01;15;05;04 – 01;15;32;07
Victoria
Welcome to Beyond Lab Walls, a podcast from the Salk Institute. Join hosts Isabella Davis and Nicole Mlynaryk on a journey behind the scenes of the renowned research institute in San Diego, California. We’re taking you inside the lab to hear the latest discoveries and cutting edge neuroscience, plant biology, cancer, aging, and more. Explore the fascinating world of science while listening to the stories of the brilliant minds behind it.

01;15;32;10 – 01;15;52;02
Victoria
En Salk, desvelamos los secretos de la vida misma y los compartimos más allá de las paredes del laboratorio.

01;15;52;04 – 01;16;07;27
Isabella
Today we’re joined by Jeremiah Minich, a trained marine biologist that studies microbial ecology, fish, fisheries, and aquaculture. Welcome to the podcast, Jake. Let’s start at the beginning. Where’d you grow up?

01;16;08;00 – 01;16;36;08
Jake
Yeah, so I’m from rural Pennsylvania. Perry County. So we don’t have any red lights in the whole county. We had, like, one McDonald’s that I worked at when I was in high school. This is very small, very rural. I grew up there my whole life. 18 years. Basically, the things you do there are, you know, sports and hunting, fishing, did a lot of hiking.

01;16;36;10 – 01;16;39;25
Jake
And yeah, that was essentially my childhood.

01;16;39;27 – 01;16;44;28
Isabella
Were you always curious about nature and science or did that come later in life?

01;16;45;00 – 01;17;16;10
Jake
None of my my parents went to college or anything like that, but I grew up hunting and fishing like most of the other kids, and just being an outdoor enthusiast, you just fall in love with nature and understanding, like how animals move around, what makes the environment important. And most hunters are pretty active, like conservationists. So it’s the sort of thing where you want your kids to have these same experiences that you did.

01;17;16;13 – 01;17;21;26
Jake
We want to protect nature and enable it for future generations.

01;17;22;03 – 01;17;23;28
Isabella
That’s a great shared sentiment.

01;17;24;00 – 01;17;48;13
Jake
I’ve always been interested in that. Science wasn’t really something I was necessarily interested in. It was more probably through hunting and my first dissection of a deer. I think I was probably like 10 or 11. My dad got a deer. And then just seeing like that process and just seeing the anatomy is pretty wild, like just was fascinating.

01;17;48;14 – 01;17;53;21
Jake
Got me super into just like anatomy and physiology.

01;17;53;24 – 01;18;02;12
Isabella
Is there a moment you remember in high school maybe where you really thought, oh, I should go to college and study science, study biology?

01;18;02;15 – 01;18;28;05
Jake
When I grew up and I was, like interested in biology and whatnot, most of us only understood that you become a medical doctor. So I didn’t really even have a sense, even knowing that, okay, there’s like conservation stuff, a game warden, like, you’re either become like a police officer of the nature or you become like a medical doctor.

01;18;28;07 – 01;18;55;15
Jake
That was kind of the extent of what I understood. So I didn’t really have like a moment that I was like, oh, I’m gonna definitely not go into marine biology. And it wasn’t until I did a year of college on the East Coast at a small school, and then I transferred out to the West Coast, and that’s probably when I really kind of fell in love with fish, marine biology, because I would fish all the time.

01;18;55;17 – 01;19;09;14
Jake
I got into spearfishing and I was like basically hunting underwater. And that’s when I really started to understand, like how many different species of fish there were and then how fish can be important for our nutrition.

01;19;09;16 – 01;19;13;16
Isabella
Were you hoping to get out of Pennsylvania when you went to college?

01;19;13;19 – 01;19;35;25
Jake
I was so like, I mean, it’s a great place to be raised, but it’s so it can be so boring, you know? I played competitive paintball throughout high school, and that’s actually what brought me to California the first time I played a tournament in Huntington Beach. And then when I visited, I was like, holy crap. Like, this is, pretty, pretty nice.

01;19;35;28 – 01;19;41;29
Jake
And then when I then went to visit San Diego, I was like, yeah, this is where I’m gonna move.

01;19;42;01 – 01;19;51;11
Isabella
And once you transferred out to the West Coast, you started studying biochemistry and taking some Spanish. What inspired those choices?

