Thomas

All right, Can everybody hear me? Okay? Thank you so much for coming to join us. This is our first science cafe and the Bangs community center and Science Cafe is now coming to you through Science Stories, which is a if you don’t know, a graduate student run science communication organization run by grad students at the University of Massachusetts Amherst.

Thomas

So in the past – Science Cafes have been running since 2011, bringing science to the Valley. In the past, we were under the organization name Life Science Cafe. We’ve merged with the That’s Life [Science] blog to create, sort of, one big umbrella science communication organization. So if you don’t know us, please check out our website and our social media pages at…

Thomas

Our website is sci-stories.org. It’s on some of our fliers. I’ll get you the website after the event. But we’re so grateful for all of you for coming out. This is one of our first Science Cafes back out in the community in person after our hiatus. So thanks for turning up, and we are excited to be here to talk about science with Dr. John Gibbons.

Thomas

So I’m going to introduce myself now. I’m Thomas. I’m a Ph.D. student at UMass and John here, we’re so excited to welcome him to talk with us here tonight. Dr. Gibbons is a professor in the Food Science Department at UMass Amherst, and he studies microbial domestication and population genetics, which we are about to hear all about. John earned his Bachelor’s in science and biology from Keene State College in New Hampshire, his Ph.D. and biological sciences from Vanderbilt University, where he worked in the lab of Antonis Rokas.

Thomas

I’m not sure if I’m pronouncing that right. Okay. Dr. Gibbons was also a postdoc at the Harvard T.H. Chan School of Public Health and then a faculty member at the biology department at Clark University for four years before moving to his current position as a scientist here in our community. So please help me welcome Dr. Gibbons. Hey, so John, we are here to mostly talk about your research in food science.

Thomas

But before we get into the technical stuff, we want to know a little bit about you. So what can you tell us about your introduction to science? What kind of got you interested, or how did you come to a career in research? 

John

Sure, yeah, I wish I had a nice back story, but I kind of floundered a little bit in high school and never, I wouldn’t say ever really was super drawn to science.

John

And I think it was college. So I played soccer my whole life and I really liked filmmaking. I made stop action movies when I was younger, and I went to – I chose Keene because I thought I could play soccer there and they had a film major. It was the only public school, I think, in the region at the time that had a film major.

John

And then I broke my ankle, which was actually like a blessing in disguise. And I, I got really serious about school and I took a non major course on speciation, and it, like, blew my mind. And I decided to major in biology after starting in film and going into psychology and then sociology. And I finally landed upon biology, kind of went from there.

Thomas

Very cool. So are you back to playing soccer at all? 

John

I am, yeah. But also breaking my ankle, I mean spraining it, all the time, but yeah. 

Thomas

Oh, no! No, that’s great to hear. I was kind of a high school flounder-er, so I love hearing from faculty who were the same. So speaking of your hobbies, as you mentioned, soccer, stop motion filmmaking.

Thomas

And before we get into science, I had to ask because you mentioned this in your email to us, that you do metal –  is it metal detecting or metal detectoring? 

John

Yeah, Yeah. I feel like, very feel very old talking about this. It’s like a very old person hobby I think. Yeah. So there are these really cool old abandoned towns all over New England and, and I go with my metal detector and try to find old coins and artifacts and stuff like that.

Thomas

What’s the coolest thing you’ve ever found? 

John

Oh, that’s kind of depressing. I don’t find much, but I find a lot of, you know, bottle tops. But we’ve had some buffalo nickels before and some really, really intricate, uh, padlocks from the turn of the century. There’s a place called Catamount in Massachusetts, pretty close by.

John

And it was a town at one point. And it’s a state park now, and if you hike it, you’re like, how did anybody live here? And farm here? It’s just all hills and rocks. So they got out, you know, by the early 1900s they were gone. But you can find artifacts all over.

Thomas

That’s really cool.

Thomas

So biology, you told us a little bit about how you took this non-major speciation course that kind of brought you to biology. So why microbes? I mean, you study food science, microbes. What was the sort of connection point for you there from the speciation course into food science? 

John

I don’t think I’ve ever been drawn to an organism.

John

For me, it was always the questions. And so, you know, I was in grad school. I was really lucky to get a great advisor, and I was his first Ph.D. student and he studied fungi. So I was like, all right, I’ll study fungi, why not? So he gave me a bunch of papers, my first, you know, the first week.

