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microbial herding, impossible garum, and the future of fermentation:

an interview with elisa caffrey
conducted by hannah wastyk

recorded december 2021 

Hannah:  Okay, so let's start with a softball question. What is fermentation? Feel free to be as creative with this question as possible.

Elisa: At its core, fermentation is just the conversion of materials like carbohydrates into energy using microbes. Microbes will use that energy and also produce other chemical compounds. In food production, which I think is more interesting, new flavors and textures are being produced.

The changes in microbial community throughout the course of the fermentation of food is also beneficial by creating an environment where pathogens can't really grow. It makes food safe. And in certain cases like with cassava fermentation, there's also this removal of toxins. So in essence, it's just this beneficial trans-kingdom transformation, which I think is cool.

H: So for all fermented foods, is that true? Is this transformation true for everything from kombucha and SCOBY starters to cheeses and cassava? Is it the same basic idea for all fermented foods?

E: Yeah. Yeah, because you're starting with a certain microbial population, and then it will change over time and produce metabolites (chemical compounds produced during metabolism) over time that are different from the initial population that you're starting with. It's a constant regeneration of these communities.

Got it. So that's the common thread through all fermented foods. How do you think about the differentiation between fermented foods? Because you know, kimchi is pretty different from cheese or kombucha. How do you bin fermented foods in what you talked about with taste and texture?

E: What we're realizing is that a lot of it  has to do with the starter ingredient. These microbes are really important, but for example, with cheese, you could take very similar strains of bacteria and yeast that you're using to make the cheese, but a lot of it comes down to the origin of the milk or the location and environment in which you're actually developing the cheese.

So it is this combination of the microbes, the environment, and the raw materials that they're starting with and how all of those interplay in order to create this final product that we enjoy.

“It is this combination of the microbes, the environment, and the raw materials that they're starting with and how all of those interplay in order to create this final product that we enjoy.”

H: Yeah. I think that's a really good point to highlight is that I think a lot of people for fermented foods right now, or like in probiotics in general, are obsessed with the strains, but forget about the context of the starting material and the origin of the starting material. The context for which the community has grown with temperature, pH, altitude, all of those things are all really important and differentiate fermented foods to be a common thing where microbes are growing, but also how they transform the starting material into different tastes and textures like you mentioned. How did you, how did you first become interested in fermentation?

E: Um, I guess there are two different parts to it. I started developing some gut issues and became really interested in the low-FODMAP diet which is basically starving your gut microbiome of fermentable foods because you have some certain microbes in your gut that are too eager to ferment fiber and cause all these GI symptoms. So the idea of the low-FODMAP diet is basically to remove all of these fibers from your diet.

There's a lot of research about this that comes out of Monash University in Australia. They have this app where you can go and look up the different amounts of these fermentable carbohydrates in different foods to help identify what might be a trigger for people with IBS. While I was looking through it I noticed that there was a difference between starter ingredients and the final fermented food. Some of these fermentable carbohydrates increased from common cabbage (green) to sauerkraut production, but when you looked at sauerkraut from red cabbage fermentation, they actually decreased.

And so that's part of the spark asking “What causes the difference when you have these cabbages that should be very similar?” They're very closely related, but there's something about the fermentation process that actually makes sauerkraut made from common cabbage less IBS friendly, but when it is made with red cabbage, it might be more friendly for people with IBS.

So that's what sparked my interest from a scientific perspective. The other part was personal. My family is from the Tyrolean Alps and my grandfather was a cheesemaker and my grandmother's family had a sauerkraut business for 200 plus years and, but for a long time was never really interested in it.

As I got a bit older I started wanting to understand my roots, especially to understand this part of my family history. I found out the sauerkraut business was closing since no one in the family wanted to keep it open, and the loss of something I never appreciated really pushed me to want to focus my research on understanding fermentation, that I needed to start making and eating sauerkraut and all these cheeses. And I wasn't a huge fan, especially with sauerkraut. I thought it was kind of gross, and also never sat well with my stomach. I was just really fascinated by the idea of bringing these two parts together, making ‘gut-friendly’ sauerkraut and understanding my family's sauerkraut history, so that I can enjoy sauerkraut in the Alps. And what I noticed is that over time, the more you eat it, the more you want to eat it. I don't know. There's something about it, where this taste preference develops.

