NEB Podcast Episode #10 -
Interview with Scott Chimileski: Microbes are Everywhere!

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Transcript

Interviewer: Lydia Morrison, Marketing Communications Writer & Podcast Host, New England Biolabs, Inc. 
Interviewee: Scott Chimileski, Post-doctoral Fellow, Harvard Medical School.

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Topics include: Microbiology, Microbes, Bacterial Art, Kombucha

Hi everyone, thanks for joining us for this episode of the NEB podcast. I'm your host Lydia Morrison, and I hope that today's podcast broadens your perspective. I'm joined by Scott Chimileski, who is currently a post-doctoral fellow in Roberto Kolter's lab at Harvard Medical School, and he's also co-curator of Microbial Life: A Universe at the Edge of Sight currently on exhibit at the Harvard Museum of Natural History. Today, Scott's here to talk about the intersection of art and science, and the important role that mentors play in the realm of science careers.

Thanks so much for joining me today, Scott.

Thanks for inviting me.

Bacteria Art

So how did you get involved in microbial art in the first place?

During the ... I would say, towards the end of my PhD at the University of Connecticut, I started to study biofilms, which are like a multi-cellular form of bacteria. I was actually working with archaea at the time, some salt loving archaea, and I had already been a photographer for a long time before that, just taking photographs of nature and landscapes and wildlife, and it was around that time when I started working on biofilms, which are a very imaging intensive field of study in microbiology, for example, at the Center for Biofilm Engineering in Montana, and I was learning how to do confocal microscopy of these biofilms, and I guess it was around then that I started realizing how beautiful these biofilm structures were.

It was also around then that I started photographing colonies of archaea and bacteria in the lab. And so, that's when the photography side of me ... if they're different sides to begin with ... and the scientist track sort of began to merge, and that's really how it got started.

Why do you feel like microbes lend themselves so well to making art?

One of the things I was noticing around that period was that these bacteria that I would cultivate or that we had in the lab, represented, for example, a whole palette of colors that you could find on an artist's palette. There's bacteria just outside this door right now in the soil where when you grow them up in the lab, they'll be bright orange, bright purple, red, pink, blue, I mean, every color in the rainbow. And so, right away, you have all of those beautiful, natural colors.

And then, as it comes back to biofilms, you also see these remarkable patterns and structures in biofilms. They have like a fractal pattern, almost the types of patterns that you see all over the place in nature. So, patterns really do repeat themselves in nature, and you can see these beautiful fractal patterns in biofilms, for example, that look superficially similar to maybe how the earth looks from space sometimes, different patterns in rivers, how rivers join each other and rejoin each other, so you see these sorts of patterns that I could find in the bacterial colonies.

That's interesting. And so they also seem to lend themselves really well to timelapse photography, in particular. Can you talk a little bit about how you decided to apply timelapse photography to capturing these images?

Yeah. The still version of, like a photograph, of a colony or something like that is only going to tell such a small part of the story because in bacteria, when you build a biofilm, this is really a type of a developmental program, so it's obviously, it's a lot less complicated than how an embryo would develop or something like that, for an animal.

But, the basic principles are there, and it is a true developmental program where you start from a single bacterium, that bacterium grows and divides and over time, you get interactions between the cells, and it's those interactions that lead to the final biofilm structure. So it's really important, I think, to capture that whole process from a single cell sometimes, all the way up to the finished biofilm.

As far as how I first started doing timelapse of microbes is, again, related to my background in photography. I was doing a lot of timelapse of nature, just clouds rolling by on landscapes, and things like that, and so I had already learned how to do timelapse. I have what's called an intervalometer that you hook up to your SLR that tells it how often to take photos, and things like that. When I was in the last year of my PhD, studying these biofilms formed by archaea, I noticed that my biofilms on my bench from one day to the next had different shapes.

So I was looking at them every day and I was thinking, what's going on here, these biofilms seemed to be doing something while I'm not around. And so, it just sort of hit me, okay, well I just need to make a timelapse and see what's happening here.

So that was when I built my first dedicated timelapse system inside of an incubator, and that was probably in 2013. That, I guess, was the first version of my timelapse incubator, and ever since then, I've just been updating and modifying that initial design. I was able to discover, in that case, a new type of a social motility in this archaeon that I was studying. The species is called Haloferax volcanii. I found that the biofilms were moving in a collective fashion, and that's what I was noticing on the bench, and I was able to capture that through timelapse. We wrote a paper about that.