John

And he said, “What’s interesting?” You know, read these and let’s talk next week about what’s interesting. And I found some papers that I thought were really cool and we designed some projects off of that. But, you know, since then, through my post-doc and even after, we’ve worked on fungi, worked on humans, we had a polar bear paper, a polar bear genomics paper.

John

You know, I’ve been involved in virus papers. And so for me, it’s always kind of been the question.

Thomas

 So what are some of the questions that you’re seeking to answer with your work these days? 

John

Yeah, thank you. That’s the big picture. So, you know, this whole idea of domestication to me is just so fascinating, how humans could shape living things just by breeding them.

John

You know, it’s really wild. And so for me, there’s this historical aspect of it that is so interesting. It’s like you’re you’re you’re looking back in time and trying to figure out why did people do the things that they did. And so, you know, humans have been around for – anatomically modern humans – for 200,000 years or so. We spend all of our, or most of our history in Africa, and successfully leave 60,000 years ago.

John

And, you know, we breed with Neanderthals and all this stuff happens. And it’s only the last 10,000 years that we’ve learned how to farm and stopped, you know, following food around. And so that’s always been really exciting to me. And then, you know, you hear about dog domestication and, you know, maize domestication, but there are microbes behind that which also, you know, that were domesticated by humans.

John

And it’s something that isn’t talked about much but was so interesting to me. 

Thomas

So a lot of the time when those of us who aren’t in this field are thinking about molds, or fungi, or bacteria, we’re kind of thinking about pathogens, sickness or issues for human health. But there are some positive or sort of beneficial relationships-

Thomas

-you’re saying that we have had, historically and presently, some of these organisms. Can you tell us a little bit about some of those areas that we may not be thinking about microbes at work?

John

 Sure. I mean, well, so okay, imagine our whole history. We were trying to find food, you know, traveling seasonally to get food and to track animals.

John

And finally we’re sedentary and there’s an abundance of food because we’re farming.

John

But how do you preserve that food right now? The first time we ate, there’s an abundance of food, but it can spoil. And so you know, we think that most of the organisms that are used, microbes that are used in food production, are there because they’ve they’ve limited spoilage. 

Thomas 

Right. 

John

They’re increasing the length that you can eat food.

John

I mean, you think about raw milk. It will spoil in, you know, hours. And if you ferment it into a hard cheese, you can travel around with it at room temperature for four months. It’s really wild. So we’re trying to figure out, you know, what was this series of events that happened with microbes, and how did humans change their traits, and how do they change their genomes?

Thomas

So when I think about domestication in that sort of sense of changing genomes, I’m often thinking about dogs, cats, corn. So how would you define domestication? And then how do you domesticate, you know, something so small as a yeast or a microbe? 

John

Yeah, that’s the big question, how do we do that? So I think domestication, you know, you can define as humans breeding something in isolation from its ancestor and selecting for traits that are beneficial.

John

So, you know, if you think about dogs, you have this huge variety of breeds and they’re all bred for a certain trait,  it could be hunting or tracking or things like that, and they look very different from their ancestor. With microbes, you look at them and they look the same.

John

The wild ones and the ones that are used in food. So the idea is that, you know, this running idea, is there’s this process called backslopping. And so imagine a long time ago, you have this really good fermented thing. It could be like sake, rice wine. Okay. And so it turned out really good. And so you take a scoop out a little bit of it, and you put it in the new batch that you’re gonna ferment, hoping that it creates the same type of fermentation or the same product.

John

And so the idea is you keep doing that and keep doing that and you keep doing that. These microbes are basically getting serially transferred in the same environment generation after generation after generation, and they start adapting to the food that they’re grown in. 

Thomas

So this is, I mean, kind of similar to the process of keeping a sourdough starter or yogurt at home.

John

Exactly. You’re engaging in that same process. Yeah. 

Thomas

So can you tell us a little bit about  – that’s the sort of big picture of the questions you’re asking. Can you tell us a little bit about what your day to day research looks like? So are you in the lab making these sorts of media, are you sequencing? 

John

Yeah. So we have two models that we’ve kind of developed a bit. One is Aspergillus oryzae and one is Aspergillus flavus. So Aspergillus oryzae is a domesticated mold that’s been used for thousands of years. It’s used to ferment rice products and soy products. So sake, soy sauce, miso. These are all products of Aspergillus oryzae. We know in the wild there’s Aspergillus flavus.

John

And if you look at their genomes, they are 99.5% identical. It’s like if you look at the person next to you, you’re sharing basically the same genetics, you know, that amount of difference. Super, super similar. So we have been studying their genomics and the evolution of Aspergillus oryzae and flavus. I started this in grad school and we’re still working on it.