Definitely, fermented foods are a strongly acquired taste. People say that about coffee, which is also fermented, people say that about beer, which is also fermented. I wonder if there's something about fermented food products where initially our body just doesn't like it. But then something about microbes create these cravings, which is something that we've also heard. A lot of people start to crave fermented foods, as if microbes are working at our gut-brain-axis in some way to create these feelings of needing to continue to eat the food that sustains the microbes.

E: Totally. Objectively, I think sauerkraut just kind of tastes gross. I also think we've changed the way sauerkraut that we eat is produced. There is a way of preserving food, where you're making it and fermenting it and storing it for a long period of time, which is different from what we now find in stores. Working with food producers in the Bay Area, some producers like Aruna from Volcano Kimchi, was telling us that she ferments at room temperature for a few days, jars the kimchi, moves the jars to the fridge, and then sells it by the end of the week. I don't know if it's to help sell more or increase palatability. I think producers have shortened the time in which they're fermenting because it does taste better. It has this crisper flavor.

It's kind of a flash ferment because in one of the last experiments that we did together was to make kimchi ferments and then sampled them over 60 days. And it definitely got danker and danker the closer to 60 days. It got to the point where we made the entire cold room smell like kimchi.

Fermented foods are obviously in the limelight more recently. And I'm interested in what you think about the cultural implications of that and how that seems to differ from your family who made fermented food products, you know, for 200 years before.

Because even then they weren't doing it just for survival reasons, but they were selling a product. So how is selling a product today differ from selling a product over the past 200 years?

E: That's a great question. I think part of it is that it’s just a food that people enjoy and want to buy. So it will always be a product. Part of the problem now is pitching it as a health food. I think it’s over-hyped and we don't fully understand what the actual benefits are of these fermented foods, or who should be consuming fermented foods. Is it beneficial to everyone? And it’s just turned more into a marketing thing.

A lot of fermented foods you can make at home, buy buying is also for convenience. I think it's great that people are consuming them, but really it's just another way of  storing, preserving and enjoying food. So it’s just another type of food. The thing that is really magical about it is that you are enjoying a complexity of flavor that you can't get with just a raw head of cabbage.

“The thing that is really magical about it is that you are enjoying a complexity of flavor that you can't get with just a raw head of cabbage”

H: I also think a lot of that hype comes from the imprecise definition of what fermented foods are. I would consider a couple of days of fermentation to be a flash fermentation of kimchi, as opposed to the 60 day. When people make kimchi once or twice a year it ferments for quite a bit of time. So if the definition of fermented foods and what particular elements of the fermented foods are important become better understood, I think it will be less hype and more targeted in terms of the very specific applications of how it impacts health. I think the implications of fermented foods in health are different from the cultural and social implications of fermented foods and how they were brought from people who have been fermenting foods for a very, very long time. So preserving that kind of cultural aspect and the health aspects of it, I think are two different topics.

E: Totally. I mean, at its core, fermentation is a way of preserving food. You ferment for six months, not because it needs to get to a certain amount of funkiness or taste that you’re going for, but because you need food six months from now when your vegetables can't grow. So there's that aspect to it, which is the primary reason that fermentation has been a common practice. Aside from, I guess, alcohol production. Production of alcohol is mainly for alcohol’s sake and not because you just really want to preserve grape juice. But in terms of food fermentation, right, it's primarily a way of preserving food. So you have all these culinary traditions that have developed around having dishes where you can enjoy something that isn't fresh, but has been fermented by these microbes for a long time.

And then you have the side of regulation and food safety, which is important but also shows a lack of understanding of what happens during fermentation. There's a lot of regulation around fermented foods and food safety that should be questioned and explored because it tends to be a pretty safe method of preserving food. There are definitely ways of doing it that are not safe, but I think that's a fascinating way of thinking about the way in which we control and regulate microbial life.

“Fermenting foods is more like herding microbes, not simply growing them…”

Are you a shepherd?

E: Yeah. [laughs] I mean, Louis Pasteur, his last name means shepherd. And so it's funny that when we think of this guy, we think of the process of pasteurization, which is to kills of most microbes. But instead our relationship should be more like shepherds, allowing us to manage and respond to the microbial landscape rather than killing everything off.

