How your skin microbiome fights infections

Maria Losito

Welcome to another episode of Interview with a Biologist. I'm your host, Maria Losito, and I'm joined today by Dr. Rosana Ferreira who is Assistant Professor with the Department of Molecular Biosciences from the University of Kansas.

How are you doing today?

Rosana Ferreira

I'm doing great, how are you? 

Maria Losito

Good, thank you. It's nice to have a bit of sunshine after having all the rain in these last few days.

Rosana Ferreira 

Just a little bit of sunshine, but 9t's nice.

Maria Losito

All right. So, Rosanna, would you mind telling us about your research interests?

Rosana Ferreira

I am interested in studying the bacteria that cover our skin that we call the skin microbiome and more focused in how they protect us against infections by different bacterial pathogens. So, I want to understand how they do that by investigating what molecules they produce and what's the impact on the infection.

Maria Losito

We sort of talked earlier that fall is your light schedule, and spring is your heavy one for classes. But would you mind telling us about your KU classes and then something that you want to share about one of those classes too?

Rosana Ferreira

Yeah, sure. So, for undergrads, I teach Bacterial Infectious Disease Lab, which is BIOL 507, in the spring. That's an advanced lab class, mostly for micro majors where we do a very interesting research experience with the students.  They basically do a little bit of what we do in the lab on research, like trying to find molecules that their own skin bacteria produce against pathogens.

So that's mostly what I do for undergrad studies and for grad school, I teach a host pathogenesis graduate class in the spring as well.

Maria Losito

What drives you as a researcher?

Rosana Ferreira

From the past couple of decades, we know a lot about the importance of the microbiome as a whole from those studies. We know by now that the gut is very important for our health, but we know relatively less of the skin and I think there's a lot of skin infections and diseases that we don't know much about and I'm sure that if we investigate closer, the microbiome has a lot to do with those. I also think like from a medical point of view, we can learn from these environments to get new ways to treat infections.

Maria Losito

You had recently published a paper titled “Cutibacterium acnes inhibits Staphylococcus lugdunensis biofilm formation through inhibition of autolysis and purine biosynthesis”? Which is quite a lot of words, but in a really broad way, what kind of scientific topics does that research touch on and what do you get into?

Rosana Ferreira

So, a while back we found that one bacteria that basically colonized all skins, which is the Cutibacterium acnes, produces something in the media that inhibits biofilm formation of these species, Staphylococcus lugdunensis, that species can be found in the skin, but it also correlates with some types of infections like more opportunistic infections. So, we've thought that was very interesting that in the presence of these molecules is bacteria cannot can grow just fine but it cannot attach to surface and produce this community that we call biofilms.

 So, in this paper, we investigated how that molecule was doing that, and we found that the molecule affects autolysis, which is the ability of the bacteria to lyes or release extracellular DNA, and also affects the purine biosynthetic genes of that bacteria. So, it was very interesting to see how like up close, how that mechanism is inhibiting biofilm, how that molecule is inhibiting biofilm.

Maria Losito

Okay and I guess for context is the staphylococcus that you're working on what is responsible for like a staph infection that you may get at a hospital?

Rosana Ferreira

Not the conventional one, the classic one that everyone thinks about-- that one is Staph aureus. So that one causes lesions in the skin abscess, and it can get very nasty and can cause death in many people. But lugdunensis has a big part of the hospitalized population that developed endocarditis, which is the infection around your heart.

So, it is very important for those kind of infections, although it has been related also to skin infections but not as commonly as Staph aureus.

Maria Losito

You had mentioned a biofilm-- that makes me think of sort of like a jelly that would form. Can you sort of describe what a biofilm actually is?

Rosana Ferreira

I love studying biofilms. I think they're very interesting. They can form pretty much anywhere.

A biofilm happens when free leaving bacteria, like swimming bacteria, can attach to different surface that can be either biotic surface, like the heart or the skin, or an abiotic surface such as the prosthetic devices or maybe pipes.

If you think about the environment, they are also very common, like the soil, rocks, they can form anywhere and once they attach, they start producing like a substance that protects them, that covers around them, and that protects them from the environment. So, they protect them from antibiotics, from the host immune factors, or even like the flow of water in a river.

So bringing this to a more like household environment when you have like that plastic bottled water like that you forget to clean every day. That brings like the little thing around the bottle--that's biofilm.