John

And we are, you know, we’re sequencing. We get as many strains as we possibly can, and we sequence genomes and we use those sequences to try to infer their evolution. 

Thomas

So to sequence the genome, to give us an image, if I walked in when you are at work, are you at a computer, are you sitting down at a machine?

John

Yeah, unfortunately, the people here do most of the work. So we have some grad students here, Adenike, and Nadia,  and Ezra is an undergrad that all work in our lab and they do most of the lab work. I wish, I love going up into the lab and putting them on to doing stuff, but yeah. So basically, we are growing these molds and they grow in anything.

John

If you give them water and a carbon source, they will grow. They’re generalists. And so we have some standard media that we grow them in. And then basically you’re taking some of that fungal tissue, grinding it up and trying to extract DNA from that. So with that DNA, you send it off to – we sequence its genome – we send it off to a company for sequencing, and then it’s always a happy day when it comes in and then we get to start processing it.

John

And UMass has this great, it’s a shared supercomputing cluster that we do all of our analysis on. So that’s usually like, you know, I will get it in that stage or, or even a little later.

Thomas

Yeah, some of the big datasets. So I want to talk a little bit more about some of this recent work that you’ve been doing with that genomics.

Thomas

But I also want to pause. So we’re going to take a couple of breaks during our conversation with John so that as questions come up for you all in the audience or on Zoom, you get the chance to ask him things. Before we move on to other topics, I’ll pause here for a minute. And if anybody has a question or if anybody in the Zoom Room has a question, raise your hand or your Zoom hand and you can come up to the microphone or I can try to bring it to you.

Thomas

Thanks. That way we will catch you online. Yeah. 

Audience member

John, I was wondering if any of your Aspergillus strains have become pathogens or degraders or have you seen that at any point in the sort of co-domestication? 

John

Yeah, that’s a good question. So Aspergillus is this really big genus of fungi. There’s, you know, 300 species or so and we call them – 

John

– My advisor Dr. Rojas used to call them the Dr. Jekyll and Mr. Hyde of fungi, because you have pathogens that cause lung infections and kill hundreds, thousands of people a year and you have these other species that are used in food fermentation and to make drugs, and to make citric acid, and you use them quite a bit.

John

So there are cases of people getting a fungal infection that work in sake brewing because they’re in constant exposure to these spores. Typically they’re not pathogenic Aspergillus flavus, the wild one is rarely pathogenic, it can happen. But there is a species called Aspergillus fumigatus that is like a super infection agent for people that are immunocompromised.

John

We have some experiments that we’re trying to go in the opposite direction. So we start with the wild one and we’re saying, All right, if we keep growing it on rice and keep growing it on rice and keep growing it on rice, can we get it to look like the domesticated one? Can we mimic domestication in the lab?

John

And that’s work that is kind of still in progress. 

Thomas 

I’m glad you’re going in that direction. The other one is kind of,  mad science, evil genius, right?

John

Yes. Right. 

Thomas

So you have this recent paper where you are looking at – Oh, yeah, sure. 

Audience member

So I have a question. You are in the food science department. Do you consider yourself more of a food scientist or more of an evolutionary biologist? And what do you think the difference would be? 

John

Yeah,  I am definitely not a food scientist, but we do a lot of research that is food based. So I’m definitely, you know, I was trained as an evolutionary biologist and as a genomicist and I’ve loved getting into the food science department. So we work on these food microbes.

John

We also work on other types of fermented foods that are spontaneously fermented, and we work on bacterial pathogens – the foodborne pathogen listeria. So we have you know, we work on other food systems, but for me, there’s so much application, it’s so much more applied. And I found that l super interesting and also very, very challenging at times too.

Thomas

It’s very present in our lives.

John

Yeah. Yeah. 

Thomas

What is spontaneously fermented?

John

Yeah. Great question. So cocoa beans are an example. Cocoa fermentation. So –  chocolate is actually fermented, it’s in these big pods. You open the pores and there are these white fruits that are in there. And they’re just basically heaped, and whatever is in nature is fermenting them. So this could be from, like insects flying in that have microbes on them, and crawling around.

John

It could be from whatever is native to the outside of the pod. Environmental dust that’s rolling around and lands on it, that’s in the wind. These are spontaneously fermented from things that are in nature. Yeah. 

Thomas

Got it, it’s really just kind of picking up on wild microbes. 

