delicious biofilm. We've talked about what I consider to be the cutest biofilm, which is the biofilm that makes the squids light up. Very cute. And now let's talk about a not so lovely kind of gross biofilm. So Jen, the listener shared the story about Legionella in the water flosser. Can you tell us a bit about what was happening there and why this is a dangerous biofilm? Yeah, for sure. So, you know, a lot of the bacteria that you find living in water, gram, negative bacteria, are good at forming biofilms. Now, I don't want you guys to leave thinking that this is always a bad thing. I mean, our wastewater treatment plants entirely depend on biofilms, often formed out of these kind of gram, negative bacteria, and that is purifying our water. So, you know, it's not necessarily bad that we have some bacteria in our water. But even after wastewater treatment processes conclude, there are usually a few bacteria left in the water. So in your tap water, there's some bacteria. In fact, in bottled water, there might be even a little more bacteria because they have time to grow in there. And those are often gram negatives that could cause disease if the right circumstances emerge. Now, when you're using a water flosser, there is a chance for some water to be kind of sitting around for a while. Anytime there's water sitting around like that, there's a chance that the density of the bacteria will increase. And if especially if you're immunocompromised, but, you know, wrong place at the wrong time, the bacteria that are sitting in standing water can cause trouble. And in fact, after the pandemic, all those office buildings that had water sitting in pipes that never got run they often actually had pretty high densities of the bacteria that caused the trouble in this water flosser, Legionella. Legionella is just a type of gram negative bacteria. But I know that there was an issue with the water in the buildings after the pandemic. And there were these protocols that you had to run the water for a long time and try to get rid of this Legionella so it didn't cause trouble. So that's exactly what happened in this water flosser incident. The reason that you have to watch out for letting standing water sit in a water flosser is that those Legionella can grow up to high enough densities to cause trouble. And so, you know, if you get a big dose of Legionella, that is not a good thing. Well, let's take a break. And when we get back, we're going to talk about why big doses of Legionella are not a good thing. And we're back and we just heard a story about a water flosser that was contaminated with biofilms of Legionella. And Katrina was telling us that that is bad. Yes. Why is that bad? Well, it's not always bad. I mean, we're often exposed to bacteria, but a higher density of Legionella can be aerosolized and get into the lungs. And that can cause a kind of pneumonia. It's called Legionnaires' disease. So water flossers can lead to aerosolization of the bacteria. And then if you breathe those in, that can cause trouble. So really, the message here is put some fresh water or like rinsier water flosser out with some vinegar so that you don't get a bunch of bacteria living in there. And what's the biofilm connection? I can imagine standing water, bacteria growing, that's bad. But do these guys form a biofilm and that makes them extra dangerous? Or what's the situation? Yeah, they just they the way they face the world is they clump up and they form a sticky biofilm inside the water flosser. That's their main motive of living. And so those they just they do form biofilms inside the water flosser. And that allows them to grow into higher densities. I mean, the thing that just blows my mind is that microbes can live in tap water. I think of that as a pretty nutrient poor environment. Like, isn't that amazing that there's enough going on in there that the bacteria can eke out an existence? But part of how they pull that off is that they share. So they live in these sticky biofilms and they share nutrients and that's part of how they can survive. And they're growing really slowly. I mean, that's a big part of the trick of surviving out in the world for most microbes. They're not replicating quickly. Their metabolisms are like super, super slow. But if you leave them for long enough, they'll grow up to a point that they could cause trouble. Could you say more about what it means to be sharing? I mean, I understand that they're in the same biofilm and so they sort of have a common purpose. But are they like passing nutrients to each other? Are they talking to each other? You mentioned earlier, you know, there's some chemical signaling. Is this a social community that's like helping each other out? I mean, to call them social and helping each other out could be accused of being anthropomorphizing the bacteria. But I think that's a reasonable way to look at it. I mean, yes, they are living in this goo that's a it's got a liquid component to it. So they can pass soluble nutrients around to each other. So they're averaging out their acquisition of nutrients by sharing them throughout the community. So in this field, there's even interesting examples of what people call cheating, where one microbe produces, say, a useful enzyme that can go and break down fibers into sugars, you know, that are able to feed the cells directly. But some of the microbes might decide not to produce those enzymes and they still benefit from getting the nutrients that the other microbes helped them acquire by producing those enzymes. And so then they're called cheaters. So, yeah, there's all kinds