A Scientist's Life: Jack Gilbert

Microbial ecologist seeks ways to collaborate with bacteria to improve human and ecosystem health

Jack Gilbert is a microbiologist and professor in the departments of Pediatrics and Scripps Institution of Oceanography at the University of California, San Diego. He earned his PhD from Nottingham University, United Kingdom, in 2002. He has previously served as a postdoctoral researcher at Queens University, Canada, a senior scientist at Plymouth Marine Laboratory, UK, a microbial ecologist at Argonne National Laboratory in Illinois, and director of the Microbiome Center at the University of Chicago. He joined UC San Diego in 2019. 


explorations now: What do you do for a living?

Jack Gilbert: I study how bacteria talk to each other and how they talk to the environment around them. It's the study of ecology.

I essentially want to understand how to hack into their language and then use them to improve the health of our planet and of our population.

It's rather unusual to find somebody who's jointly appointed between a department of marine biology and a department of pediatrics. I probably am the first person in the world to have that kind of joint title, but it really does speak to the fact that you can find microorganisms anywhere. There are microorganisms in the ocean that can affect human health. There are microorganisms inside people that can influence environmental health. They are dynamically interacting all the time, so for me, there is no boundary, there is no border between those fields. They're the same fields just with slightly different context. We are interested in microbes, full stop. Wherever you find them, we will try and listen to them and learn from them.

en: What are some of the main questions in your field?

JG: I'm really interested in understanding how to stop virulent, dangerous bacteria from infecting people and, by doing that, help to create ecosystems that can promote health in our buildings, in our water supplies, in our environments, to make sure that the next generations have the best quality of life possible.

We've been using this kill-all strategy to get rid of microbial life because for hundreds of years, thousands even, it was microbial life that was our biggest threat, not war, but disease. We've gotten rid of diseases thanks to treatments such as vaccines and antibiotics, but we've gone a little bit too far. There's been too much collateral damage. And so now we're trying to pull that back a little bit and make people healthier by adding bacteria back into their lives, back into the things they do every day.

en: What do people need to understand about how we interact with bacteria?

JG: There is a common misconception about microorganisms that if you wash your hands, they're gone. You are literally a microbial bag, just a bag of microbes. There are some 30 to 40 trillion microorganisms living inside you, the same number of microorganisms as you have human cells. You are one-to-one a ratio of bacteria to human and that massive load of microorganisms is continually being shed from your body. Thirty-eight million bacterial cells leave your body every hour. That's even if you're sitting down and not doing anything. It's phenomenal.

So it’s a misconception that you can somehow get rid of them, that you can somehow sterilize your environment and everything will be fine. That's just not true. Barely 1 hour after you have sterilized a surface, 400,000 bacteria can be found.

Instead of trying to eradicate this world, we're trying to work with it. We're trying to figure out how to be the best stewards of the microbial world so that we can manage that microbial garden and create it to improve the health of our planet and of ourselves.

There's been antibiotic resistance on planet Earth for 3.5 billion years because bacteria have always been fighting among each other for supremacy. If you were to look at the intestines of Ameri-Indians living in the Amazon rainforest who have never, ever taken an antibiotic, you'll see antibiotic resistance in their microbiome to the kinds of antibiotics that we take every day. That's everywhere.

What we are interested in doing is to create a living blanket, almost like a rainforest of microorganisms on surfaces, so that when a pathogen leaves your body or your friend's body, and lands on that surface, it can't compete. Imagine I take your potted plant from home and I throw it in the Amazon rainforest. It likely won't survive. The Amazon rainforest is too complex, too rich. There's too much competition. We want to create competition for microbes on surfaces, and by doing that, make them less of a threat to human health.

en: What are you working on right now?

JG: We're exploring many different things to do with how microbes interact with different animals and plants in the ocean. For example, we look at bacteria growing on microplastics, which have become a major pollution source, and how those bacteria promote pathogenesis in oysters, which then infect people when they eat raw seafood. 

We're also interested in understanding how microbes interact with each other in the ocean and how we can predict those interactions because that could help us to understand how climate change would influence the productivity of our oceans.

 We're also trying to explore ways of taking bacteria and adding them back into mangrove forests into the soils of the trees so that those forests can be more resilient to pollution and also be better at handling the threats of climate change. We also try to understand how microbes interact with different plants and animals in a way that helps us to make those plants and animals more productive for the food consumption of people around the world, so that we can have better fish stocks, more productive shell fisheries, and even make algae or seaweed available to food production in a broader way.


en: What are some of the tools you use in your research?

JG: One of the key things we do is we look at microbes in different environments using molecular approaches. That just basically means we would sequence your genome in order to figure out what kind of diseases you might have, or your prevalence of particular diseases. We do the exact same thing just with bacteria. We sequence their genomes and we use that information to infer how they interact with each other, what they need to eat, what might make them sick, what in them might make us sick. So we read out their genome to tell us how they function in their environment.


en: What got you into this field?

JG: I actually stumbled into it accidentally. I wanted to be an entomologist. I went to study that at university and even had a job after university working in a natural history museum, studying insects and butterflies. It wasn't until someone gave me an opportunity to go and live and work in Antarctica for nearly two years that I got interested in bacteria. Down there there's no other life, definitely no insects.

I got interested in how the smallest forms of life were surviving in this incredibly harsh landscape and that really got me excited. Bacteria are the ultimate survivors on this planet. They've been around the longest and they've figured out how to adapt themselves to all the wonderful variance that the world could throw at it.

So that's my main driver. I was like 21, 22 years old, and I thought, what the hell am I doing on this frozen continent? Well, there's all this life around. You just can't see it. Well, how am I going to understand that life? How am I gonna talk to it? How am I going to figure out how it can talk to me? What tools can I have at my disposal to investigate it? And that has led to the last 22, 23 years of my career trying to figure out how to unpick that question. Sometime maybe long after I'm dead, I'll have figured it out, but right now I'm still a student.

en: Why did you want to come to Scripps Oceanography?
JG: The beach! (laughs) I was actually interested in coming to the University of California San Diego because of its collaborative spirit. I mean, I've worked in a lot of different places, but there are few places where I can be a person studying human health diseases in children in a hospital. And then five minutes later be in the world's premier marine research facility. It was an extraordinary opportunity to combine all of my interests in how microbes work in the oceans, in the rivers and lakes around us, inside our bodies, even in our hospital buildings and put it all into one package at one university. There are very few places on Earth where all of that opportunity is compacted down into an area where I can walk between the buildings.

About Scripps Oceanography

Scripps Institution of Oceanography at the University of California San Diego is one of the world’s most important centers for global earth science research and education. In its second century of discovery, Scripps scientists work to understand and protect the planet, and investigate our oceans, Earth, and atmosphere to find solutions to our greatest environmental challenges. Scripps offers unparalleled education and training for the next generation of scientific and environmental leaders through its undergraduate, master’s and doctoral programs. The institution also operates a fleet of four oceanographic research vessels, and is home to Birch Aquarium at Scripps, the public exploration center that welcomes 500,000 visitors each year.

About UC San Diego

At the University of California San Diego, we embrace a culture of exploration and experimentation. Established in 1960, UC San Diego has been shaped by exceptional scholars who aren’t afraid to look deeper, challenge expectations and redefine conventional wisdom. As one of the top 15 research universities in the world, we are driving innovation and change to advance society, propel economic growth and make our world a better place. Learn more at ucsd.edu.

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