John

Yeah, but very reproducible, which is really interesting. 

Thomas

Yeah. So I think – are there any other questions at this point, or we can keep going, we’ll have more breaks for questions.

Thomas

Do you have a question? Okay. So I want to ask you about this Aspergillus? Aspergillus research you’ve been doing. So you were looking at these Aspergillus strains that are used in sake fermentation in this recent paper that just came out of your lab, and looking at populations that are used in food production and comparing them to their wild ancestors.

Thomas

So first question, can you make sake from both of these organisms? And if so, are the domesticated ones better? 

John

Oh yeah. Cool. Really cool question. So you wouldn’t want to do it from the wild ones because they produce – many of the strains in the wild produce toxins, and some of them are super potent. So you’ve probably heard not to eat moldy peanut butter.

John

It’s because it can be Aspergillus flavus or Aspergillus parasiticus, which produce aflatoxin, which is the most carcinogenic compound that we know of that’s naturally occurring, which is wild, right, that a fungus produces this. And so in the U.S., it’s federally regulated because it can contaminate crops, stored beans dried in silos. If it’s too moist, you can get fungal growth.

John

It’s regulated in milk, because of feed. So, you know, you’d never want to have the wild fermented sake.  

Thomas

So domesticated sake definitely is better. 

John

Yeah. But thanks for bringing this question. We actually haven’t published this yet, but Dylan McCarthy, who is a master’s student in the lab, has done just that. He’s basically fermented rice with some of our wild ones and some of our domesticated ones.

John

And then we do something called GC Master, where we’re trying to pick up on the volatile compounds that are present in our samples. So while it’s fermenting, what kind of odors and aromas is it giving off? And you know, in some of the literature they say that the wild ones give off like more of a musty, earthy smell, and the domesticated ones give off what someone has described as like this sweet grapefruit smell, a little bit cheesy too – 

John

Which, you know, it doesn’t sound great for sake. So we did this analysis and we figured out, you know, we identified which volatile compounds are present in the samples. And what was amazing is the domesticated ones actually produce like 25 or 30 more compounds than the wild ones. And these are – many of them, or most of them were associated with these very pleasant floral odors.

John

Which is really cool. 

Thomas

But a taste test is off the table.

John 

Probably with the wild one, yeah. But, it used to be a hobby before I had kids, yeah, was home brewing sake.

Thomas

Yeah. Cool. Yeah. So you found some of these differences recently in these volatile compounds. With the population genomics work you’re doing, comparing these lineages –

Thomas

– what kind of difference did you find? 

John

Yeah, so the work I think that you’re talking about is actually with a different pair of species, something that Kim Acevedo, who’s a PhD student in OEB has been working on for her thesis work and has done some really exciting work. So, sojae is the domesticated one and parasiticus is the wild one.

John

And sojae is really used for soy fermentation, not for rice fermentation. And so she sequenced the genomes of 20 of these. And then there’s all this public data. So we’ve analyzed maybe 40 strains of the two different species. And when we look at how they’re related to each other, what comes out is that there are four major groups of the wild one, which is consistent – like you have, different populations in nature. And the domesticated one is a very tight population with almost no genetic diversity.

John

And so that’s telling us is that, you know, whatever strain was used initially was then, you know, was basically clonally evolved. And so it’s used in all these other…  we have them  from Korea, from Japan, from China, and they’re all pretty much the same genetically. So it was kind of a little bit surprising because the other comparison we look at the oryzae – flavus comparison is a little different, you know.

Thomas

So that’s kind of a strong indication that it’s this really specifically domesticated or cultivated population?

John

Yeah. Yeah. 

Thomas

Is that indicating that it’s from a single source lineage? 

John

Yeah, that’s one of the cool parts. So one of these wild populations is most closely related to the domesticated population. And when you look at the genetics, the wild ones, you see both the signatures of the wild genetics and some of the domesticated genetics, which means that, you know, much of the genetic variation that you see in sojae was already existed in nature and what we call it is standing genetic variation that already existed.

Thomas

Yeah. So sometimes we think of reduced genetic diversity in a population maybe as being a bad thing or,  for our food systems, a point of vulnerability.  Is this sort of  – in this domesticated population where you’re seeing less genetic variation than the wild type – is that kind of comparable to what we would see in maybe other domesticated food crops or other domesticated species?

