This week's PhDetail is with Jeffrey Letourneau who does his PhD at Duke University in the Molecular Genetics and Microbiology department. Before his PhD, Jeffrey did his undergrad at Worcester Polytechnic Institute (WPI) in Massachusetts, US, where he got his BS in Biology & Biotechnology (minors in Spanish and Bioinformatics & Computational Biology). During this time Jeffrey worked in an animal behaviour lab studying bumblebees, then in a cell culture lab working on the development of a plant-derived scaffold on which mammalian cells could be grown, and he completed his thesis in Dr. Reeta Rao’s microbiology lab studying the pathogenic yeast Candida albicans. You can find Jeffrey on twitter @letourjeff or at his website HERE!
Well let’s start off talking about completely unscientific stuff: What is your favourite band/musical artist pre 1980?
Fleetwood Mac
Favourite band/musical artist post 1980?
It kind of changes every year as I discover new music; currently Sufjan Stevens.
Favourite movie?
That’s tough. I wish I had a list of every movie I’ve ever watched. Of the movies I’ve seen recently, I really enjoyed Horse Girl. In terms of ones that have stuck with me… maybe It’s Such a Beautiful Day. In general I tend to like psychological thrillers and dark comedies.
Do you listen to podcasts? What are some of your favourites?
Not that often. In the past I have on long car rides or if I’m doing repetitive lab work for a long time. My favorite science-related ones are This Podcast Will Kill You and Ologies. I also enjoyed a few fictional podcasts like Welcome to Nightvale and Limetown. Lore also has these great narratives about mythology.
Where do you study and who is your supervisor?
I am getting my PhD in Molecular Genetics and Microbiology at Duke University. My advisor is Lawrence David.
What year of your PhD are you in?
Third year
Who’s giving you the money – and for how long?
I am funded by the National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP). That provides my stipend for three years, which will cover me through the end of my fifth (and hopefully final!) year of grad school.
Do you have any publications?
No, not yet, but I am currently prepping my first ever publication for submission.
Did you do a masters before your PhD?
Nope, I applied to PhD programs straight out of undergrad. In my field, there’s a good mix of people who came direct from undergrad, did a master’s, or worked as a lab tech for a few years before applying.
Do you ever do fieldwork?
I have not done fieldwork (though I would love the opportunity to do some someday). I’ve been trying to get good at plant and mushroom identification, but that’s the closest I’ve come.
What is the best bit about your labwork?
My favorite part of lab work is getting the data. In my research, there can be a delay of weeks or even months before I get the results, especially for sequencing, and so that’s when I can actually see and interpret what happened. The worst part about lab work is when things suddenly stop working for no apparent reason. Also, working with fecal bacteria, sometimes the smell can be pretty bad.
How many PhDs did you apply for – what were you looking for?
I applied to PhD programs at seven universities. The most important factors were the labs and the location. I knew I wanted to study microbiology, but I didn’t know what specific type, so I wanted a department where I would have options to rotate in labs that studied all different types of microbes – viruses, bacteria, fungi, etc. As far as location, I wanted to find somewhere I could really see myself living, with a good stipend to cost of living ratio. I had this whole spreadsheet with details of each different program to keep these and other factors organized.
I was rejected from two schools (ironically, the ones I thought I had the best chance at) and invited to interview at the other five. I accepted four of those invitations. At the interview weekends, the main questions I tried to answer were: Do the students seem happy? Does there seem to be a work-life balance? Do the faculty seem like supportive mentors? Is the program well-organized? Is this somewhere I could see myself living for 5-6 years?
What is the most bodged piece of equipment you have had to use during field/labwork – did it work?
I don’t think I’ve used anything too sketchy. I had one plate shaker that I partially disassembled and attached a plastic storage container to so that I could shake things of different sizes. Back when I worked in a bee lab, we made fake flowers out of Eppendorf tubes with foam petals, and then pipetted sugar water into the tubes to be nectar. Those were very effective.
What one piece of advice would you give to a masters student applying to PhDs now?