01;19;51;13 – 01;20;15;27
Jake
So biochem is, I mean, it was silly. Like, I just. I was on the med school route, and somebody was like, I heard somewhere that “Oh, you should do, like, the hardest thing. That way you’ll have a better probability of getting into med school.” And I thought biochemistry is harder than biology, so I just did biochem and then Spanish. So I had a really amazing Spanish teacher in high school, Señora Simonton.

01;20;16;00 – 01;20;51;05
Jake
She was the best teacher I ever had. And I took all four years in high school. And I’m not really even sure why I decided to do it in college, and then it turned out, yeah, in San Diego, it comes in, it comes in handy pretty often. And ironically, I married a Brazilian, so now I basically speak Portuguese and most of my Spanish has disappeared.

01;20;51;08 – 01;20;53;25
Isabella
So after all that, what did you do?

01;20;53;27 – 01;21;23;21
Jake
I got really bad grades, and I couldn’t go to med school, so I basically, I lived in a tent on Sunset Cliffs for two summers and trying to figure out my life. I worked in a restaurant and I think during my senior year, I basically I just started emailing the different fisheries, NOAA fisheries offices around the US and like cold emailing, saying, “Hey, are there any internships?”

01;21;23;23 – 01;21;47;20
Jake
Now of course this was like 2008, 2009 right at the around the housing crisis. So there are a lot of challenges with funding and stuff, which I didn’t understand at the time, but I very luckily somebody from Northwest Fisheries like, “Hey, yeah, you can come volunteer on a three week cruise where we, you know, catching hake.” I didn’t know what that fish was.

01;21;47;23 – 01;22;15;29
Jake
But basically, if you eat fish sticks from like Costco or anywhere, it’s it’s probably made out of hake. I basically took off from my restaurant job and went on this cruise was amazing. And then I got back and didn’t have a job. It was a, it was a hard time. And then, you know, at Southwest Fisheries, I basically was just applying for stuff and they had got a bunch of money from government or whatever to hire a lab technician.

01;22;15;29 – 01;22;23;29
Jake
So I joined Southwest Fisheries in their genetics lab doing genetics of marine mammals.

01;22;24;02 – 01;22;29;10
Isabella
Did you feel like when you were there you are really happy doing that, working in the lab? What was that like?

01;22;29;10 – 01;22;49;20
Jake
You know, young kids that grow up, they’re like, oh, I want to be a marine biologist. I want to work with dolphins and whales. And I was like, oh, this is okay, but I want to work with fish, you know? So in that sense, I wasn’t super stoked, but I realized that a lot of people wanted to be in that position.

01;22;49;22 – 01;23;25;17
Jake
But in terms of the lab space, like doing stuff in the lab, it was all pretty new to me and I learned all my molecular biology there. So I was there for three years and I got to do some field work, and I realized that I was pretty good at that. And I think just from my time as a kid, spending time outside, I was really like, good at just whether it was like counting whales migrating, you know, being able to just sit there for hours looking for spouts or like go out and we would take biopsy samples of dolphins so you’d have a crossbow be over the bow of the ship as a dolphin or

01;23;25;17 – 01;23;34;11
Jake
whale would, you know, surface and you could take a small skin biopsy. And then I kind of fell in love with the field work aspect.

01;23;34;13 – 01;23;43;15
Isabella
That’s super interesting coming from rural Pennsylvania ending up out in the ocean. It must have been very fun. What made you decide to go back to school?

01;23;43;15 – 01;24;11;10
Jake
So after I worked at fisheries for three years, and then I always had this passion and interest in aquaculture and sustainable fish production for the purposes of human nutrition. And I then worked at Abbott for three years. And then while I was there, I basically was like, okay, my undergrad grades are really bad, so if I want to do more schooling, I need to, I probably need to go do a master’s.

01;24;11;10 – 01;24;35;12
Jake
So I applied to a bunch of PhD programs—didn’t get in, didn’t get in, didn’t get in. And then I was like, okay, I’ll just do a master’s. So then I got into a master’s program. And during that time, that’s when I started learning about metagenomics and microbiome stuff, worked on seaweed at the same time as working as basically a scientist in an R&D division at Abbott.

