A Day in the Half-Life

Biomanufacturing: Making Stuff with Microbes

April 23, 2021 Berkeley Lab (Produced by Aliyah Kovner) Season 1 Episode 3
A Day in the Half-Life
Biomanufacturing: Making Stuff with Microbes
Show Notes Transcript

What do advanced medicines, renewable fuels, vegan burgers, smart fabrics, petroleum-free plastics, and cruelty-free cosmetics have in common? They're all produced with specially engineered microbes! Yep, microbes. 

In episode three, we explore the fields of science making this 21st century industrial revolution possible: synthetic biology and biomanufacturing.

Our guests discuss how humans first developed the tools and knowledge to harness the natural capabilities of bacteria and yeast, and chat about where this rapidly accelerating industry could go next. (Hello painless vaccines and eco-friendly air travel!)


Jay Keasling, CEO of the Joint BioEnergy Institute (JBEI),  senior scientist at Berkeley Lab, and  professor of both Chemical & Biomolecular Engineering and Bioengineering at UC Berkeley. Jay is also the Philomathia Chair in Alternative Energy at UC Berkeley, and cofounder of the biotech company Amyris.


Deepika Awasthi, a project scientist in Berkeley Lab's Biological Systems and Engineering Division and an affiliate at JBEI.

Produced and hosted by Aliyah Kovner

Aliyah (00:11):

Hello, and welcome to episode three of a day in the half-life a podcast about the fascinating and often unexpected ways that science evolves over time today, we're focusing on making stuff with microbes, otherwise known as biomanufacturing and synthetic biology.

Jay (00:31):

Let's talk about the definition of synthetic biology. The definition of synthetic biology is the engineering of biology to develop some type of function or to produce some kind of product.

Aliyah (00:47):

That's Jay Keasling. He's a big name in synthetic biology and has a lot of experience in getting microbes to produce useful compounds. He is currently CEO of the Joint BioEnergy Institute, senior scientist at Berkeley Lab and a professor at UC Berkeley.

Deepika (01:06):

And I have been following Jay's work on synthetic biology since my grad school. And that I think the advantage or one of the uses of synthetic biology comes very handy in biomanufacturing. So biomanufacturing is a field where we employ living organisms, could be microbes or plants, to produce, basically manufacture commercially relevant bio-molecules: could be chemicals, could be valuable materials or fuels.

Aliyah (01:36):

And that was Deepika Awasthi, a project scientist at Berkeley Lab focused on developing new biomanufacturing processes. These days, many of the everyday products we encounter are made by engineered microorganisms, including a large number of medicines, new materials, beauty product ingredients, and meat and dairy substitutes. And the list of products grows every year. As manufacturers are replacing traditional production methods with more efficient and eco-friendly biomanufacturing processes, or, are turning to biomanufacturing to create valuable products that would be impossible to make otherwise. Deepika and Jay are a great pair to give us the backstory on biomanufacturing and tell us how this field works.

Aliyah (02:28):

So, Jay welcome. Let's start at the beginning. When would you say synthetic biology first arose and what knowledge and tools had to come first before we could even dream of programming cells to perform new functions?

Jay (02:43):

Wow, that's a great question. I, I would say that it's been more of an evolution than a revolution, so we gained the ability to cut and paste DNA to recombinant DNA in the early seventies. And since that time scientists have engineered microbes to produce human growth hormone, human insulin. And those were generally engineering one gene at a time into an organism. And with time, we gained the scientific know-how to control many genes to build genetic circuits. And some of those genetic circuits first appeared, complex genetic circuits that is, first appeared in the early 2000s.

Aliyah (03:38):

What is a genetic circuit?

Jay (03:41):

If you think about an electrical circuit, an electrical circuit would take in information and it would then have an action: turning on a thermostat, turning on a light switch, taking in some information from the outside world and having some action. Similarly, for biology, circuits became possible because the biology could sense some change in the environment. You add a chemical to a microbe, or you do something, like it sees light for instance, and then it has some action. It turns on the expression of a gene that maybe turns the microbe green, or it produces a product, or it oscillates on and off; green and not green, green and not green. So, so those kinds of complex circuits first kind of became possible or were demonstrated in the early 2000s. And, and with time it's grown to or, or the field has demonstrated that you can engineer microbes to produce really complex products and materials that wouldn't have been able to be produced any other way, to sequester carbon from the atmosphere in new ways and transform it into new products and even to produce some extremely valuable therapeutics.