of social dynamics that people study inside biofilms. And yeah, imagine you're living in a water flosser with some tap water coming by and there's the occasional molecule of iron or something useful that pops up. And if that molecule of iron lands in the biofilm, the energy that can be acquired from using that iron is averaged out across the cells as opposed to just helping one cell at a time. Is there a way to punish the cheaters? Like, do the bacteria have ways of enforcing compliance? Multicellular animals have punishment methods for going after cheaters? Yeah, what a cool question. I really think that's a science question. I know people study that. But my understanding is that it's pretty hard to punish the cheaters inside a biofilm, but it's still worth it for the other cells to produce those enzymes because they need them themselves as well. So, there's really interesting dynamics there and evolutionary biologists who are studying whether or not there are selection mechanisms like that, but I personally don't know about them. But the social analogy makes me think that the right way to think about this is not as a bunch of cells that are sort of approximating a multicellular organism, but more like a bunch of cells building a little society the way multicellular organisms do. Right, like humans live in little groups that help each other out and average over the food and share tasks. Is that a fair way to think about a bunch of bacteria sort of living together? Yes, I think so, but they also don't have as much capacity for specialization. I mean, our bone cells and our blood cells are extremely different, and it really blows my mind that there's the same DNA underneath those two cell types, right? They just, you can't imagine them being more different. Bacteria don't, they have some differences in physiology and structure in different parts of a biofilm, but they're not that different. In my opinion, I mean, maybe there's a listener out there who has a counter example, which I would love to hear, but I have a really cool example when you're ready about the structures that biofilms form in the face of nutrients that they need. I was born ready, let's go! Yeah, we had on us. So there's this one kind of bacteria, pseudomonas, that you've got, you've probably heard of it, it can cause infections, it's a gram-negative bacteria, it lives in our tap water, and it's really good at forming biofilms. Now, the thing about the biofilm is, you might think of it as just a uniform glop, but the problem is each cell in that biofilm needs oxygen and other nutrients to be able to run their metabolism. And so actually, pseudomonas has these really cool molecules that initially got described as toxic virulence factors, they're literally being identified because of their capacity to cause disease virulence factors, but from the perspective of the pseudomonas, that's not what they're doing at all. These molecules are critical to the energy flow in the biofilm. And so it turns out, when you let a pseudomonas culture grow for a while, it kind of turns bluish-green, you might have even seen it before, like, I don't know, actually the places you would have seen it, or I see it in my lab all the time, or like a gross toe infection or something, but that's hopefully not something anybody's seen. But anyway, they turn this bluish-green from these beautiful molecules that are sometimes thought of as virulence factors, but in reality, the reason the pseudomonas cares about having these molecules is because they help with the energy flow in their biofilms. So the cells that can't get to the surface to get the oxygen instead have access to these molecules that I sometimes call snorkels, because they basically are like, they're like transferring the same function that the oxygen would be playing in the community, that same function can be performed by these green molecules, blue and green molecules, they're called phenazines, and they can act as electron acceptors, so they're like alternatives to oxygen in the energy flow for the biofilm. And so the amazing thing that I've seen, this is also from Caltech, Diane Newman's lab at Caltech, they'll make mutant pseudomonas where they take away the capacity to make these molecules the colorful so-called virulence factors. And when you try to grow a pseudomonas biofilm without those virulence factors, it forms these beautiful structures that increase the surface area. And so instead of having just like a smooth top, they have all these like invaginations so that the surface area isn't expanded. And so the only way the biofilm could come up with to like breathe without the help of these molecules to act as snorkels was to form all these extra structures that expand the surface area so that each cell is closer to some oxygen. So these guys really are more sophisticated than just like a glop of cells, they have like infrastructure that lets the cells in the middle that can't access the oxygen still breathe. And if you're saying if you take that infrastructure away, then they all basically push to the surface and make all these ripples. Exactly. Yeah, I think that's such a beautiful example. And yeah, Google a phenazine mutant of pseudomonas and you will see this beautiful structure. They're very cool looking. You know, the other day Daniel said Google raccoon eats baby's face. And I gotta say, I really don't say don't. I really prefer Katrina's Google search suggestions to Daniel's Google search suggestions. You're just drinking the kombucha over there, Kelly. I'm glugging the kombucha. Give me more. I mean, drinking kombucha