01;24;35;15 – 01;25;06;09
Jake
And at that point, after about a year or two, I had the opportunity to go to Malawi and basically work with this NGO to kind of figure out their aquaculture situation. So they’re basically an organization that takes care of kids, kids that have 1 or 2 parents who are not with them, and then they also have homes where these kids are taken care of and you have all these kids, they need to be fed.

01;25;06;09 – 01;25;38;29
Jake
So they had farms, production systems, and they had had aquaculture systems in the past, and they were interested in really beefing those systems up, getting them back online. So I went there as a consultant to basically try to figure out what needed to be done to have a sustainable aquaculture system. I had the opportunity to go there, and it’s when I met these kids and work with them and I realized like, wow, this is, a way that I could produce fish for these kids.

01;25;39;01 – 01;25;42;12
Isabella
Yeah. You were really able to see your impact in action.

01;25;42;15 – 01;26;06;22
Jake
That was really awesome. And then I later on applied for a Fulbright program, which if you’re out there and you are an undergrad, you should absolutely look into a Fulbright and apply for it. It’s basically a study abroad in most countries around the world, and you get about nine months of stipend. You can either do research or you can do teaching.

01;26;06;25 – 01;26;33;23
Jake
And basically I applied to do a research program to go back to Malawi to look at how can we do better in terms of sustainable aquaculture production. And when I, when I was living in Malawi doing this, this Fulbright, that’s really when I was like living there with these kids—I lived with recent high school graduates—and that was when I was like, yeah, I need to like do a PhD.

01;26;33;26 – 01;26;54;20
Jake
I need to go as far as I can because a lot of these kids, right, they don’t have the opportunity to go to college, even or even high school. And so that’s why I wanted to go back to school and do a PhD and to go as far as I could so that I could one day leverage that education to to then help these communities.

01;26;54;22 – 01;27;06;14
Isabella
Was the reason you originally went out there related to food scarcity, or was it more like looking for opportunities and then finding out you did have this passion for helping with food scarcity problems?

01;27;06;16 – 01;27;30;25
Jake
I should back up and say that when I was in fifth grade, my mom was in a car accident and she survived, but she became physically disabled and eventually that led to her going on disability. And through all that time, my community there would basically, she had so many surgeries, I don’t even remember, but I do remember getting meals all the time.

01;27;30;25 – 01;27;54;03
Jake
Every time she was in a surgery, our community would bring us meals, and that was something that really struck me. A lot of times I didn’t like the food, but it didn’t matter because later on in life, I realized that food is something that everybody has to do, has to participate in. Right? Eating. And it’s one of the most, like, intimate things that we can do as a society.

01;27;54;06 – 01;28;19;07
Jake
And when I started fishing in Point Loma, I learned that fish is like one of the healthiest forms of food that you can eat. And so that’s what spurred my interest in aquaculture, fish farming. And I had always had an eye towards actually Latin America, South America in particular, because of my Spanish background. But in Africa was nowhere on my radar.

01;28;19;07 – 01;28;41;27
Jake
But when I met this other NGO, yeah, I got super excited because this was an opportunity to actually create fish production to help the nutrition in these communities. And you can read about malnutrition and see it on the TV. But until you’re there, you don’t really understand it.

01;28;41;29 – 01;28;47;02
Isabella
That sounds like a very fulfilling way to engage your interest in fishing and community.

01;28;47;05 – 01;29;09;25
Jake
One of the challenges when you work in these communities, because like, there’s so many challenges with food security and poverty and all these things, right? And it’s really easy to just kind of tell that side of the story. But the people in Malawi, it’s called the warm heart of Africa. So, you know, the people are just so friendly.

01;29;09;25 – 01;29;28;21
Jake
The whole community structure is totally different than what we have. Everybody is part of the community. When you meet somebody, you, you say hi. You shake their hand and you do that to everybody in that group. If you walk into a room and and there’s somebody there like you don’t just sit down and get on your phone.

01;29;28;21 – 01;29;53;10
Jake
You actually like, look them in their eye, shake their hand, and say hello. And I think your your relationships and that community strength is way stronger, than it is here, right? I mean, there are just kids everywhere running around, running around free and just playing. And it’s like here in the US, like you would never go to a park and just see like thousands of kids running around without their parents.

01;29;53;10 – 01;30;16;01
Jake
But it’s different because the community structure is such that if something bad happens, the community takes care of it. And that can be, you know, good and bad. There’s no police rights to communities. There’s a safety in that and there’s just such strength in the community. You just can’t imagine until you go there. The food is really not that good.