In your teeth as well. So when you haven't cleaned for a while, you haven't gone to the dentist, every six months that starts forming around your teeth and that can cause problems.

Maria Losito

Yeah. So brush your teeth, people. Yeah. Just a reminder, twice a day. Fascinating. Thank you.

I just realized I, I never asked about Cutibacterium acnes. Just based on the word that's there, is that the bacteria that causes acne on your skin?

Rosana Ferreira

Yeah. So that's, the classic way of thinking about C. acnes I guess, the historical way it was isolated from acne patients and for a long time and received the name because of acne. So for the longest time, we, the scientists, thought that that was the cause. Right now, we don't think it's the cause. Definitely, there are some strains of C.acnes that are more related to acne, but we think about acne as a more like a disbiotic environment where other bacteria is also are not there or reach there and this is just an imbalance of the bacteria in the acne lesion and there are certainly strains of C. acnes that are not related to acne at all and in fact, they have been investigated as beneficial for our skin mircobiome. So the fact that you have C. acnes in your skin is not a bad thing and I tell that to my students in the undergrad lab that they are always like, kind of surprised that they swabbed their skin. And there's a lot of things going on.

Some of them are kind of grossed out and some of them are, ‘oh, that's cool’ but it is actually very cool, like, we want to have this bacteria in our skin and in other places, in our bodies and it's a good thing.

Maria Losito

Yeah. I guess it's just in a way, it's so antithesis to the common thought process that to have good bacteria on your skin or in your gut, like those probiotics and it's neat to hear that, like, you know, something that has the word acne in it is actually good for you.

Rosana Ferreira

It's a good thing. and there are a lot of other bacteria that like people are scared of but It's like, ‘no, no, if you have this bacteria like, Staph aureus in your nose, it doesn't mean much, you know, like just having it in the wrong place. Right. That that makes a problem’. But, yeah, a lot of bacteria like that. Like, if you get them from one place, it's fine and then another. Not so much

Maria Losito

So with that context, can you tell us a little bit more like, in depth what your research publication was about?

Rosana Ferreira

Yeah. So bringing more like we as scientists, we are always interested in understanding what are the molecular mechanisms around some activity that we found out. So,in this paper we started with this interesting phenotype that we saw inhibition of biofilm. So, you want to see like how the genes were affected by those molecules, how the whole cell was affected.

And so we started by analyzing gene expression, for example. We saw that those genes related to autolysis and the purine biosynthesis were affected by growing the presence of these molecules and we end up figuring it out that that was due to process of release of extracellular DNA and the extracellular and DNA is important for that substance that I said in the beginning that covers the biofilm. A lot of that substance for this bacteria is extracellular DNA and by inhibiting the extracellular DNA release, the bacteria is less able to form biofilm.

Maria Losito

And the biofilm helps protect it from essentially getting killed off. 

Rosana Ferreira

So, if you think about the infection and endocarditis biofilm protects the bacteria around the heart, and that makes the infection much worse to treat. Right? So, if we can find a molecule that can inhibit the process, we will be able to treat that infection more easily by adding antibiotics or other drugs that can and killing that bacteria.

Maria Losito

With that inhibition of the biofilm that we just talked about, why is it important that we research this?

Rosana Ferreira

In a basic knowledge context, it's very important for us to study what is happening in this key microbiome. Right? That maybe not be directly applied to say, a treatment or some like technological application. But just by understanding that mechanism, maybe we can extrapolate to other pathogens. Maybe now that we know that by inducing, or repressing Autolysis and the purine biosynthetic pathway, we can maybe see if in other bacteria that applies and that can have an indirect benefit to treating other infections.

Maria Losito

Can you tell us about the methods that you utilize to find your results?

Rosana Ferreira

Sure, we grow, of course this bacteria in the lab Cutibacterium acnesis, an aerobic bacteria. So, it means that it doesn't do well, it doesn't grow in the presence of oxygen. So for that in our labs, me and Dr. Antunes, we have an aerobic chamber where we can grow the bacteria without the presence of oxygen.

Other than that, we do biofilm assays which are made in a polystyrine plate where we can see the attachment that I said in the beginning, and then the big mass of biofilm being formed. For this paper we use a technique called RNA seq, which is the sequencing of the whole RNA transcripts of that bacteria in that condition. So we compare what genes were expressed in one condition versus the other.