I think the most important advice I can give is to choose an environment where you will be happy for 5-6 years. I’m very fortunate to be in a lab with a supportive PI and awesome labmates. Talk to students in the lab, and talk to students that left the lab (or rotated but didn’t join). If you know early on that it’s a toxic environment, but think you can handle it… that’s great, you probably can handle it, but it’s not worth being miserable for 5 years of your life no matter how cool the research is. There’s also nothing wrong with switching labs if that’s what you need to do.
How often do you meet with your supervisor?
I meet with my advisor one-on-one once every other week. Then on alternating weeks we also have small group meetings for specific project teams. I like this system because it means I’m only attending the meetings that are relevant to me, and that each project has a designated time where everyone involved can touch base. Finally, we have a weekly lab meeting with food (usually bagels if it’s in the morning and pizza if at lunchtime) where one person presents on what they’ve been working on for the past two months or so.
What supervisor traits are important to you?
A good supervisor understands work-life balance, works with trainees to help them get what they are looking for out of a PhD, and works to foster a happy working environment (through building a sense of community, being cognisant of potential conflicts, etc.). I also think it’s important for a supervisor to be excited about the research. I often walk out of meetings with my advisor with a renewed excitement because of his own enthusiasm.
What do you think are the worst supervisor traits?
I think the worst supervisors are those who perhaps were great at research but never took the time to work on the skills needed to be a good manager or mentor. That may manifest as treating trainees like robots who exist only to work, criticizing trainees (in a non-constructive way), or providing inadequate feedback and guidance.
In one sentence what is your PhD about?
I study how complex communities of bacteria in the gut work together to break down dietary fiber and transform it into chemicals that benefit human health.
What has been your academic highlight of the last year?
Probably getting awarded the NSF GRFP. I had previously applied as an undergrad, and my application was not even reviewed because the topic was deemed too relevant to human health, so it was really exciting to get it the second time around.
Have you had an academic lowpoint of the last year – if so what happened?
Not a single low point, but repeatedly missing self-imposed deadlines for submitting my paper definitely wore me down and caused some burn-out.
Do you have any academic idols?
I really don’t tend to idolize people. The people who most inspire me are not the most famous scientists, but rather I have found role models in my labmates (current and past), classmates, and early-career researchers I follow on Twitter. For example, when I first started getting into science, my PhD student mentor, Melissa, really helped me to develop some fundamental research skills and provided a window into the ups and downs of PhD life.
That said, I have had a few opportunities to meet some big-name researchers in the field. I have served on the committee for an annual lecture in my department for several years, and last year we brought in Jeffrey Gordon, who is practically the founder of gut microbiome research. This year I am also excited that we will have Yasmine Belkaid speaking, who is a renowned immunologist studying host-microbe interactions at the skin and the gut. Other scientists I would love to meet in the future include Elaine Hsiao, who studies how the gut microbiome can influence behaviour, and Rachel Dutton, who uses cheese as a model system to study microbial interactions.
Do you have a favourite paper?
I don’t know that I have a favorite, but of research in the past year, I really like “Effects of microbiota-directed foods in gnotobiotic animals and undernourished children” from the Gordon Lab. Jeanette Gehrig and co-authors do a great job of connecting specific foods with trends in the composition of the gut microbiome, and the work directly addresses a really important problem.
What has been your favourite conference so far?
I’ve only been to one conference, a Keystone Symposium in Killarney, Ireland. It was a really awesome experience. I got to go with the two other grad students in my lab, Zack and Brianna. We attended four days of scientific talks, presented on our own research, ate a lot of really good food, and then ended the week by climbing the tallest mountain in Ireland together. Great lab bonding experience. The talks were also really interesting too, in part just because they were all microbiome-related, so very relevant to my work. There was also a very inspiring talk by David Zilber, a chef at Noma, one of the top restaurants in the world. He talked about how his research on fermentation at Noma, and I have since bought their cookbook, The Noma Guide to Fermentation.
What hours do you typically work?
I typically try to do a 9-5, with occasional night or weekend work if an experiment requires it or there’s a deadline I need to meet.
How do you avoid procrastinating?
Not very well. I often “productinate” by doing lower-priority tasks rather than the important thing I should be working on.