means you avoid alcohol, but you still get to have a sophisticated, you know, terroir of fermentation e goodness that otherwise you might get from your wine. Daniel's just such a like fun killer, isn't he? That's what I think. Staying alive, staying alive. Overrated. Anyway, Daniel will eat cheese, yogurt, he'll drink beer, he'll drink wine. I do not understand the the line with the kombucha. It's arbitrary. Seems arbitrary to me. I will not eat homemade cheese. I'm sorry. No, homegrown funk. I hate to feel like I'm giving Daniel a win here by transitioning us to conversations about disease. But should we talk a bit more about disease? So what I'm wondering is like, say you were going to get infected by a million pathogenic bacteria, would you rather get infected by a million pathogenic bacteria that are individuals or a million pathogenic bacteria that are part of a biofilm, which would likely be worse for you to get infected by? Wow, that's a really cool question. I mean, overall biofilms are the hardest to get rid of. So I think I would probably prefer not to have the biofilm. But I mean, then I want a little more rules on what the non biofilm bacteria or microbes could be. Because I mean, I wouldn't want to get infected by like Ebola viruses. They'll just take you down so quick. So I think I'd prefer, you know, the biofilm is going to be a slow disaster. Okay. So I guess it depends on the time scale. Do viruses make biofilms? Oh, what a cool question. I don't know. I mean, not tech, the definition of a biofilm kind of requires cells and viruses are not cells. But do viruses ever kind of like clump up together and help each other? And I think that can happen actually. So that's a cool question. But what is it that makes a biofilm harder for our immune system to protect us against? Great question. So I mean, when a biofilm forms one of these structures, then imagine you're trying to get antibiotic drugs into that or imagine you're an immune cell trying to get rid of that, you know, they're bigger and they're able to hide out. So it's much harder to get rid of every last cell in a biofilm because they have more structure and density that makes it harder to reach. So getting antibiotics into a biofilm is really hard. So yeah, so that's one reason. And in general, they also just grow really slowly. So it's not even only about getting antibiotics in there, it's about if the antibiotics mode of action involves stopping replication, the biofilm can just be like, yeah, well, I'm not replicating until 20 years from now. So I don't really need, I don't care about you. I mean, they really can be very, very slow growing in the biofilm. So those are reasons that they're hard to get rid of. So people who are immune to compromise for different types of reasons, like for example, if you have cystic fibrosis, which already predisposes you to having a lot of mucusy build up in your lungs, that's a perfect environment for a biofilm bacteria to take hold. And as a result, people can have lung infections that go on for decades. That's a tough situation, but I guess it's a slower situation than a terrible virus could have. So it seems like it's an advantage for the bacteria to make a biofilm. Do all bacteria make biofilm? And if not, why not? The super majority of bacteria do make biofilms, but there are some bacteria that prefer to grow planktonic, like one at a time in liquid. Planktonic, awesome word. That's the new word for being an introvert, huh? No, I'm just planktonic. It's so funny that that's a new word to you. That's really interesting. Yeah, I never thought of it that way. I like that. And then, so then your first instinct might be like, oh, so you mean in the ocean, the bacteria just are all by themselves planktonic in the ocean, but they're actually not. Cyanobacteria, for example, are famous for making clumpy biofilms even in the ocean. But yeah, there's some types of bacteria that tend to grow planktonically. I don't actually have a good reason why. I mean, I can tell you in my own lab, if you grow shaking cultures of bacteria, they tend to grow planktonically then. Shaking cultures? Yeah, like most of the bacteria in labs are grown in rich media, so just think of it like kombucha. And then, and then we put them on what we call a shaker, which shakes at 300 rotations per minute and like really mixes things up. And that's a case where the bacteria often do not go biofilmy because they're just like, they're a lot of the advantages of a biofilm to get nutrients and so on are removed. If you're shaking around like that and you've got all the nutrients you need, they don't bother to make biofilms in that circumstance. But then, which tells you how our lab conditions are actually terrible for mimicking infections, which is a big topic to talk about because the overwhelming majority of microbiology in labs happens with planktonic bacteria in fast growing conditions. But the overwhelming majority of infections are in essentially low nutrient conditions, even though that's ironic because obviously a human is full of delicious nutrients. But if you're growing in a hidden corner in a biofilm, you won't be getting that many of those nutrients. So that's a big issue is getting our lab cultures to do a better job of mimicking infection conditions. Do you just call humans delicious? Oh, yes. I mean, in terms of richness in useful nutrients, yes. So when you want like neighborhood parents to trust you to send their kids over to your house to drink your kombucha, they're calling their children delicious. I'm not sure if you're helping yourself out there. I think we need a special sound effect for when we've hit a DKEU bingo spot on our card and cannibalism just got... There we go. There we go. That is definitely not where I was going. Well, now feels like the perfect time to take a break. And when we get back, we're going to talk a little bit more about how you study this stuff in the lab and why it involves stakes from Trader Joe's. Rural Britain, you've suffered too long. Your days of sluggish broadband are over. We're connecting rural homes to full fiber with thousands more joining every month. T-minus five. The gigaverse is expanding before my very eyes. Three. Giga clear. Faster broadband for rural Britain from only 19 pounds per month. We have lived off. TZZ apply. 