01;30;16;07 – 01;30;40;11
Jake
It’s and this is like a joke that the, you know, the, the places that were colonized by the British are like has the worst food. But some things are good like the fish is good. The chambo, the somba, is the general word for fish, but but the people, it’s the people. That’s that’s the main thing in their culture.

01;30;40;13 – 01;31;01;09
Jake
I’ve been there like, I think six times. I was planning to go back in 2019, 2020 and then Covid hit and then I just haven’t been able to. But I’m hoping to go this year, potentially next year.

01;31;01;11 – 01;31;38;22
Victoria
If you’re enjoying this episode of Beyond Lab Walls, be sure to check out our other channels at Salk.edu. There you can join our new exclusive media channel, Salk Streaming, where you’ll find interviews with our scientists, videos on our recent studies, and public lectures by our world-renowned professors. You can also explore our award winning magazine, Inside Salk, and join our monthly newsletter to stay up to date on the world within these walls.

01;31;38;24 – 01;31;46;07
Isabella
Speaking of travel, how did you end up at Salk and permanently in San Diego? What kind of research are you working on now?

01;31;46;10 – 01;32;15;12
Jake
Sure. So I should say during my PhD, I pretty much studied the microbial ecology of fish, trying to think about, hey, can we modify or how can we use the microbiome to maybe improve fish production or improve the nutritional capacity of fish? And at Salk, I was fortunate to get an NSF, postdoc grant to basically investigate host microbiome interactions in fish.

01;32;15;15 – 01;32;43;15
Jake
I joined the lab of Todd Michael. He’s an expert in genomics and comparative genomics. He primarily works on plants, but the methods are pretty much the same. So I’m doing a lot of comparative genomics of fish trying to understand what makes fish special, how are they unique. And I’m really interested in some of the more highly nutritious fish that we can consume.

01;32;43;15 – 01;33;02;26
Jake
So like mackerel, sardines, these are fish that are are small and are caught regularly on the Eastern Pacific. They’re not always readily consumed, but they are some of the healthiest fish just because of their high amounts of omega three fatty acids.

01;33;02;28 – 01;33;06;00
Isabella
Does that relate at all to the Harnessing Plant Initiative?

01;33;06;03 – 01;33;37;22
Jake
I work, I do work with HPI a little bit. So I mean, I’m involved in some of their projects and specifically some of their microbiome interests and trying to understand, okay, hey, we want to store a bunch of carbon in the roots, but it turns out the roots are and the rhizomes are pretty much the most microbially diverse, systems or biomes on Earth.

01;33;37;25 – 01;34;11;28
Isabella
Salk’s Harnessing Plants Initiative, abbreviated as HPI, is working on a bold, scalable solution to climate change that relies on Earth’s pre-existing carbon storing mechanisms. HPI is comprised of two programs: one that is engineering crops, called Salk Ideal Plants, that can store more carbon in the ground for longer, and the other project is working to restore and preserve the world’s wetlands, which act as significant carbon sinks.

01;34;12;01 – 01;34;47;19
Jake
So we’re talking about, you know, hundreds or thousands of more genes in the soil microbial community as compared to the plant or the hosts. And there has been some data I’ve been working on with Sorghum Project, where we’re starting to look at that, and that’s in collaboration with the Danforth Center. And some of the techniques that I’m working on developing with long read sequencing will ultimately apply to trying to look at the metagenome, bacterial species in these communities.

01;34;47;22 – 01;35;10;11
Isabella
Long read sequencing is a new technique for cataloging the line of nucleic acids that make up DNA or RNA. Instead of short read sequencing, which can only read small parts of genetic code at a time, long read sequencing can read more code at once, saving scientists time and resources.

01;35;10;13 – 01;35;27;26
Jake
But we’re at this moment where long read sequencing has become the new standard, and this is the case for whether you’re doing plant genomes, fish genomes, if you’re doing, microbial genomes or even transcriptomes looking at gene expression.

01;35;27;28 – 01;35;33;27
Isabella
Do you have any specific goals for the next few years? Questions you really want to ask or really want to answer?