What motivates you in your day to day PhD life?
I guess for me it’s about sharing science. You can “know” something in the lab in minutes, but often to get that knowledge out into the world (in the form of a paper) can take years. I’m excited to really get my research out there and start some new discussions about how gut bacteria do what they do.
What do you do when you’re not working – how do you balance it with your PhD?
Even when I’m not at work, I still enjoy experimenting in the kitchen with fermented foods, baking, and new high-fiber foods. I also like getting outdoors and I on-and-off rock climb. I also enjoy art, reading, and writing, but am not always good at making time for those.
If a genie could grant you one wish to help with your PhD what would you wish for?
Ability to shrink down to bacteria size and ask, “Hey little microbe, what are you up to?”
What would be your dream job?
I think in my dream job, I’m working a different job every day of the week. There are too many different things I want to do – microbiology research, outreach, writing, teaching, mentoring, food science… Currently I think that becoming a professor is my best shot at synthesizing these interests. Maybe with some sort of food business side hustle.
Where do you see yourself in 5 years?
Hopefully working as a professor :)
One word to sum up your future in academia:
microbial
What do you want to achieve outside of academia in the coming year?
I would like to publish my first paid science writing piece this year. I’m currently writing for several blogs and enjoying that, but if I could successfully publish something and get paid (even a very modest amount) that would feel really validating and would be a huge step for me towards reaching a broader audience.
Also, to successfully grow chicory root.
What essential tool hardware/software could you not do your PhD without?
R
Where is somewhere you would like to work in the future?
I lean slightly towards a state school, one with a strong microbiology program.
Do you have a favourite organism?
No. Maybe garlic, because it is delicious. I study complex communities of bacteria, so not a single organism.
If you could change one thing about your group/department structure what would it be?
Better policies on harassment and discrimination, making reporting easier and eliminating protections for perpetrators. This in part stems from involvement with the Duke Graduate Student Union, which is currently launching a campaign at the Duke Graduate School level to address these issues.
What major question in your subject area is yet to be addressed – why is it important and why isn’t anyone addressing it?
I’d say a big one is understanding how individual differences in the gut microbiome lead to differences in health outcomes and responses to specific foods. People are beginning to realize that these differences are important, but it’s really difficult to study because every person is unique. Maybe ten years from now, though, we will be able to take a stool sample from someone and use it to determine which drugs they will respond best to or what foods they should be eating.
Well let’s start off talking about completely unscientific stuff: What is your favourite band/musical artist pre 1980?Fleetwood Mac
Favourite band/musical artist post 1980?
It kind of changes every year as I discover new music; currently Sufjan Stevens.
Favourite movie?
That’s tough. I wish I had a list of every movie I’ve ever watched. Of the movies I’ve seen recently, I really enjoyed Horse Girl. In terms of ones that have stuck with me… maybe It’s Such a Beautiful Day. In general I tend to like psychological thrillers and dark comedies.
Do you listen to podcasts? What are some of your favourites?
Not that often. In the past I have on long car rides or if I’m doing repetitive lab work for a long time. My favorite science-related ones are This Podcast Will Kill You and Ologies. I also enjoyed a few fictional podcasts like Welcome to Nightvale and Limetown. Lore also has these great narratives about mythology.
Where do you study and who is your supervisor?
I am getting my PhD in Molecular Genetics and Microbiology at Duke University. My advisor is Lawrence David.
What year of your PhD are you in?
Third year
Who’s giving you the money – and for how long?
I am funded by the National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP). That provides my stipend for three years, which will cover me through the end of my fifth (and hopefully final!) year of grad school.
Do you have any publications?
No, not yet, but I am currently prepping my first ever publication for submission.
Did you do a masters before your PhD?
Nope, I applied to PhD programs straight out of undergrad. In my field, there’s a good mix of people who came direct from undergrad, did a master’s, or worked as a lab tech for a few years before applying.
Do you ever do fieldwork?
I have not done fieldwork (though I would love the opportunity to do some someday). I’ve been trying to get good at plant and mushroom identification, but that’s the closest I’ve come.