We're manipulating them to grow in the way we want, but there's also this level of precarity where you never really know how you're fermenting, mainly due to limitation in our (genetic) sequencing approaches and access to sequencing. Which is why people then try to control fermentation, where they sterilize or they pasteurize before inoculating with certain microbes that you want in order to get a stable product, and then you can sell it on the market. I prefer to just see what happens. Let's ferment this cheese and see what it tastes like. And so it becomes more of a craft instead of an industrialized process. I'm not a fan of the industrialization of fermentation for that reason.  It is just tasty and safe and you can enjoy something that you're making and that your environment is making for you.

H: Okay. So we're jumping a little bit to the end, in which we're going to talk about the future of fermented foods, but I'm interested in where do you see the future for fermented foods being in that balance between craft and an industrial product? Because obviously if it's an industrial product, some might argue that the possibility of impact in spread is larger if it's an industrial product. Whereas if it's an artismal or craft-based thing, I think that often it is co-opted into something that's a boutique product and is more expensive.

How do you see the interplay between artisanal and industrial fermented foods? And then how do you see the artisanal and craft kind of branching off into the health benefits– in an ideal world, do you see fermented foods being consumed as a health product or do you think they really should be focused more as a cultural and traditional type product?

E: Great question. So I think that the future of fermented foods, because of capitalism, will just be more industrially made ferments in grocery stores. But I think part the preferred future should be on fermented foods with a focus on more sustainability. So preventing food waste, for example, in your kitchen. You could clean extra carrot tops and ferment them and learn how to use these products that you would typically waste. Becoming more creative in the kitchen to feel empowered, to create your own flavors that are unique to your households and your kitchen.

H: So you no longer have a compost bin, you have a ferment bin?

E: A ferment bin, right. Um, I mean, don't ferment dirt… [laughs]

H: [laughs] I don't think we should get into tricky waters here…

M: Yeah. I mean, you have to be careful. You're not going to, you don't want to get a bunch of random soil bacteria rotting your food, but there are ways of taking meat scraps and turning them into garum, or cleaned radish tops and fermenting them. And maybe part of it is rethinking the way we design kitchens to have a fermentation cupboard that's built in to control humidity and temperature, something like that. That to me is really exciting.

When it comes to making certain things more palatable, there's taro and cassava fermentation which is known to help reduce toxins. But maybe there are also other foods out there that might not be easy to digest without fermenting. And we can just start doing that at home. I think that's a really exciting future and developing this kind of community-based or familial appreciation for your local fermented foods and local products.

Yeah. I love that vision.

E: What was your second question? 

H: The implications on health... This is a funny question because both of us literally study it for our graduate thesis and PhD, looking at the effects of fermented foods on health. So the fact that both of us are excited, but also have a clear understanding of what the boundaries of fermented foods as health products are.  It's really difficult for me to see artisanal fermented foods as health products as opposed to something that's an industrial practice, whether that be engineering specific strains or figuring out what is beneficial in fermented foods and then turning those into therapeutics.

So how do you think about the future of fermented foods in health, and what you want to see in that arena?

E: Yeah, totally. In the gut microbiome, the imperfect metric that is used to define a healthy microbiome is the idea of having a very diverse microbiome and consuming diverse types of fiber. So I think consuming diverse fermented foods will also play a role. I would love for the answer to be that it's not one metabolite that's causing all these effects, but it's the constant diversity of metabolites you're being exposed to through all these ferments that you're eating that come from different sources and all the flavors that are being produced. Those are what are really contributing to your overall health, whatever health ultimately means.  I think personally and politically, I would love for diversity of metabolites to be the answer and that we'll all be driven by not one final metric. All you have to do is just experiment with your ferments, eat as many different fermented foods as possible from different sources, swap with your neighbour, and that overall it will help to improve these health scores.

H: Yeah, that reminds me of the blue zones and people going to Japan or Italy where people just live well into their hundreds. And people come and try to figure out what their secret is. It always turns out to be not one thing that they're doing, but a collection of habits and consistent behaviors like socializing and having a really strong community, drinking wine and getting enough sleep and exercise and all of these things. But there's not going to be one specific fermented food that people can just buy and eat a lot of and expect to feel healthier. It's going to be like integrating it into their lifestyle, like you said, through home ferments, decreasing food waste and eating a variety of different fermented foods to kind of create this holistic profile of microbes that we want to, that's not necessarily something that we can point at and then industrialize.

