What is the lung microbiome and why is it important to study it in CF research?
What is the lung microbiome?
The lung microbiome is the name for all of the different species of bacteria, viruses and some fungi that live in our lungs, where they live and interact with each other. Studying the lung microbiome in people with CF can help us improve the detection and treatment of CF lung infections in the future.
The microbiome contains both helpful and harmful bugs. The helpful ones, called commensals are normally found in the body and help keep it healthy. The harmful ones, called pathogens can cause infections, produce toxins, and make you unwell.
Precision-CF Innovation Hub
The Precision-CF Innovation Hub is led by Professor Jane Davies and Professor Darius Armstrong-James at Imperial College London and involves around 40 researchers across the UK and internationally. It is part of the Translational Innovation Hub Network for CF Lung Health and Infection, funded by the Trust and LifeArc.
The aim of the Precision-CF Innovation Hub is to improve the detection, diagnosis and treatment plans of lung infections in people with CF. One workstream within the Innovation Hub is looking at what happens when more than one bug causes infections in the lungs of people with CF. The goal is to understand how these bugs survive, interact and affect lung health - to help find new ways to detect infections and develop better treatments.
Introducing Lillie and Heritage
Heritage
I’m a first year PhD student at the University of Newcastle, working in Professor Tracy Palmer’s lab. I studied Biochemistry as my undergraduate degree. During my Masters, I did a microbiology course and chose to do a microbiology project studying the bacteria Staphylococcus aureus. I genuinely had the time of my life! I really enjoyed it and I loved the people there. I wanted to carry on studying Staph aureus, so I applied for and got this PhD.
Lillie
I’m a post-doctoral research associate at Imperial College London, working with Dr Dom Hughes and Professor Jane Davies. I really loved studying microbiology during my Biology degree. I was inspired by an amazing lecturer, and did a research project in her lab investigating bacteria on the skin in eczema. After that I focussed on studying the bugs in the lung microbiome during my PhD and first post-doc.
What studies are you working on?
Lillie: Pseudomonas aeruginosa and Aspergillus fumigatus are bugs that frequently co-infect the lungs of people with cystic fibrosis.
I’m now studying how they grow together in biofilms. Biofilms are tough, complex structures that communities of bugs develop to protect themselves. Infections caused by bugs in a biofilm are much harder to treat. I’m trying to replicate biofilms in the lab, making them as similar as possible to the biofilms that form in lungs of people with CF.
Heritage: Staphylococcus aureus is commonly one of the first bacteria to infect the lungs of children with CF. It used to be believed that Pseudomonas aeruginosa completely killed off Staphylococcus aureus as people get older, but now we know they can survive together in the lungs of people with CF.
I’m studying a clever defence system in Staphylococcus aureus that it uses to produce toxins which kill other bugs - but we don’t know if this defence works in the same way in CF. We hope to understand how this defence system might influence competition with and survival of other pathogens in the CF lungs.
What does a typical day look like to you?
Heritage: I’m working on ways to grow the bacteria as close to what it is like in the lungs of people with CF as possible. This includes adjusting what goes into the liquid that the bacteria grow in. A researcher from Imperial sent me a new recipe to try out. So, in my latest experiments I am testing how well Staphylococcus aureus grows in that.
A good thing about a PhD is that it’s quite flexible and you can work your own hours, as long as you get what you need to get done. It’s all a balance, I can come in later if I want to, but when I’m running long experiments, I can be in the lab until 8pm. Sometimes I have to pop into the lab on the weekends to keep the bugs growing well.
Lillie: It depends on the day of the week. I try to make Mondays my admin day. That means replying to emails about advice on protocols or looking at data or meeting with my supervisors. Then from Tuesday all the way through to Friday, I’ll be working in the lab. That might be prep work for experiments or running the experiments themselves.
Growing bacteria and fungi separately is different, but not that different. Combining them is a whole different game - it starts to get challenging!
What’s it like working within the Precision-CF Innovation Hub?
Working in the Precision-CF Innovation Hub there are so many of us working towards a joint end goal with related work packages. I haven’t experienced that before.
Lillie
We have our own individual part of the project, but there is overlap between us, so we really do have to work closely with each other.
Heritage and I have met online, but we haven’t met in person yet. It’s nice to have this ready-made collection of people who are all working on similar things and who you can reach out to for help if you need to.
I just find it quite exciting. I think it’s really cool that there’s an entire lab group over at Imperial that I can go and talk to and ask for advice. My project has funding for me to be able to go there to learn new techniques in person. It’s also just very nice to have this group of people that are doing similar things to me and to have that external support as well.
Heritage
What do you love about working in research?
Heritage: I like being surrounded by smart people! Whenever I hear people in my lab talk during lab meetings, my jaw is on the ground, astonished and amazed by everyone’s brains. These are some of the funniest, silliest people ever, but also the smartest people I know, which is just so cool to me.
Lillie: I love how varied it is. No day is ever the same. Even if you’re doing the same experiment, there’ll always be a new challenge to overcome or a new result to look at. I love hearing about other people’s projects and getting to hear them be excited about an interesting result. The fact that there are so many people around that I can troubleshoot my own work with. I also love the flexibility; there’s no specific kind of day that anyone ever has to do.
What do you do to switch off from work at the end of the day?
Heritage: I’m part of the university volleyball team, I play for the women’s seconds. Along with that, I go to the gym. When I’m at home I play video games.
Lillie: I’m a very arts and crafts person. I love learning new hobbies. I’m learning to knit at the moment and learning to sew my own clothes, and I really love that I get excited when I get home to go and carry on with whatever project it is I’m working on.