What is the best bit about your labwork?
My favorite part of lab work is getting the data. In my research, there can be a delay of weeks or even months before I get the results, especially for sequencing, and so that’s when I can actually see and interpret what happened. The worst part about lab work is when things suddenly stop working for no apparent reason. Also, working with fecal bacteria, sometimes the smell can be pretty bad.
How many PhDs did you apply for – what were you looking for?
I applied to PhD programs at seven universities. The most important factors were the labs and the location. I knew I wanted to study microbiology, but I didn’t know what specific type, so I wanted a department where I would have options to rotate in labs that studied all different types of microbes – viruses, bacteria, fungi, etc. As far as location, I wanted to find somewhere I could really see myself living, with a good stipend to cost of living ratio. I had this whole spreadsheet with details of each different program to keep these and other factors organized.
I was rejected from two schools (ironically, the ones I thought I had the best chance at) and invited to interview at the other five. I accepted four of those invitations. At the interview weekends, the main questions I tried to answer were: Do the students seem happy? Does there seem to be a work-life balance? Do the faculty seem like supportive mentors? Is the program well-organized? Is this somewhere I could see myself living for 5-6 years?
What is the most bodged piece of equipment you have had to use during field/labwork – did it work?
I don’t think I’ve used anything too sketchy. I had one plate shaker that I partially disassembled and attached a plastic storage container to so that I could shake things of different sizes. Back when I worked in a bee lab, we made fake flowers out of Eppendorf tubes with foam petals, and then pipetted sugar water into the tubes to be nectar. Those were very effective.
What one piece of advice would you give to a masters student applying to PhDs now?
I think the most important advice I can give is to choose an environment where you will be happy for 5-6 years. I’m very fortunate to be in a lab with a supportive PI and awesome labmates. Talk to students in the lab, and talk to students that left the lab (or rotated but didn’t join). If you know early on that it’s a toxic environment, but think you can handle it… that’s great, you probably can handle it, but it’s not worth being miserable for 5 years of your life no matter how cool the research is. There’s also nothing wrong with switching labs if that’s what you need to do.
How often do you meet with your supervisor?
I meet with my advisor one-on-one once every other week. Then on alternating weeks we also have small group meetings for specific project teams. I like this system because it means I’m only attending the meetings that are relevant to me, and that each project has a designated time where everyone involved can touch base. Finally, we have a weekly lab meeting with food (usually bagels if it’s in the morning and pizza if at lunchtime) where one person presents on what they’ve been working on for the past two months or so.
What supervisor traits are important to you?
A good supervisor understands work-life balance, works with trainees to help them get what they are looking for out of a PhD, and works to foster a happy working environment (through building a sense of community, being cognisant of potential conflicts, etc.). I also think it’s important for a supervisor to be excited about the research. I often walk out of meetings with my advisor with a renewed excitement because of his own enthusiasm.
What do you think are the worst supervisor traits?
I think the worst supervisors are those who perhaps were great at research but never took the time to work on the skills needed to be a good manager or mentor. That may manifest as treating trainees like robots who exist only to work, criticizing trainees (in a non-constructive way), or providing inadequate feedback and guidance.
In one sentence what is your PhD about?
I study how complex communities of bacteria in the gut work together to break down dietary fiber and transform it into chemicals that benefit human health.
What has been your academic highlight of the last year?
Probably getting awarded the NSF GRFP. I had previously applied as an undergrad, and my application was not even reviewed because the topic was deemed too relevant to human health, so it was really exciting to get it the second time around.
Have you had an academic lowpoint of the last year – if so what happened?
Not a single low point, but repeatedly missing self-imposed deadlines for submitting my paper definitely wore me down and caused some burn-out.
Do you have any academic idols?
I really don’t tend to idolize people. The people who most inspire me are not the most famous scientists, but rather I have found role models in my labmates (current and past), classmates, and early-career researchers I follow on Twitter. For example, when I first started getting into science, my PhD student mentor, Melissa, really helped me to develop some fundamental research skills and provided a window into the ups and downs of PhD life.