E: And I think that’s something you also got into with your paper. You weren't looking at one metric, right? To look at immune health, you were looking at a bunch of different metrics and looking at the consistency in trends across these different metrics, instead of just optimizing for one, which showed there was this positive effect of fermented foods. I think it’s a bit problematic when we fixate on just one metric and it would be the same if we fixated on one metabolite, because the body's a crazy thing and everything will affect everything and also affect absolutely nothing overall. What is the saying? When you have a hammer, everything's a nail…So if you want to study one metabolite, you can find the receptor in any cell type and say, this is the effect, but if you're actually trying to understand overall health you can't do it by just looking at one metabolite. So I think looking at diversity is going to be really important.

H: Definitely. I think not having optimization perimeters makes it really difficult to industrialize, and so that's why it's not quite turned over to that side yet, but I don't know. I'm interested in the future. If more research that we do comes out that fermented foods hit a specific receptor it'll kind of lose that diversity and craft aspect of it so that it optimizes on a specific perimeter that people have identified for being a marker of good health or that fermented foods are able to hit.

E: Oh, so you're saying if there's one fermented food receptor and all metabolites hit that one receptor…

H: Yeah, and people are just going to crank it out on that…

E: Right, right. That's a cool idea, a fermentation receptor…

E: So we talked a little bit about fermenting at home and your family's tradition of fermenting at home. So why don't you tell me a little bit more about that? Like what do you, what do you ferment at home? Interesting stories. Big fail.

E: I think I've always been more interested in the act of fermentation itself and less about cooking with it, I guess. And I am saying that because I started with sourdough and this was pre-pandemic. So just putting that out there, I did it before the pandemic [laughs].  But I was always more interested in just making as many sourdoughs as I could. From going to the farmer's market and getting flour, and then I went to Italy and got flour from there and brought it back. It was more about trying all these different ways of fermenting sourdough and smelling it than it was about actually baking bread.

H: Did you even eat it?

E: I’m also gluten-free, so I didn't even eat it…

H: You just baked it, sniffed it, and gave it to people…

E: Yeah [laughs] I went through a phase where I trying it. It smells so good and also it feels weird to make something and then just hand it off to other people.

H: But yeah, you’re always pushing to see how far you can take your gut [laughs]

E: Yeah, I'm always down to taste everything, but…

Anyway, I'm one of those people that just will set up a bunch of sourdoughs, and then I would freeze them and then share them. And that was really great. What else have we done? Now I'm pretty consistent with red cabbage sauerkraut, big fan of that.

I'm really into garums, um, which are a meat ferment. So you can take fish, to basically make a fish sauce, or ground beef and then you add koji, which is rice that has Aspergillus oryzae, a type of yeast, that grows on it, and those will break down over time. So it makes this really savory umami flavor packed liquid that you can cook with. And, and so that has been a game changer in home cooking. And I really love that. What else have I made? Vegan cheeses.. I've tried making vinegars which are something that I want to get more into. I also always have some misos going. I have a fermentation closet, which is great.

H: I can confirm she has a fermentation closet. It's very funky in there.

You mentioned vegan cheeses. I know an angle of fermented foods companies or microbiome companies is going after alternative proteins. Alternative proteins are very popular right now, and fermented foods have been kind of thrown at it at any angle in terms of making tastes and texture of alternative proteins more palatable. I know you said you made garum with regular ground beef. Did you also make it with Impossible meat or Beyond meat?

E: I did. Yeah, I did make it with Impossible meat. As is typical for me, I just experiment with stuff first and then figure out what's actually worth keeping later. So I did the Impossible beef and ground beef at the same time. I did the ground beef for six months and the Impossible meat I set up at the same time and within three weeks it smelled amazing. But I was like, “No, no, I'll keep it going, I'll keep it going.” So I waited the whole six months, same as ground beef. And it was disgusting. It was inedible. It was one of the worst things ever tasted in my life. So if you want to make garum from Impossible meat, three weeks is best, less than a month. I would not go for six months. At three weeks it smelled just insanely yeasty and just cheesy. It was really, really amazing. More than that, no.