That's cool. So it really gave you sort of a new window into viewing the movement and the changes of the biofilms to be able to really catalog those movements, I guess?

Yeah. So it's, in my mind at least, equal parts capturing the beauty of what's happening, and then the beauty of the structures, and the intricacy there, and also documenting it for scientific purposes.

Choosing a Scientific Mentor

Cool. So let's talk about your mentor, Roberto Kolter. It seems like the two of you have a pretty unique relationship. Do you have any advice that you could share for graduate students or post-docs who are deciding which lab to join, or tips for what to look for in a mentor?

Start Early: The first advice that I would give is actually advice that came to me from Roberto, as I was seeking out his lab for a post-doc, and that is to start early. Roberto's advice to me, at the time, was like 18 months, so if you're a grad student, or a PhD student finishing up, 18 months is not too early to start seeking out your post-doc lab and making contacts to that person. That is around the time that I started contacting Roberto, and you're right that we do have a special relationship, and I think that that really also comes out of us having a lot of time to plan these projects, because I was joining his lab as a post-doc and doing research, and as an imaging specialist in the lab, but we were also, from those early days, planning to write a book together already, and planning to make these museum exhibitions. Those projects were really part of it from day one. And of course, if we hadn't started planning those things way back, even before I joined the lab, then they could have never come to fruition.

Find the Good Match: In my own experience, I had been reading papers from Roberto for a long time, and not just ... I mean, they were all scientific papers, but I could also see this streak of creativity in the papers. For example, like I said, I was studying biofilms as a PhD student, and he has this one paper that's titled something like 'Thieves and Assassins of the Microbial World' or something like that. There's a lot of examples like that if you look through his papers, and so I thought, he's really a creative person, and somebody who, not just creative, but somebody who values creativity, and who really looks for that connection between art and science. I also knew, at that time, that he was the cover editor for the Journal of Bacteriology, so he's the person who picks the cover every month for that. So I definitely knew ahead of time that he was going to be receptive towards these types of projects and that made all the difference, versus just going to somebody randomly and then saying, "Hey, you know, let's write a book, or make a museum exhibition."

So lots of research up front and time in thinking and planning about what you want to get out of your post-doc or your graduate school experience.

I've been certainly impressed to learn all that you've accomplished in your three years at your post-doc. You've had two museum exhibitions and a book, among other things, and having your photography displayed, and it's like 30 different places that have used your photography, everything from CBS to scientific journals, so that's pretty impressive.

Yeah, yeah. I don't think that either of us thought that it was going to go exactly how it did, as far as how well it went. One thing that we were really pleased with was the timing of the book and the exhibition. They were always parallel projects, but we probably assumed that they wouldn't come out at the same time, and then they ended up coming out within days of each other.

The museum exhibit opened and the book launched, which made it really fun, because we took the book to the museum and took photos there with the book, and we were super excited. That was about a year ago now when the book and first exhibit opened. So yeah, I mean, I think that luck certainly ... hard work. We wrote the book pretty quickly, but also luck comes into it as well. Yeah, we've been really happy with it.

And a good deal of planning, it seems like.

Yeah, a good deal of planning, for sure.

So your latest publication with Roberto was entitled 'The End of Microbiology.' What does that mean?

I'm really glad you asked about that because, as you might guess with such a controversial title, it's something that I'm really happy to talk about. The title, 'The End of Microbiology', was meant to be provocative, but really the paper is all about how we make divisions between different disciplines, as scientists. And so, The End of Microbiology was a piece that we were asked to write, which was a vision piece. We were specifically asked to write by The Environmental Microbiology Journal, what's going to happen 20 years from now in microbiology. What we see happening, and what we hope will continue to happen, is sort of a breakdown of these barriers between disciplines which, in my view, these are really false divisions.

Between divisions within science or between divisions within like art and science, in sort of a broader thinking about subjects?

Yeah. Certainly art and science as well, but right now, I mean just between different scientific disciplines. So, for example, microbiology. Microbiology came about as a separate discipline really because a few hundred years ago, we invented a microscope, and so then, we all of a sudden started using a microscope and we say, "Okay, everything that we see through the microscope is a microbe, and so this is now microbiology." But meanwhile, those organisms were there all along, way before we had the microscope, from the beginning of life itself, and so we kind of put up these artificial boundaries around different disciplines.

