PhD candidate Joseph Pennycook of UCC is currently trying to peer into the mysterious world of the gut microbiome and the bacteria that inhabit it.
After completing his undergraduate degree in evolutionary biology at the Cornwall Campus of the University of Exeter, Joseph Pennycook stayed put to complete a master’s degree in biological sciences.
In 2018, he moved to Cork to begin his PhD to study gut bacteria with the University College Cork (UCC) School of Microbiology and APC Microbiome Ireland, funded by Science Foundation Ireland.
He was recently a participant in the finals of the FameLab Ireland science communication competition.
‘Some people imagine bacteria as interchangeable, boring specks of living dust, but they’re actually really diverse and interesting’
– JOSEPH PENNYCOOK
What inspired you to become a researcher?
I’ve always really loved animals, so I spent ages as a child filling in the pages of birdwatching books, hunting for bugs in my garden. I also played games like Pokémon and Animal Crossing, where discovering all sorts of different creatures was the main appeal.
I suppose whenever I’ve had to decide what to do next, I’ve chosen to keep studying biology and the natural world, even when I’ve found it difficult or less exciting because it’s always felt like an important part of my life.
But honestly, I don’t feel like a ‘spark of inspiration’ is a very important part of doing research. Research can have opportunities to be tremendously creative, but other times it can be pretty tiring and repetitive. At its core, it’s just the work of trying to thoughtfully organise information.
I certainly don’t think I have any uncommon spark of talent or passion that makes me uniquely capable of research, but I am doing work that I think needs doing, and that on my best days I think I can do well.
Can you tell us about the research you’re currently working on?
At the moment, I’m studying the bacteria that live in the human gut and trying to figure out how they are affected by very small amounts of antibiotics.
Antibiotics have been used so much that they’ve begun to pollute some natural environments to the point where humans might be exposed to low levels even when we aren’t taking them deliberately. Along with my supervisor Dr Pauline Scanlan, I’m trying to find out what this might be doing to our microbiomes.
It might seem strange that I’ve ended up working with bacteria after starting out with a focus on animals, since bacteria aren’t animals, but there’s a lot to love about both.
I began to study bacteria because I was interested in evolution and it’s a lot easier to study evolution in bacteria than animals since they reproduce so much more quickly and you can fit massive populations into small bottles. And really, bacteria are just as diverse and interesting as animals – they’re just harder to see.
In your opinion, why is your research important?
It certainly feels important to me to understand how we’re being affected by antibiotic pollution.
I don’t want to oversell the point, so it’s worth mentioning that we really don’t have a clear idea how much antibiotic contamination there actually is in the natural world. It’s a very difficult question to answer for every type of antibiotic in every possible environment, and it’s not something I’m even trying to tackle in my work.
So, we might be lucky. We might not be exposed to very high levels of antibiotics, and if we are, they might not have a meaningful impact on our microbiomes. It’s possible. But I certainly think it’s worth finding out.
What are some of the biggest challenges you face as a researcher in your field?
Lots of bacteria have very flexible lifestyles. So it’s really difficult to be confident how they’re actually living in their natural environment of the gut where we can’t easily see or measure them.
For a simple example, the bacteria E coli can survive in environments without oxygen (like the gut) or with oxygen (like most labs) but produces energy in very different ways in each setting.
It’s fairly simple to grow E coli without oxygen to mimic conditions in the gut, but most of the microbiome species probably change in various ways in response to different levels of temperature, acidity, concentrations of different chemicals and more.
Staying on top of all these conditions is a massive challenge. Hopefully, through a combination of genetic research and experiments with living cells, we’ll eventually be able to get a clearer picture of everything these bacteria are capable of.
Are there any common misconceptions about this area of research?
I think some people imagine bacteria as interchangeable, boring specks of living dust, but they’re actually really diverse and interesting. Some bacteria have sophisticated ways to sense the world around them and swim towards places that suit their needs, while others link together into chains hundreds of cells long and stay rooted in place.
Some can unpick complicated knots of sugar molecules that no animal alive could digest, while others can survive entirely on hydrogen and CO2 with no other food.
With the right push, there’s no reason why bacteria couldn’t feel as exciting to the general public as dinosaurs or distant planets.
They certainly have more impact on people’s lives than either of those things. I think almost any field of science can be made approachable and interesting to a wide audience, and making that connection is a skill I’m excited to practise and improve in the future.
What are some of the areas of research you’d like to see tackled in the years ahead?
There’s so much left to learn about the microbiome, but I’m personally really interested in finding out more about how gut bacteria travel between human hosts. We know bacteria must travel between different people or else species of bacteria could never outlive a single human.
But the journey is a dangerous one and we don’t really know how they manage it.
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