18 month contract. Prices may rise during contract. Check availability at gigaclear.com. Okay, we're back and we're talking to Katrina about how she's working hard to be a delicious target for just the right microbes. Yes. Definitely true. I mean, if you drink your kombucha and you eat your fiber, hopefully you will attract the right community of microbes to form healthy biofilms in your gut and not disease related bacteria, biofilms, which are less common. And if that doesn't work out, you can always get a fecal transplant. And if you want to learn more, you can listen to one of our previous interviews with Katrina. We only talk about the best stuff when we have Katrina on the show. But I think that's an important point. We've been talking about bacteria and how biofilms make it harder for our immune system. But of course, lots of bacteria are not clearly pathogens, right? They do helpful stuff. And those helpful bacteria also make biofilms. Tell us more about how biofilms can help us out. Yeah. I mean, most bacteria are living in biofilms. So every time you've heard about a bacteria, just imagine it in the sticky community with other like-minded bacteria and other microbes. So the microbes that live on our teeth, they're in biofilms. You've seen that before. In fact, that's the first microbe we ever saw as humans when Dutch draper Antonin van Luwenhoek took a clump of his own dental plaque and used the hand-grown glass he had made to view the animal cules in his teeth. And those are the same microbes we all have in our teeth. And they're definitely part of our health. Gut bacteria, many of them are forming biofilms against the mucous in our guts. And I guess maybe an example that really affects humanity, arguably one of the more important parts of our civilization is wastewater treatment and the biofilms, which are often coming from gut bacteria. Let's face it, those are formed in the wastewater treatment tanks that purify our water. Hmm. Thank you, biofilms. In your lab, are you studying the good biofilms or mostly just studying bad biofilms? Oh, what a good question. I mean, we are studying good biofilms in fecal samples, but when we actually do experiments in the lab, it's more about the disease-causing biofilms, specifically the kinds of bacteria that infect people who get cystic fibrosis. And then they have these long-term infections in their airways with bacteria that are really good at forming biofilms. And so we actually have clinical isolates from people with cystic fibrosis at different points in their infection. And the types of biofilms they form change a lot. So if you grow a pseudomonas that is from a fresh infection of somebody, of a human, it will form some biofilm, but it doesn't make all that much mucous. If you grow a late pseudomonas isolate from somebody, from an infection that went on for decades, it will be called mucoid. And literally after a couple of days growing on a plate in the lab, it will make piles and piles of this mucousy gunk. And that clearly is a phenotype that is helping it stay in the lung inside all of that goo. Oh, man. Yeah. So to transition to a paper of yours that I'd really like to talk about today, I'm wondering why Trader Joe's hasn't reached out to fund your lab, given that you have been growing biofilms on Trader Joe's stakes. Can you tell us a bit more about that? I'm sure they're thrilled. Yes, I can. I would happily. So we were trying to think of ways to grow bacteria to mimic the conditions inside the human body. And that's not going to be rich, nutrient shaking 300 times per minute, which is how most experiments are happening in our field right now. And so we were just thinking of different substances that we had available to us that would mimic a human infection. I mean, there's actually a lot of people who we got ideas from like Freya Harrison in the UK. She has been studying cystic fibrosis microbes for a long time. And she goes to the butcher and buys pig lungs and uses them for her infection model. And actually, when I was in Malta last week at that cystic fibrosis conference, I saw one of her collaborators presenting how they were using pig lung as a model. We've also tried like making media that has all the stuff we think will be in a cystic fibrosis mucus plug. But the stake came up because we could do it, you know. So my student Joanne fan literally went to Trader Joe's and we actually bought quite a bit of steak and cut it into cubes and put it in the freezer so that we would have the same batch to go back to again and again for the experiment. And then we infected the steak with, it was, Pseudomonas was one of the ones we were using. And then we hooked it up to some pumps that could flow media through. So that was kind of mimicking how you would have nutrients arriving in an infection. This sounds like Act One of a horror movie, doesn't it? Yeah. It is kind of