But now, because of the microbiome fields, in particular, we're seeing how intimately connected microbes are to macroscopic life. So there really is like no true division, and this is something that we talk about in the book, too. In fact, the title of the book 'Life at the Edge of Sight' kind of deals with this idea of the edge of sight and how humans, based on our visual acuity, defined what a microbe is, and what is not a microbe.

Meanwhile, there might be another organism that has a different visibility, a different vision system, that might be able to see what we call microbes. And so, that's one way of realizing that it's sort of a false boundary that's really relative to only humans. And so, the paper really just argues for the fact that microbiology, and all disciplines of biology, are really just all biology, that nature is indivisible, and that, in certain cases, you might have an advantage to studying microbiology apart and studying it in its own right, but I think that in most cases, you're putting yourself at a disadvantage if you say, "Okay, I'm a microbiologist, so I only study these bacteria."

Meanwhile, those bacteria are in your body and they're so relevant to how your body functions, and to how the whole biosphere itself functions that I think that you're putting yourself at a disadvantage if you sort of wall yourself off and say, "I'm only going to study microbes." So, it's really just a sort of call to arms and a plea that we start to break down some of these divisions and look at biology as a whole.

NEB Passion In Science Awards^®

An interesting concept. So you were a 2016 Passion in Science winner, and we're about to launch the application process for our 2019 awards, how has being a Passion in Science award winner impacted your career?

I would say it comes back to, like you mentioned that my photography has been used in a lot of different outlets, and has gotten all over the place, and I think that there was a certain momentum there that happened. I started my post-doc in 2015 and then this award came about a year into my post-doc. That's also when we were working on the book and a lot of the exhibit intensively, but I think it really did help me to gain momentum. I can't say for sure how much that momentum mattered, but I think it mattered a lot as far as pushing me forward into all of these other opportunities that have happened since then. So I would say it definitely gave me a lot of exposure and just added to that momentum that takes me to today.

Yeah. It's always nice to be recognized for doing things that you excel at, and things that you enjoy, too. So that probably just sort of helped to be like, oh, people are interested in this. The exhibit is going to work. The book's going to work.

Exactly. Yeah. Adding to the momentum is both in terms of exposure, externally, and also adding to my own confidence. That further cycles into the positive feedback loop of pushing that work out there.

Yeah. And certainly, you've done a lot of work in terms of science communication. And that end, you're currently a guest co-curator with Roberto, of the microbial exhibit at the Harvard Museum of Natural History, which I have visited both of your exhibits there, and they were very engaging and educational in completely different ways. Could you tell our listeners a little bit about those exhibits?

Yeah. The museum project started, in my mind, in 2013 when I visited the Harvard Museum of Natural History. I love this museum. It's a really historic museum, but like so many natural history museums, there was very little emphasis on bacteria or microbes there. I went there one day and I searched the whole place, and I found this one room called the New England Forest, and within the New England Forest, there was a rotting wood exhibit, and then on there, there was a tiny little cartoon of bacteria.

And so, that just like ... I literally was freaking out on that day at the museum, and texting my family, and that time ... I knew I was going to start the post-doc and things were lining up, so I was like, "This is what we're going to do. This is a big problem. We have to fix this." Of course, I didn't expect it to actually come to fruition. That was the moment that really started to catalyze it.

And so, after that, Roberto and I met with the director of the museum and we sort of pitched the idea to her, and she ... Her name is Jane Pickering, is a great director of that museum, and she loved the idea, from that moment forward, from when she approved it, and we were sort of off to the races. The museum ended up breaking it apart into two different exhibits. One was a teaser exhibition, which was more poetic and photographic. That was up for six months. That was called World in a Drop: Photographic Explorations of Microbial Life. That photography exhibit is currently traveling to the Eden Project in the UK, and also to a place in Colombia. So that's done pretty well. But then, at the Harvard Museum, that came down and made way for the Microbial Life exhibit, which opened this past February, and that will be open till September of 2019. So they ended up breaking it up into those two different exhibits.

And yeah, the idea is that the natural history of this planet is mostly microbial. So even though we're biased, like I've been saying in other answers, by our vision, as far as what we think makes up the biodiversity of the planet, most biodiversity of the planet is microbial. And so, in a natural history museum, we really have to have a strong emphasis on microbes.

What is Kombucha?

Well, thank you, from the general public, for adding to the natural history museum and sort of opening everybody's eyes to the invisible. Can you tell our listeners what kombucha is?

Yeah. Kombucha is part of our exhibit at the Harvard museum. It's actually part of our live demo where we have some microbial scientists there with kombucha that they show to the visitors. This is a type of microbial food, we would call it. It's a tea product that's made by microbes.