John

Yeah. Yeah, it’s a great question. One of the big signatures of domestication in plants and animals is seeing a big reduction in genetic variation in the domesticated populations. And the same is true for fungi. So with our examples, with Aspergillus sojae and Aspergillus oryzae, there are some groups in France that look at the Penicillium fungi that are used to make Camembert cheese and blue cheese, and they’ve actually said the genetic variation is so low in the blue cheese fungi that we have to, we have to think about conserving it.

John

How do we conserve these? The caves are getting warmer because of climate change. And they’re trying to figure out ways to actually preserve the fungi. 

Thomas

Wow. That’s an interesting question. And I mean, I was going to come to this later, but maybe that’s a good time to ask this question. So since you’re working on these organisms that have these significance for food systems and kind of these histories of domestication and cultivation, what are the cultural impacts of your work? Is this shaping how people are thinking about these historical traditions, thinking about carrying these foodways into the future with changing climate and that sort of thing?

John

Yeah, that’s a good question. I don’t think our work is that exciting, but I do think it gives you a window into the past. And I think that is worth a lot. And when you think about the history of fermented foods, I mean, they’re like sacred in human culture, especially the ones that have alcohol.

John

So like, sake is used, in traditional Japanese religion in, Shinto, it is sacred, sake is. You know, and  wine is quite literally in the Catholic Church, you know, the blood of Christ. And pulque, which is a traditionally fermented Mexican drink from agave sap, is sacred. And there’s, you know, Mayan paintings that depict it. So, you know, culturally fermented foods are really really important.

John

And I think that’s what I always kind of come back to. 

Thomas

So to kind of get to that historical perspective that you started out with, can you imagine – this is kind of speculative, but if we had never domesticated these microbes or kind of entered into this relationship of domestication,  I don’t want to like, attribute it all to humans…

Thomas

Who knows? Maybe the fungi have some agency in this process, and maybe you can speak to that. But if these organisms had never been domesticated, how do you imagine our world might look different today? I mean, no sake?

John 

No sake.

Thomas

So that’s a bummer.

John

It is a bummer. Yeah. I mean, they’re such an intricate part of our lives, and so many food systems use microbes and, you know, it’s weird.

John

They’re popular now, like fermented foods, right? People like kombucha. And you can find it everywhere. And, you know, we don’t have life, we don’t have food without microbes. So much of traditional food is fermented, you know, traditional pickling and so on. 

Thomas

Yeah, yeah. So when we think about, like the contemporary context of that fermentation, you know – I’ve done some home brewing, I’ve baked with sourdough and that sort of thing, and I get yeast like online and it comes in a little packet and I keep it in my freezer and I have no idea.

Thomas

I’ve wondered, with baking yeast or brewing yeast, where is that coming from? So for these domesticated any of these sort of organisms that you’ve touched on that are used in food production, where they’re being domesticated, are there farms? Or factories? Or where is that being grown? What does that process look like?

John

Yeah, that’s a really good question. So the process of – maybe I could back up. So the way that the sake is fermented is, you steam your rice and you put it on a very flat surface and sort of cool it down.

John

And then you’re adding this mixture called Koji, which is… it’s wood ash and it’s spores and it’s dried rice. And that is what’s actually like sort of sprinkled onto the rice to start fermenting. And so that can be dried, and that’s grown for a few days and it can be dried and used again as your, you know, your new batch of Koji.

Thomas

Got it. So kind of making a starter. 

John 

Yeah. 

Thomas 

A little bit of the previous batch.

John

Yeah, but the nice thing about molds is that you can … they are super resistant and resilient and once you have spores you can keep them almost indefinitely. 

Thomas

Right. Dry them out and wake them up again. 

John

Yeah, exactly. 

Thomas

Now it’s going to be a good time, maybe for any other questions from the audience or from the zoom room. Take another little question break. Yeah, Elsye, yeah. 

Audience member

So in thinking about what you just talked about with the whole sprinkling of your inoculum onto the rice. How stable, or like how much fidelity do you have, in any given thing? Like if you think about Richard Lenski’s evolution experiments, those microbes are just like splitting all the time.

Audience member

How phenotypically stable are these microbes?

John

Yeah. Huh. Well, they haven’t started metabolizing new stuff like the Lenski experiment which is, I guess that’s good. They’re pretty stable. But like with oryzae especially, you have strains that are specialized for different things. So for different sensory attributes, for different, you know, protease activity or amylase activity, things like that.

John

Actually, that’s one of the cool stories with Aspergillus oryze and Aspergillus flavus. So when we’re eating food, and you’re chewing food, in your saliva, you have the salivary amylase enzyme that’s being produced, helping you break down carbohydrates. And in human evolution, that gene has actually duplicated within the genome in populations that have starch rich diets, which is really wild. The same thing has happened in Aspergillus oryzae.