That said, I have had a few opportunities to meet some big-name researchers in the field. I have served on the committee for an annual lecture in my department for several years, and last year we brought in Jeffrey Gordon, who is practically the founder of gut microbiome research. This year I am also excited that we will have Yasmine Belkaid speaking, who is a renowned immunologist studying host-microbe interactions at the skin and the gut. Other scientists I would love to meet in the future include Elaine Hsiao, who studies how the gut microbiome can influence behaviour, and Rachel Dutton, who uses cheese as a model system to study microbial interactions.
Do you have a favourite paper?
I don’t know that I have a favorite, but of research in the past year, I really like “Effects of microbiota-directed foods in gnotobiotic animals and undernourished children” from the Gordon Lab. Jeanette Gehrig and co-authors do a great job of connecting specific foods with trends in the composition of the gut microbiome, and the work directly addresses a really important problem.
What has been your favourite conference so far?
I’ve only been to one conference, a Keystone Symposium in Killarney, Ireland. It was a really awesome experience. I got to go with the two other grad students in my lab, Zack and Brianna. We attended four days of scientific talks, presented on our own research, ate a lot of really good food, and then ended the week by climbing the tallest mountain in Ireland together. Great lab bonding experience. The talks were also really interesting too, in part just because they were all microbiome-related, so very relevant to my work. There was also a very inspiring talk by David Zilber, a chef at Noma, one of the top restaurants in the world. He talked about how his research on fermentation at Noma, and I have since bought their cookbook, The Noma Guide to Fermentation.
What hours do you typically work?
I typically try to do a 9-5, with occasional night or weekend work if an experiment requires it or there’s a deadline I need to meet.
How do you avoid procrastinating?
Not very well. I often “productinate” by doing lower-priority tasks rather than the important thing I should be working on.
What motivates you in your day to day PhD life?
I guess for me it’s about sharing science. You can “know” something in the lab in minutes, but often to get that knowledge out into the world (in the form of a paper) can take years. I’m excited to really get my research out there and start some new discussions about how gut bacteria do what they do.
What do you do when you’re not working – how do you balance it with your PhD?
Even when I’m not at work, I still enjoy experimenting in the kitchen with fermented foods, baking, and new high-fiber foods. I also like getting outdoors and I on-and-off rock climb. I also enjoy art, reading, and writing, but am not always good at making time for those.
If a genie could grant you one wish to help with your PhD what would you wish for?
Ability to shrink down to bacteria size and ask, “Hey little microbe, what are you up to?”
What would be your dream job?
I think in my dream job, I’m working a different job every day of the week. There are too many different things I want to do – microbiology research, outreach, writing, teaching, mentoring, food science… Currently I think that becoming a professor is my best shot at synthesizing these interests. Maybe with some sort of food business side hustle.
Where do you see yourself in 5 years?
Hopefully working as a professor :)
One word to sum up your future in academia:
microbial
What do you want to achieve outside of academia in the coming year?
I would like to publish my first paid science writing piece this year. I’m currently writing for several blogs and enjoying that, but if I could successfully publish something and get paid (even a very modest amount) that would feel really validating and would be a huge step for me towards reaching a broader audience.
Also, to successfully grow chicory root.
What essential tool hardware/software could you not do your PhD without?
R
Where is somewhere you would like to work in the future?
I lean slightly towards a state school, one with a strong microbiology program.
Do you have a favourite organism?
No. Maybe garlic, because it is delicious. I study complex communities of bacteria, so not a single organism.
If you could change one thing about your group/department structure what would it be?
Better policies on harassment and discrimination, making reporting easier and eliminating protections for perpetrators. This in part stems from involvement with the Duke Graduate Student Union, which is currently launching a campaign at the Duke Graduate School level to address these issues.
What major question in your subject area is yet to be addressed – why is it important and why isn’t anyone addressing it?
I’d say a big one is understanding how individual differences in the gut microbiome lead to differences in health outcomes and responses to specific foods. People are beginning to realize that these differences are important, but it’s really difficult to study because every person is unique. Maybe ten years from now, though, we will be able to take a stool sample from someone and use it to determine which drugs they will respond best to or what foods they should be eating.
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