Typically, when you buy kombucha in the store ... and it's become a multi-billion dollar industry, all different types of brands ... you see just the tea part of it, but how kombucha is made is by starting off with a very sweet tea, with a lot of sugar, and then you add some microbes to that sweet tea in the form of what's called a SCOBY, which stands for Symbiotic Community of Bacteria and Yeast, and that's basically a biofilm that sits on top of the fermenting tea and develops there. The microbes that live inside of that biofilm are fermenting the tea, and as they do so, they're adding different flavors to the tea. It's truly a product that relies upon microbes.

So when someone picks up a bottle of kombucha at the grocery store and drinks it, are they ingesting microbes?

Yeah. They're definitely ingesting microbes, just like beer or how yeast makes bread, things like that. The SCOBY biofilm that I just described, that part of it is removed from any kind of commercial kombucha. You would really only see that biofilm if you made your own kombucha, which a lot of people do make their own kombucha. The one that we have in the museum is homemade kombucha. Otherwise, you would never see all those microbes at the top, however if you look closely, there's usually, in any kombucha, still some sort of fine material that settles at the bottom.

Sediment?

So there's definitely some microbes in there that you're drinking.

And are those microbes part of what's beneficial about the beverage?

This is a question that we get very often at the museum. I have to give a kind of boring answer, which is that we really don't know if kombucha is beneficial or not. It's one of many products that contain probiotic bacteria that have a lot of claims behind them, but we really don't know. There's not a lot of studies that show their beneficial effects. So it's kind of an early field, the microbiome field in general, and it's kind of early to say whether or not kombucha is beneficial.

The other thing is that because, for example, you and I have different microbiomes in our gut, you and I have some different microbes, and the microbiome varies, in general, from person to person. That means that we can drink the same kombucha and it might affect your gut community in a way that it doesn't affect mine, or vice versa. So it's just a very complicated field that we're just sort of getting a foothold in. That's why when people ask about these probiotic products, we have to kind of take a step back and say, "We really don't know right now if it's beneficial or not."

Recently, a friend told me that she drank a kombucha that she picked up at the grocery store, and she felt like she'd had a glass of wine or two. Does that happen frequently? Is that over-fermented? What's the explanation of that?

The explanation of that is definitely a microbial explanation, and that is because what you have happening, as this biofilm forms in kombucha, you have what's knows as an ecological succession that happens. It's really neat, if you think about the biofilm almost like a microbial forest, you can think about this ecological succession almost like a forest that's burned down. You know when a forest burns down, there's a certain order to how the saplings and the grasses come back, and recolonize.

Sure.

The same thing happens in the sense that you have an order of the different microbes that form that biofilm, and so the yeasts are the ones that come in first. They're growing off of the sugar in that sweet tea, and they're producing alcohol. That's where the alcohol is coming from. Then you have acetic acid bacteria that come in and they are feeding off of the products of the earlier microbes, and they're producing acetic acid, which is vinegar, so then it gets to be vinegary.

So it really does depend on the different kombucha, and particularly if you're making homemade kombucha, you can get all sorts of different flavors. You could get some that are more alcoholic than others, some that are more vinegary than others, depending on the SCOBY that you started it with, and depending on how long you let it ferment, et cetera.

That's interesting. I don't ever see on the kombucha in the grocery stores, I don't see like 1.2% alcohol. Are they not reporting on that or is it just not that well controlled yet?

Yeah, it should be one of those products that has some small percentage of alcohol, but not really enough to intoxicate you. But certainly, if you're making your own kombucha, and something goes haywire, then you could have more alcohol in there than in most products.

Interesting. Thanks so much for joining us today, Scott.

Thanks. It's always a pleasure to be at NEB.

And I just want to remind our listeners that if you have the opportunity, you should go see Scott's exhibit at the Harvard Museum of Natural History. It'll be there through September of 2019. You can also follow Scott on Twitter and Instagram @socialmicrobes. And, if you want to check out some of his amazing photography and learn a little bit more about him, then check out the website microbephotography.com.

I hope you enjoyed this episode of our podcast. Be sure to check out the transcript of the podcast for links to additional information. This is also a great time to mention that we're currently accepting application for the 2019 Passion in Science awards, so be sure to nominate yourself or someone you know who's passionate about their work in science. You can find more information about the awards as well as how to apply at nebpassioninscience.com.