John

So the wild ones have a single copy of this Alpha amylase gene, and the domesticated ones have two, three, four, sometimes five copies of the same gene, which is really amazing. And some of our work from a couple of years ago with Katherine Chacon-Vargas, who was a Ph.D. student here in MCB, she actually discovered that they have evolved completely differently.

John

So there are copies that are on chromosomes that we wouldn’t expect them to be on. They’re kind of hopping around everywhere. And the more of that gene you have, that typically correlates really strongly with the amount of amylase that you’re producing. So they are actually evolving, you know, they are actively evolving. Yeah. 

Thomas

So I’m going to cut in because I have a kind of a related question. So I work with plants, I have a little bit of background with agricultural mammals as well.

Thomas

And I know in some cases of domestication, when we look at these histories, we see like domestication syndrome where certain traits kind of come along with domestication, by accident in some ways. So like coat color patterns or floppy ears in mammals, there’s sort of a set of traits in plants. Are there across maybe some of the different species that you’ve worked with, for domesticated species, obviously not floppy ears, but some some other kind of patterns of, you know, consistent changes in some phenotypic traits?

John

Yeah, Yeah. That’s how we got a grant for this – trying to say, is there like a fungal domestication syndrome that we can define? And you know it’s tricky because there’s exceptions for everything.

John

But in fungi, it looks, in filamentous fungi, at least, it looks like there’s a loss of secondary metabolism. That’s one of the big domestication syndromes. So secondary metabolites in fungi are these compounds that many times are defense chemicals. So they’re used to… imagine, you know, fungi are weird and they digest their food externally, and then they try to like, reabsorb the nutrients.

John

And so when the nutrients are out in the soil, there are competitors also on it, because it’s like very easy nutrients, right? So they’ve evolved this amazing array of arms, of different toxins and secondary metabolites. And actually aflatoxin is one of those that we talked about before. And when you look at the domesticated ones, it looks like, for the most part, they’ve lost a lot of that ability to produce some of these toxic secondary metabolites for these toxins.

John

And there’s, you know, a few different explanations or hypotheses. One is that they don’t need them anymore. You don’t have any competitors in the food environment. You have all the food you could ever want. You know, and it’s stable and there aren’t competitors. And so they’re wasting energy producing these. And these compounds take a lot of energy to produce.

John

So you’re freeing up energy now from making toxins, to actually eat for primary metabolism. And so that’s one of the big ideas, this is probably the biggest characteristic of fungal domestication. 

Thomas

Yeah, that makes sense. I mean, that sort of sounds like these mutualistic relationships we have with other species, they don’t need to hunt anymore or whatever it is, spend so much time foraging.

Thomas

Great. Any other questions? 

Audience member

Yes. All right. So, you know, go co-ops. We love co-ops, but also, it’s kind of an oversimplification to think that we can have local ag and local meat production in every town, in every city. And so, you know, I think from a public health lens, you have to consider that there’s going to be really large industrial suppliers of meat ag.

Audience member

And then, you know, as you think about macroeconomics with that, you’re going to increase your supply chains by having single distribution points. But with that –  Boar’s Head listeria outbreaks, etc. What advice would you give to major industrial suppliers of these products so that you can continue to do this cheaply and, you know, make sure people can afford them, but also, you know, prevent adverse public health dynamics?

John

Yeah, I don’t know if I should be answering this. Yeah, I’m going to get sued or something. 

Thomas

We’ll redact that company name mentioned. 

John

Yeah. I mean, having large scale food processing facilities is really scary, right? Because a pathogen can be introduced at almost any point and you’re in trouble and it could just sort of replicate.

John

So, really we know what practices we have to sanitize surfaces and things like that. It’s just harder to do it on a big scale. I don’t know if I should be giving advice on that. So yeah. But, you know, really good sanitization is probably the best that we can do. 

Thomas

Other questions from the audience right now,  a couple more?

Thomas

Well, maybe following off of that, you know, in terms of public health or consumer safety, there’s the side of it that you just mentioned with the scary of listeria outbreaks. But then also, like you said, fermentation is really hot right now. You’ve got kombucha, everybody started making sourdough. And there’s all kinds of information out there about prebiotics and then probiotics and all kinds of… I don’t even know all kinds of other things.