crazy that we did this. I know. Yeah. And then we tried exposing the infection to different types of antibiotics so that we could study the response of the bacteria to antibiotics in more realistic conditions. And I remember the title of the paper had thriving under stress in it. But it never like pulled itself together into some weird monster to attack your grad students? I mean, not that I know about. Hopefully not. Do you count them regularly? Still missing one student though, yeah. And actually, Daniel, our friend, Alon Hawkbaum, an engineer here at UCI, he was my collaborator in that project. And we had very serious meetings weekly for years discussing how to do this. And then the results when we got them back, which is kind of funny. And about those results, did it work about the way you wanted it to? Is this now a helpful model for studying biofilms? Yeah, that's a good question. It was not easy to set up. So it's not something we've done again, to be honest. I think it would require, the right person and the right funding to be able to support being able to do that. So it's not our current go to. But we did have really nice results out of that paper. The growth rates of the bacteria were much more realistic. And the antibiotic responses were, the antibiotics were less effective in that model, which is exactly what we were going for. So I would say it's a really useful model in that sense. It's just kind of hard to set up. So what we're actually doing right now is we like to do things higher throughput. That method is not very high throughput. So we were doing everything in 96 well plates these days. And we're buying media. One of my colleagues in Georgia in Atlanta has started a company where he's making artificial sputum media. So we used to make our own artificial sputum media, which has things like pig mucin and egg yolks and all kinds of rich things that are trying to recreate the environment of the lung. But the problem is there's a lot of variation batch to batch and lab to lab. So now that there's a company making that media, we can all buy that media. And then when we compare results across papers, at least we know we're using the same stuff. And so that actually has worked really well. And to me, it's fascinating how we'll have a really slow growing bacteria when we're using the kind of typical media. And then we'll put it into the artificial sputum media, and it'll actually grow better. So I think it is helping us recapitulate infection conditions to use that media. And then we have 96 well plates, and we have this plate reader that can hold four plates. So we have really high throughput. So we can, for example, test whether a phage can infect 90 different strains in triplicate all in one day using that plate reader that's got the four plate capacity. We got the phages. I was hoping we'd get to phages. Okay, so could you remind us, one, what phages are? And then two, could you tell us, I've been dying to know, like you mentioned that antibiotics, not great for killing a biofilm, probably because like the bacteria hiding in the center of the biofilm, antibiotics probably don't really get to them. But maybe a phage can sneak into the middle. So yeah, what are phages? And are they the solution to the biofilm problem? Phages are the viruses that can infect and kill bacteria. And so we're using them as alternatives to antibiotics sometimes. So if your bacteria is resisting antibiotics, it might be susceptible to phage. So that's the idea. And so yeah, there's actually really cool reasons that phages might work better than antibiotics to attack biofilms. Some phages carry enzymes that break down the gunk that forms a biofilm. So I mean, what a great combination. I mean, imagine, you know, an antibiotic is just one molecule and it might not really be able to get in there. But the phage is a package that contains its own scissors for cutting open the biofilm. And then it can get in there. And if it can infect a cell and locally multiply, then you're increasing the dose right where you need it. So there are bacteria phages, viruses that specialize in infecting biofilms. I personally have tried to find those ones, like we intentionally make up the gunkiest biofilm we can and then hunt for phages that are good at breaking it down. We haven't actually had a lot of luck with that strategy. But I know other labs that have found phages that can break down the biofilm matrix. And yeah, that's a real reason for trying to use phages as alternatives to antibiotics. And if most bacteria make biofilms, then phages in the wild that are around because they've been succeeding against bacteria must somehow be able to attack biofilms, right? Yeah, exactly. Yeah, they've been evolving for four billion years, whether or not they can infect the biofilm. I mean, part of the bacterial strategy for avoiding viruses is forming the biofilm. I mean, it is a good defense mechanism. So we're like stepping into a four billion year old arms race here. That's right. Yeah, it's like that show Neighbors, except they've had four billion years. I don't get the reference, but we don't want to talk about that show. So what other ways are folks using to try to battle biofilms? Are antibiotics and phages the main things we're working on right now? Oh, good question. No, there's people who have all different kinds of strategies. Like you could imagine molecular adjuvants that kind of dissolve the biofilm before the antibiotic gets there. So making combinations of antibiotics that are soluble in the context of a biofilm. Yeah, I mean, there's actually a lot of different