01;35;33;28 – 01;36;04;23
Jake
There’s going to be a lot of interest in basically a lot of the questions that we looked at with basic microbial ecology and genomics, host microbe interactions, these these new technologies are going to allow SAS different questions or to revisit old questions where maybe we could only resolve things that are very coarse level, but now we’re going to be able to look at things that are much more high resolution method. I think, in the, in the next five years

01;36;04;25 – 01;36;44;00
Jake
Personally, I want to be involved in understanding to what extent fish consumption can prevent acute malnutrition. So combining these various genomics methods to try to understand and identify biomarkers associated with progression to kids who become malnourished and to try to see, hey, can we know ahead of time which kids are going to get sick or are going to have poor growth. And also at the same time being able to understand, hey, to what extent is fish, to what extent is fatty acids, either reduce inflammation or improve the growth of these kids.

01;36;44;02 – 01;36;55;03
Jake
So that’s kind of, where I see the next stage of my career going.

01;36;55;05 – 01;37;01;27
Isabella
Are there any projects you’re working on related to solving food scarcity that you’re particularly excited about right now?

01;37;01;29 – 01;37;28;00
Jake
So one of the, one of the big challenges to aquaculture is that there are like maybe over 1000 species of fish that are being farmed. Whereas if you look at like cattle, there’s like one or two species, chicken, like one or two, pigs, I think it’s just one. So there’s very little genomic resources. There’s very few high quality genomes.

01;37;28;00 – 01;38;09;06
Jake
So the genome is kind of the start to where you can start to build upon that and do selective breeding and try to like identify which genes are associated with like fast growth or climate resistance, right, like a low oxygen tolerance or a high temperature tolerance, a sort of any phenotypes of interest. So in order to address this big challenge, one of the things that we’ve done this year is basically try to figure out, is there a way that we can collect samples and to preserve the specimen so that we can actually generate genomes, high quality genomes, from what’s called indigenous or orphan crops?

01;38;09;06 – 01;38;20;16
Jake
So these are anytime there’s a crop that’s not a big export product, it’s labeled as an orphan crop. Or now there’s terminology to call it an indigenous crop.

01;38;20;18 – 01;38;22;03
Isabella
Oh, interesting.

01;38;22;07 – 01;38;49;20
Jake
And these are high globally low value food sources. But they’re really important for those specific countries or communities. So Todd has a grant to be doing plant genomes of cassava and also looking at sorghum. And these are types of food that we may not have heard of, but in order to actually do any of these genomics and using long reads, it turns out that the sample preservation is really important.

01;38;49;26 – 01;39;17;12
Jake
So if the cells breakdown, if the DNA, the DNA will get sheared and fragmented, and then we don’t get along DNA, we would sequence it. So we basically developed this methodology that allows you to collect either plants or fish samples from the field. And for plants, we showed that if it’s stored in ethanol for up to three weeks at four [Celsius], we can still get a really high quality genome.

01;39;17;15 – 01;39;39;09
Jake
And for fish, we showed even up to six weeks at room temperature and ethanol that we can still get a high quality genome. So this will really enable the old type collections and to be able to start producing genome resources for a lot of these, these crops or these animal species, fish species that really we don’t know anything about.

01;39;39;12 – 01;39;50;01
Isabella
That’s super interesting. It’s it’s weird to think about how little we know about fish varieties when, like you said, there’s just a few types of chicken, a few types of pig. And then there’s all these different types of fish.

01;39;50;04 – 01;40;28;12
Jake
Yeah. And it’s it’s even, you know, I mean, this is something that you and I can relate to because of the price of eggs, right? Because of influenza. So what happens is, and even a few years ago, there’s a huge viral outbreak in China and tons of pigs died. And so what happens when you have these, like, single species that are just, like, produced everywhere, different breeds, whatever, but is that you get one big viral outbreak and it like, wipes out, you know, 70, 80, 90 percent of the population. And this causes real problems in the food availability.

01;40;28;12 – 01;40;55;21
Jake
So having a diversity of fish species, for instance, actually buffers against this. And yeah, fish are interesting because of the the micro nutrient, the macro nutrient profiles, just the really high amounts of fatty acids that can be in them, which are, you know, important for your heart health, important for cognitive performance. So I think it’s a really interesting food system and something that needs more funding.