“So I waited the whole six months...and it was disgusting. It was inedible. It was one of the worst things ever tasted in my life. So if you want to make garum from Impossible meat, three weeks is best, less than a month.” 

 H: I mean, that kind of gets to fermentation where you're controlling microbial communities, but obviously you don't want to get sick. Controlled rotting is how you describe fermentation to me one time that just really resonated. So for Impossible meat versus regular meat, I'm interested in what you think those communities' differences were. Is it the proteins that it was breaking down? What do you think is the difference between those two fermentations?

E: I think it was mainly just the raw ingredients, because I was using the same starter, I added the same koji from the same bag. Same temperature, they were in the same incubator.

H: What is Impossible Beef made out of?

E: Soy protein, I think. I should look it up. I believe it's mostly soy protein, and then they add heme. And then a bunch of other stuff. So I think whatever it was, it broke down a lot faster and then the off flavors it was giving was gross. I tasted it and I didn't get sick. I think it was totally safe. It just tasted so bad. [laughs] I honestly wasn't a huge consumer of Impossible meat, and I have not had it since then. I don't know if it's because I just developed an aversion to it.

I was going to ask if you would try to ferment it again, but do the three weeks and see. It'd be interesting if it created a more umami or intense meat flavor…

At Noma they have the recipe for garum from egg whites or mushrooms, so you can make it from other proteins. I feel like that's a better use of your koji than buying Impossible meat for however much a pound and then fermenting it, if you want a vegan or vegetarian option.

H: Okay. You're right.

E: You don't need to additionally ferment stuff that's already been fermented in huge bioreactors for a long time to make this product. You can just go straight to the original ingredient.

H: That's fair. That's fair. I think something else that’s interesting is that you told me about that experiences was you were making the garum you opened up the garum and your roommate's cat was there and she was like standing on your leg, and when you opened it the cat's claws immediately came out and it became primal. I think that's interesting in terms of, presumably the cat smelled meat before, but fermented products  and microbial products can interact with the brain, create cravings, create different reactions at a gut-brain-axis level.

E: Totally. Yeah, the cat was in the other room and I opened the Impossible beef jar and nothing happened. And then I opened the beef and it just pounced on my leg with its claws and I screamed. So it knew something. It could smell the difference if you right away, which is fascinating, but yeah.

H: You’re onto something. You could be a cat herder or something. [laughs]

So we talked about home ferments and how you're interested in them from a taste and texture profile, but going back to something that you talked about at the beginning, in terms of you becoming interested in fermented foods through your own issues. How has your own medical issues influenced your understanding and experimentation of fermented foods?

E: Since I make the fermented foods myself, or when I get them from producers I know, it makes me more open to trying them. But, it has also made me realize that even within the same group of fermented foods, so even across a bunch of sauerkrauts for example, where you would expect would have a very similar final metabolite or microbial profile I have different responses.  

We talk about  engineering fermented foods to have a certain profile that might be “safe” for people with IBS. But there are different methods that people are using to produce their fermented food, their sauerkraut, and there are different types of cabbage. And there's something about the differences where I'll see in certain sauerkrauts and not in others. I think that's incredibly fascinating, because it means there's really no need to engineer the microbes. We just really need to understand how the production or the raw material effect the microbial ecosystem, and how the microbes impact IBS-associated metabolites in the fermentation process. But those are actually harder problems than just engineering strains [laughs] 

“I think that's incredibly fascinating, because it means there's really no need to engineer the microbes. We just really need to understand how the production or the raw material effect the microbial ecosystem, and how the microbes impact IBS-associated metabolites in the fermentation process.”

H: Do you feel like part of the engineering that is most exciting to you is at the strain level, like literally engineering the genetics of specific strains? Is it at the community engineering we're putting the right microbes at the right ratios or is it the starter material in terms of where the food comes from and what the quality is? Or number four is the conditions in which the fermentation happens?

How about you rank them conditions, starting material, community, single strain?

E: Okay. Conditions is number one, two starting material. I'm not super excited about engineering strains. Not because I think it's dangerous, I think it's totally fine, and I think they're really great uses for engineered strains, especially if you want a certain protein specifically that you're trying to optimize for.