Thomas

So it feels like a sort of a complicated information landscape, you know, on this complicated topic that I don’t know much about. So what do you think that those of us who aren’t scientists in this field should sort of be thinking about in terms of taking care of our bodies, our food, but also finding information and you know, where should we turn to to learn what we need to know about these topics?

John

These are the hardest questions. I wasn’t ready for these. I mean, diet-wise study and study and study, again, have basically shown that the more fiber you eat, there is no upper limit. The more fiber you eat, the healthier you are. And part of that is because you’re feeding your microbes, Right? The fiber has all these really complex carbohydrates that your body can’t digest, that are feeding your microbes.

John

And there’s so many benefits to, you know, to having a healthy gut microbiome in terms of like, inflammation, you know, anti inflammation and things like that. You know, my partner had a product recently and I looked at the label and I was like, Hey, it says Aspergillus oryzae on there! And you know, they were using alpha amylase, this enzyme in this product as like a, you know, as a probiotics or a prebiotic.

John

So, you know, the FDA isn’t involved in a lot of the probiotic research. You know you don’t have this governing body that looks at this stuff. So it is hard to get good information. And I’m not sure I want to lead anyone down the path to a certain source. 

Thomas

Yeah. Sure, well, now that I’ve asked you maybe erroneously to give advice to anybody who eats food, let me, let me narrow it down a little.

Thomas

Does working in this field generally, in any way, has that changed how you cook, or how you shop, or how you eat? Are there things that you will eat that other people won’t or things that you won’t eat, that other people will? 

John

That’s a good question. I’m pretty adventurous eating, I think. But we have kids who are kind of picky, so I cook the same kind of stuff every week. But yeah, I’m trying to think, I just lost my train of thought. Sorry, what was the big picture question?

Thomas

Just sort of, has it changed how you shop, or…? 

John

Oh, yeah. So yeah, thank you. So I went, when I gave my teaching talk at UMass, it was on the gut microbiome and diet and how they influence each other and that actually – just by creating that lecture and really thinking about it, did change the way that I eat.

John

And I am mostly plant based now, and it’s really changed. It has changed the way that I eat. Yeah. I don’t think I thought about it as much before I got into this department

Thomas

Do you have a particular favorite fermented food or drink?

John

I do love sake. I have a special place in my heart for sake. And there’s actually a sake brewery in Massachusetts now near Boston called Farthest East and that makes unbelievable sake. It’s one of the only sake breweries I think in New England and there’s only a few in the U.S.. 

Thomas 

Wow. Thanks for the recommendation. All this sake talk is making me wish we could have sake here tonight. 

Thomas

Do a little a taste test, but we have to get all this approved through the UMass Finance office. So you wouldn’t believe what that process is like. I think it would be a no-go. Um, so I want to ask you a little bit. We kind of have talked about your research work, but you’re an educator, too. You know, I’m so glad some of your students are here.

Thomas

Um, can you talk a little bit about how you see your role as an educator? 

John

Yeah, sure. I mean, for me, the most exciting thing about teaching is helping people find what makes them curious. You know, what, what actually makes you curious? What are you driven to think about?

John

And so,  in all my classes, that’s kind of what I strive for. Like what? What are you passionate about? And maybe you don’t know what it is. And that’s part of the fun. So there are some courses that I teach that are kind of more applied in terms of doing analysis and I teach a graduate genomics course.

John

It’s called Food Science for Genomics, but I’ve had students from all different departments take it.  And many of them don’t have any experience doing genomics work. And so part of the class is actually doing your own, your own original projects that you have to take ownership of. And it’s amazing because some people end up using this in their PhD work after or get a job in the bioinformatics field or genomics field and figured out that they actually really like it.

John

And so it’s like empowering people to find, you know, what makes you curious and, and giving people new tools.

Thomas

 That’s great. So in terms of that support of your students’ curiosity, you’re also the chair of your department’s workplace climate committee. Can you say a little bit about what you’re hoping to do in that role or sort of what you do to build community?

John

Yeah, over the last few years…So one, one thing we did last year was we had a graduate student town hall. We have so many graduate students in Food Science. I think there’s over 60, maybe 70 or 80. And our building is very tight and old and, it was just basically we held this town hall, basically as a forum to ask graduate students, what is going well? Or what’s not going well?

John

What do you like about our department? What don’t you like? And the idea is to get, you know, confidential feedback back, honest feedback, and see what we can do better as faculty. I’m really looking forward to presenting that to our department to say, here’s what we have, here’s what we need to do better, here’s what we need to improve on, and here’s what’s going well.