01;40;55;21 – 01;41;27;22
Jake
And in the US, like we need to have fish in our, in our elementary schools, right. In our middle schools. There are some programs like in the South, there’s a ton of catfish production. USDA is is trying to work that into school feeding programs and that sort of thing. So it’s not something just important for, you know, low middle income countries, but it’s also really important and developed or Western countries as well, because our diet is generally not that good.

01;41;27;24 – 01;41;33;10
Isabella
The parallel with plants is also really interesting. Like it makes a lot of sense you’re working with plant biologists.

01;41;33;10 – 01;42;05;01
Jake
A whole nother side of things is that fish sustainability, like one of the criticisms of aquaculture, is that you oftentimes you have very high protein diet, so these fish. And that protein often comes from the sardines and mackerel, o these baby or smaller fish, these pelagic fish or forage fish, sometimes called trash fish. And so what we’re doing is we’re like harvesting and catching all these fish to turn them into feed so that we can farm and grow other fish.

01;42;05;04 – 01;42;33;20
Jake
And probably about 20 years ago, there was a huge push against this and say, hey, if you’re going to do aquaculture, we need to figure out a way to feed them plants. And so that has changed. And there are salmon, there are yellowtail, there’s like all these marine aquaculture, highly carnivorous fish that researchers have been able to basically feed them a fully plant diet and to be able to grow them.

01;42;33;22 – 01;43;09;24
Jake
There’s challenges with doing that because they’re not adapted to eating like corn, right, they’re in the ocean. So that’s another interest with plants and especially like, some work with duckweed, is trying to figure out how can we, you know, make better, more sustainable fish feeds using plants. Can we engineer these plants to actually, get rid of some of these compounds which basically cause, like diarrhea in fish?

01;43;09;26 – 01;43;14;13
Isabella
So are you still fishing? What are you what are you up to outside of the lab in San Diego?

01;43;14;15 – 01;43;46;25
Jake
I love to do anything in the water. So, spearfishing, regular fishing… I lived on a sailboat for a little while. I love to surf. I do have two little kids now. Maria Luisa, she is just over two. And Juda Caleb, he is almost, he’s about eight and a half months. So the reality is my past three years of life has, yeah, I don’t really do anything except take care of them.

01;43;46;27 – 01;43;57;17
Jake
It’s a challenge, but it’s totally worth it. So now. Yeah, like going to the zoo, going to parks, that sort of thing is pretty much my main activities.

01;43;57;19 – 01;44;09;16
Isabella
Do you ever think back about your young self who thought medicine was the only option, and wonder what would have happened had you not realized research and marine biology and what you’re doing now at Salk was an option?

01;44;09;22 – 01;44;38;04
Jake
I think if I was financially stable, I would just like sail around the world and fish and spearfish and do that, and surf. In reality, I would I would love to do fish farming, and basically like, have a farm where I’m like growing fish. I always wanted to have a bison farm because that’s also a really healthy terrestrial meat that you can eat.

01;44;38;07 – 01;44;50;16
Jake
If I really wanted to make money, I mean, data science in business, there’s that’s that’s kind of what my wife does. It’s a pretty data rich world right now, which is pretty, pretty interesting.

01;44;50;18 – 01;44;58;26
Isabella
Okay I’m curious, how many languages do you speak now with Spanish and traveling to Africa and your wife and Portuguese?

01;44;58;28 – 01;45;32;01
Jake
I, so, my Portuguese, my Portuguese is, probably, hmm, probably like an advanced beginner stage. We pretty much speak to our kids just in Portuguese, so that’s improved. And my mother in law and father in law, they they don’t speak English, so I only speak Portuguese to them. My Spanish is, is still okay. And then I do speak some Chichewa, which is the native language of Malawi.

01;45;32;03 – 01;45;37;20
Isabella
Well, thank you so much for talking with me today. It’s been really great to hear about your life and your science.

01;45;37;20 – 01;45;53;13
Jake
Thank you. Appreciate it.

01;45;53;15 – 01;46;24;02
Victoria
Beyond Lab Walls is a production of the Salk Office of Communications. To hear the latest science stories coming out of Salk, subscribe to our podcast and visit Salk.edu to join our new exclusive media channel, Salk Streaming. There you’ll find interviews with our scientists, videos on our recent studies, and public lectures by our world-renowned professors. You can also explore our award winning magazine, Inside Salk, and join our monthly newsletter to stay up to date on the world within these walls.