I think engineering yeast for recombinant protein production to produce a certain protein or certain metabolite is a great method. But I think in terms of making things at home, there is a microbe out there that is doing whatever you need it to do. Nature is pretty amazing. Any sort of enzyme you need, nature has already created it. You just need to figure out how to find it. It’s the same with microbes. You could have a microbe that has a gene that could ferment something specific. But if it's not in the right environment, it won't do it. You know, they have a mind of their own.

H: True. Okay. So conditions.

E: Yeah, creating the right conditions I think are the most important. And then also the raw starting material would be second to that.

But I think a future where every kitchen has a little incubator and fermentation station would be sick.

H: That reminds me of like in the Great British Bake Off when they want their little breads to rise and they put it in a proofer.

E: Yeah, exactly. But instead of a cabinet have a full incubator.

H: Like your closet?
E: A kitchen closet. Yeah. Kitchen design is fascinating [laughs]

H: We can talk about kitchens later. It’s all about hiding appliances. You heard it here second, someone else in that first. Okay, let's go to another topic. So you talked about your own interest in home ferments, you have your medical issues. Now going back into how that's been influenced by your family history.

E: Growing up in Italy and going to see my grandparents… I mean, in most places, fermented foods are just part of life. You don't even think about it. You don't think about it as a fermented food. My grandfather made cheese, he did his whole life. He retired and then he would just make cheese at home. And he made his own wine, which he had every day at lunch or dinner, and then let it turn into vinegar. My grandmother's side of the family is really interesting because my dad, and I’m talking about my maternal grandmother, would always joke around about how she was a sauerkraut heiress. And I always thought that was stupid. But it turns out she technically was--  her family had a sauerkraut business, and they have receipts going back to the 1830s showing they sold sauerkraut jars in the valley. Then of course she didn't inherit anything because she's a woman, and so her two brothers got everything. Also I am not sure how much there is to inherit running a sauerkraut business in the middle of two World Wars... Anyway, in the winter of 2019 as I was thinking about my next move and was applying to graduate school, they actually shut down. There was no one really that wanted to keep running the sauerkraut business.

Then COVID happened. And so Crauti Comandella... So in the Northern Italian dialect they are called cauti, not sauerkraut. Comandella is her family's last name. So Crauti Comandella  closed down and all the machinery is still there. And so if this PhD thing doesn't work out, I'm just going to move back there and make sauerkraut in the Alps.

H: So it's the meme where it's like “I'm just going to move to Vermont and make like a nice bakery”

E:  The female urge to move to the Alps and make sauerkraut [laughs]

H: Exactly. Yep. Well, you'll know fermented foods have made it when that's the new pipe dream.

E: Yeah, exactly. I just want to make cheese in the woods in Vermont. I mean, it sounds sick. I'm a very pro but I also, yeah.

H: Okay. So we ran the whole gambit with your interest in fermented foods, where it came from, where it's going. Where do you see the important gaps in the field as a whole?

E: I think food safety is a big gap in terms of understanding a lot of the basic biology of fermentation. I think updating some of these food microbiology regulations. A lot of regulation prevents producers from making certain fermented foods and exploring the fermented food landscape because the regulations that are largely based on our understanding of microbes as good or bad, instead of understanding that it is the community as a whole, that actually makes a difference in fermentation production, and also in food safety.

So I think that's what should be really focused on. If anyone's interested there's a scholar, Heather Paxson, that wrote about microbiopolitics and fermented foods and she looks at this using Foucault’s biopolitic as the basis of her argument, we need to move to a post-Pasteurian understanding of fermentation. It is not just good or bad microbes, it is this community understanding.

I think that's where the energy really should be put to understanding fermented foods is, trying to create a better understanding of microbial ecology, community and diversity and not about whether or not your food is positive for E. coli, for example.

H: It's just funny that, you know, you could say a lot of things should be the focus of a lot of things should be on community and diversity.

E: Yeah, that's true. Yeah. Well, that's why fermentation is so cool! Because you can use it as a metaphor, shout out to Sandor Katz.