So in the absence and in the presence of the molecule and that tells us how the bacteria changed that profile of expression of genes in the by being grown in the presence of the molecule.

We also did autologous assays that measuresthe ratio of lys, cell lysis of the bacteria in the presence and absence of the molecule. We also measure the extracellular DNA release, in the presence and the absence of the molecule and we also tested how guanine which is a purine affected the biofilm formation of those of the Staphylococcus lugdunensis in the presence and the absence of the molecule. So it took a lot of different methods. So genetic methods, phenotypic methods of all kinds to really, to really get to a point that we can say for sure this is what's happening.

Maria Losito

it's really fascinating that you tried all these different pathways for this analysis. I mean, I'm sure that they all show different things, but the fact that they all ended up proving the same, or at least adding to that proof, like, is really cool that there are these sort of multiple pathways that you could take.

Rosana Ferreira

Yeah, and we need that, right? So we cannot, just by doing one task or one methodology, we cannot say for sure that's what is happening. We can indicate, but you kind of have to do it all different ways to really get to a real answer. Right? To make sure that what you're  putting out in the world is what's really happening in your science.

Maria Losito

You had mentioned, extra DNA release. What exactly is that? And then how is it impacting your specific specimens?

Rosana Ferreira

Extracellular DNA is DNA in the inside of bacteria. When there is some of the bacteria on that population, some of the cells in that population lyes, they release the DNA in that environment and the DNA that's released can develop different folds and that becomes part of the matrix that the extracellular substance that protects the biofilm. So that substance can be formed by polysaccharides, proteins, lipids and also extracellular DNA. And that that is in the beginning people would think that's just contamination. And now we know that for certain species of bacteria is crucial. If you inhibit the extracellular DNA, the biofilms are weaker. So we can take that information to have another tool to fight those biofilms.

Maria Losito

Was there a reason you chose C. acnes to pair with the staphylococcus? Was there like previous research or you know, what made you choose those two?

Rosana Ferreira

So there was previous research. So both C. acnes and other species of Staphylococcus in general are very common in the skin. So we started this this work like that was in 2016 or 17, where we decided to test if C. acnes produces molecules that affect any of the other staph bacteria that we can find in the skin, and then we end up seeing that there was a very specific phenotype for lugdunensis and another one that I didn't include in this paper, but two out of like tens of different species.

So we this this is was very interesting to us. It's very specific. Even though those Staphylococcus species are very related genetically to each other. There was something going on with and that's why we decided to look at a little bit deeper in what was happening there.

Maria Losito

Was there anything that we haven't talked about that you think would be good to touch on?

Rosana Ferreira

So yeah,we can talk about like other projects that we have in the lab. 

We had other Staphylococcus species that not also produced molecules that affect different bacteria. So we are doing this work more like concentrated to finding a mechanism and we also do this work related to one of our classes. The BIOL 507 class where we have this, the students collect their own skin microbiome and test that skin microbiome against Staph aureus which is an important pathogens.

So from that class we ended up publishing another paper where a lot of students were involved. Doctor Hotzee was involved as well. And we ended up publishing very well. It was surprising, but it was great work, like great teamwork. A lot of students writing a paper and doing the bench work. So that was exciting for us.

Maria Losito

What an amazing opportunity, it's so cool that a paper came out of that like class work. Usually think it's like, you know, this research has been going on for years and years and years before you ever get a paper.

Rosana Ferreira

But yeah, just it was it was a very, happy moment for us because we were like, wow, this is super cool because these students are having the opportunity to publish a paper and they are still undergrads. And I was just part of a class. So we are very excited about that.

Maria Losito

Yeah. That's amazing. And I'm excited to see what your lab does in the future with these things that you've just mentioned to us and it's gonna be good.

Rosana Ferreira

Yeah, I hope so.

Maria Losito

Thank you for joining us today Rosana I really appreciate you stopping by.

Rosana Ferreira

Yeah it was great. It was my pleasure. Thank you for inviting me.

Maria Losito

Of course and thank you to listening to Interview with a Biologist. You can you can check out the notes show for more information about Dr. Ferreira’s work, as well as a link to the research paper discussed in this episode. A full transcript of this episode is available at biology.ku.edu.