Thomas

Yeah, that’s great to hear about. So, kind of the results of that are pending, and then you’re presenting that to the department? 

John

Actually, we’re waiting for the grad student organization in Food Science to approve of our notes so that we can then have that discussion.

Thomas

Yeah, yeah, it’s great to hear about. I want to pause for – I’ve got one or two more questions but if anybody else, we’re getting close to the end of the hour here… so if there’s other things that come up, on anything we’ve covered… Anything in the chat, Matt? 

Audience member

Hi John, on this aspect of mentorship what advice would you have to graduate students who are thinking of pursuing research? 

John

So yeah, that’s a really good question.

Audience member
Or are in grad school right now?

John

Sure. So finding the right fit, finding the right advisor. And I know that I’m probably not the right advisor for certain students. Really, really, really finding the right fit. You know, some people like to be micromanaged and want to have more structure, and some people want to have, you know, be kind of free to do their own thing.

John

So I think it’s so important to find the right advisor. You could love the project, but have a really bad relationship with an advisor if you don’t align well. So I always encourage, whenever someone is applying for our lab, I really encourage them to, like, reach out to every graduate student, every undergraduate in our lab, and talk to them about how their interactions and their relationship with me is, because it might not fit for you.

John

And, you know, if you’re going to graduate school, you’re gonna be working on something for two, three, four, five, six years. And so you want to really love what you’re doing or it’s going to make that period really tough for you. Yes. 

Thomas

Other questions from the audience? Maybe I just have like two more questions as we kind of close ourselves out and then if any folks want to chat in the last few minutes we can. Sticking on the topic of sort of mentorship and teaching. When you think you know, over your career so far, are there any lessons, big or small, that really stand out that you’ve learned from your students?

John

Yeah, I mean, I know when to say “I don’t know”. And I think that’s such a valuable lesson. We’re not supposed to know everything. So I actually love getting stumped. And it happens often. But, you know, it’s a chance to really think about things. And to be honest, I think, you know, the way that we think is more important than what we actually know.

John

So a lot of times it’s just thinking about things deeper. Um, you know, for me, I was always very nervous to go to graduate school because I didn’t think I was good enough, you know. And most people have, a lot of people have imposter syndrome. And, um, you know, everybody feels that way.

John

It’s a really important message also. At some point, that feeling is held by almost everybody. So just knowing that you’re not alone in that feeling is really important. 

Thomas

Yeah, that’s good. Thanks. So what’s kind of what’s coming up next for you? Maybe even idealistically, what do you hope is coming up next for you?

John

Yeah. So with the domestication work, I feel like every time we do something, it uncovers a thousand new things to look at. So, getting more into the food science aspects of the volatile compounds and the sensory attributes and all that stuff is super exciting to me. So that’s one place that we’re moving into is really trying to figure out, how are these things different based on the compounds that they produce and the smells and the taste that they produce.

John

And then we’re also so Ezra and Kim are – we have this hypothesis that… so, miso fermentation, for example, there are many, many different bacteria and fungi and yeast that are involved in that fermentation process. And we want to know how they interact with each other. You know, how do we get this consistent product every time?

John

How are they not dying off at certain phases? And it follows a very clear path of fermentation. And so we’re trying to figure out, we’d really like to know some of the interactions between… how are they feeding off of each other. Um, figuratively and literally, you know, how are they actually feeding off of each other? So that’s another kind of big place where we’re going.

Thomas

Yeah, I’ll look forward to hearing about that and it sounds really interesting.  So last question, unless there’s any other audience questions after this. What’s your favorite thing about being a scientist?

John

Oh, by far, my favorite thing is like discovering something new. There’s nothing like that feeling. It’s like scoring a goal or something, you know.

Thomas

It’s like finding a buffalo nickel. 

John

Exactly. Thank you. Yeah, well, we’re full circle now. Yeah. Yeah. There’s nothing like discovering something that’s never been discovered before. It’s the coolest thing you can ever experience. And, you know, I feel so lucky in this job that I get to just ask questions. And try to answer them. And sometimes they don’t get answered. But you get this rush from finding these very, very interesting things.

Thomas

Yeah. Well, we’re lucky to have you answering our questions tonight. We’ve got some good recommendations, too, for the sake distillery, brewery and for the best metal detecting spot so I think we’re all taking home a lot. Anybody else want to ask any last questions of John? And otherwise, we can wrap up and chat and eat some pizza.

Thomas

All right. Thanks so much. Please join me in thanking John.