H: At first, when you said you want to see microbiome or fermented foods being used as food safety, the initial thing that I thought of was using microbes as a tool for foods that aren't fermented, if they're safe for consumption. Do you see that as being any type of future? I know that’s an idea a colleague of ours had was using microbes for testing whether or not food is counterfeit, like very expensive honeys or counterfeit, or like very expensive artisanal salamis are counterfeit. Do you see microbes as being used for a tool in terms of food safety on not just fermented foods, but whether or not food is safe to consume period?

E: Um, that's a good question. To just basically sequence the food?

H: Not even sequence, but… I'm going to riff, so you can edit this out. Let’s say  a food is left out and Salmonella starts to grow. If you pretreat that food with a strain that will outcompete Salmonella, can it be used for food safety in that way?

E: Oh, that's really interesting. Like a probiotic for the food. I was thinking of using microbes as a marker in some way of food safety. So if it was a counterfeit food, it wouldn't ferment in the same way. But I feel like there are other methods  that don't involve fermentation that work well to identify adulterated foods.

H: Yeah, I guess at that point mining microbes for preservatives is I guess what I had in mind....

E: Yeah. I mean, in essence that's what fermentation is for. It's a way of preserving food. So you're going full circle Hannah.

H: Yeah, I just reinvented fermented foods [laughs]

So to wrap up here, what do you think is next for fermented foods and the next year, five years, 10 years. Where do you see it going?

E: I actually think that we're going to see more fermentation as a technique applied to alternative protein production. I think just because that's where the money is right now. Everyone's really interested in alternative protein. But using fermentation as a way of creating these proteins in a method that I am not interested in. Just thinking about all the different types of yogurt that are out there, and all the different methods and strains that are important in yogurt production that create all these really cool textures. Right? And so maybe it's more useful to understand why these microbes are creating these different textures instead of just applying precision fermentation and using a big bioreactor full of engineered yeast to create some polymer that can be used to texture alternative meat. But that's currently what commercial fermentation is looking like. So it's actually less about this intuitive culturing of flavor and more about optimizing fermentation for a very specific outcome.

H: It's hard to scale things that you don't understand. So I think that is kind of a blockade in the reach of craft fermented foods, that you can't scale it. So everyone has to kind of do it in their own little pod, but I think that's what you're getting at is what makes fermented foods special in cultural traditions.

E: I think that's what makes it really interesting and cool. Giving people the tools to just start doing it themselves is really interesting, even as a campaign to increase science education. I think it can be incredibly beneficial as a whole, of appreciating the cultural context of fermentation, and getting your hands dirty, making food and  flavors is really cool.

In terms of how the actual market is going to move, it's just going to be more precision fermentation and alternative protein. I mean, there are also other really cool companies that are making chocolate without cacao, or coffee without coffee beans. So they're able to ferment and produce chocolate flavor and make chocolate bars without actually having to use cacao, which is a really hard to plant to grow and cultivate, and there are a lot of issues with slavery and labor. And so I think that is also incredibly exciting. I think that's a really, really cool use of fermentation as well. There's something different about optimizing for a flavor because you're not optimizing for a compound, you're optimizing for a feeling, right? It needs to be the right combination of texture and taste and scent in order to get the right flavor. But if you're just optimizing for a metabolite that will gelatinize in a certain way and produce the right texture of a patty, that's different.

“There's something different about optimizing for a flavor because you're not optimizing for a compound, you're optimizing for a feeling...It needs to be the right combination of texture and taste and scent in order to get the right flavor” 

H: Very interesting. I mean, you're for the cacao flavor and taste, that's like optimizing for food as opposed to optimizing for specific aspects of that food.

E: Right. So if you're optimizing for food, you're still maintaining the diversity of metabolites and microbes.

H: Exactly. Yeah. Awesome. All right, well, we'll leave it at that. Thank you for letting me interview you, but mainly thank you for sharing all of your thoughts about fermented foods, where it's going and giving a primer for where the genesis of this project came from and why it's so why this is such an exciting field.

E: Totally. Thank you Hannah, thanks for having me.

Elisa Caffrey
is a graduate student in Sonnenberg lab at Stanford university studying the impact of fermented food metabolites on health.

Before coming to Stanford, Elisa was a research associate at Kallyope,  a biotech  studying the gut-brain-axis.  Outside of work she  ejoys experimental film and using dried SCOBYs as home decor.


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