kinds of strategies. I mean, there's also more physical strategies. So some of the main treatments for people with cystic fibrosis include chest compression vests or exercise with the hope of dislodging the mucus that accumulates as part of the disease so that you can cough it back up or in the context of a wound, you can clean up and de-bride the wound and remove some of the biofilm. Yeah, I think there's lots of different types of strategies for trying to go after biofilms. Katrina, I remember when you were on the show talking about phage therapy, you had a patient and you were growing phages specifically for their infection. And a bunch of folks wrote in and wanted to know how is that going? How is that patient? Oh, thanks for asking. So it's now March, 2026, and the treatment happened in July and August of 2025. So now it's been six months. And so I was so curious how it was going to go. We need time to tell. And so far, they are still doing really well. So they had 10 years or maybe even 12 years of chronic fevers from sinusitis. It was a staph infection in the nose. And so they still don't have fevers. So that's a really good sign. And I met with the doctor a few weeks ago, and we were saying, hey, we still have these approved phages sitting in our fridge. We could repeat the treatment if that would help at this time. But actually, the doctor thought that they were doing fine and did not need further treatment. So that's really amazing. They also went to have an endoscopy. And overall, the conditions look really a lot improved. There's not big signs of inflammation. There's still healing going on from all those years of infection. So that's a biofilm, for sure. I mean, that was a staph biofilm in the nose, very hard to get to. And so we did daily treatment in the nasal rinse with the phage for six weeks last summer. A phase that you grew in your lab specifically to target this infection? That's right. We got the isolate from the clinical micro lab, a student in our lab slogged away for months, failing, and then finally succeeding at finding a phage, grew up a big vat of the phage, purified it in very complicated ways that we had to learn how to do. And then we had a third party testing to show that it was sterile and didn't have any toxins in it to get FDA approval to be allowed to use it. So yeah, that's really personalized medicine, that's for sure. Wow. And did this patient have to sign a waiver similar to our kombucha waiver? Oh my gosh. They had to sign a consent form which looked nothing like our kombucha waiver because it didn't have jokes in it. It was very serious. So you're saying people take it really seriously when somebody grows a microbial community? All right, I'm getting eye rolls over here. Two pairs of them. All right, well, I think that's amazing. Congratulations. And we have to of course end on Daniel's alien question. So Katrina, when we eventually land on alien planets and describe a microbial life, do you think those microbes will be forming biofilms or will they be planktonic? Oh, I think they'll be forming biofilms. That's an easy one. Because it's such an obvious advantage? Yeah, I mean, if that's the overwhelming majority of the way most microbes are growing, I could imagine them banding together and sharing nutrients. I would imagine the conditions would somehow be really tough, but from the perspective of the microbes, they might be great. So I don't And when the alien citizens of that planet offer you their locally brood confection, are you drinking it down? Are you signing the alien waiver? Oh, man. You mean I'd be the first person to drink alien kombucha? Yeah. She's thinking hard here, folks. She says yes. All right. Sure. I do it. I mean, I wouldn't mind like, you know, I think of maybe I wouldn't mind a little time to test it out in other ways before I drink it. But kombucha is ancient in human culture and think of all of the people who have survived and thrived while drinking kombucha through this, not just the centuries, but the millennia. So is kombucha the most delicious form of biofilm? I think so. Yeah. So the kombucha has this disc floating on top of it called a scoby, which is the symbiotic culture of bacteria and yeast. And it's actually pulling the sugar out of the sweet tea you put in there to form this like cellulose mat at the top. And so it really is a biofilm that's very visible. And I know to some people it might come across a bit disconcerting, but that's not how I view it. I'm like, man, that's so cool, you know, and like all you added was sugar and tea. And it makes this thing that has all these fruity flavors in it. I think that's so amazing. Like when we shared it with a bunch of friends on Saturday, they were like, what fruit did you add? Well, I didn't add fruit. I just let the scoby do its work, you know? And so, yeah, I don't remember your question anymore. And there you have it folks. Katrina is pushing the big booch. And I'm pushing right behind her. Well, thank you so much for being on the show, Katrina. As always, we had an absolute blast. And we can't wait to have you on to talk about some other aspect of what you do in the not too distant future. Well, thank you very much for the opportunity to promote the microbes. They rule the world anyway. So might as well talk about it. Always happy to have you here and thank you for your patience with Daniel. I did actually really need to exercise my patience in today's episode. I'm going to stop recording. Bye everyone. Until next time. Bye. Thanks everybody for listening. 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