Aliyah (05:12):

And so what microbes in particular have been used for these functions and why those microbes?

Jay (05:20):

Early on the most popular microbes were the microbes that were known the best. E. coli, the organism that lives in the human gut and is widely studied, in fact, one of the most widely studied organisms. It was first used because it was easy to get DNA into and out of it, it was easy to turn on a gene's expression. It expanded into organisms like yeast, which we use to produce bread and wine and beer, because again, the organism was well-known, it was well studied. And it was really used as a model eukaryote, to study higher organisms like humans and other organisms, but what's great about the field of synthetic biology is that now it's advancing into other organisms, organisms that are not as well known, but with tools like CRISPR, we can now engineer those organisms almost as easily as we could engineer E. coli and yeast.

Aliyah (06:28):

And so what are some early examples of products that were made using these microbes?

Jay (06:34):

Well, the most early products, things like human growth hormone and human insulin of course were made for, as human therapeutics and replaced the versions that were extracted from cadavers or extracted from pigs or some other form. As we got better at making complicated products, those go into things like materials. There are flavors and fragrances out on the market now that are made using engineered organisms. We see a form of yeast being engineered to produce the heme that goes into the impossible burger to make the flavor that you get when you grill the impossible burger and, and to make it look bloody as well. So the, the range of products is growing dramatically, as we become better and better at engineering the biology.

Aliyah (07:35):

And Jay, you were involved in a lot of those early experiments to sort of first harness and utilize microbes, utilize their ability to, to produce compounds. What was the earliest pathway that you worked on?

Jay (07:49):

Well, one of the earliest pathways was a pathway to produce isoprenoids. So isoprenoids are a large family of natural products. They include some really great therapeutics like Taxol, an anticancer drug; artemisinin, and anti-malarial drug, as well as the the, the scent of mint and the flavor of mint and a lot of other flavors and fragrances as well as the red color in tomatoes. For instance so we engineered this pathway first in E. coli and then in yeast. And then we learned about artemisinin, this anti-malarial drug. And so we launched into engineer an organism to produce a low-cost version of artemisinin, and that, that product got commercialized. It's been out on the market in Africa and Southeast Asia and then launched a company called Amyris that is using that same organism that was engineered to produce artemisinin, but now to produce other products.

Aliyah (09:02):

So what are the benefits of using microbes in these situations? I mean, for these compounds, you know, why not just grow a field of the plants that produce these compounds? You know, why has it turned out to be that microbes such as E. coli and yeast are just so amazing at becoming natural factories?

Deepika (09:22):

I mean, look at the size, how many plants you'd have to grow, right? When you have big plants, that's the amount of material you have to throw out in the waste as residue. With microbes as smaller you get, the less biomaterial you throw out in residue and you can make a more purified product. Like sometimes it is 90% of the dry weight of the microbe is actually the product. Whereas in plants, you can never achieve that. Then the cost and everything of making that molecule drastically slows down. Because if you have to grow a plant, you need land fertilizers water. And I think microbes are also easier to genetically manipulate the life cycle of the product. Like, you know, you can make that product within 24 hours, 48 hours in a microbe, that's the whole life cycle.

Aliyah (10:10):

Right, you don't have to wait for the plant to grow.

Deepika (10:12):

Yeah, those are the various advantages that's like, as Jay was saying that there are so many animal farms, why one has to produce heme? It's for the same reason for an animal farm, you still need land resources, food for the animal and everything. But when you start making these meats, you can isolate the actual content, which is giving you nutrition, not every other junk that you have to eat with it. So microbes give you a very directed and focused approach with, you know, reduced cost.

Jay (10:41):

And many of these molecules is as Deepika mentioned are super rare inside the plant. And so you'd have to grow huge quantities of the plant to get just a little bit. Taxol, which is this anti-cancer drug, $2 billion a year drug, it's extracted from the bark of the Pacific yew tree. And you would extinct all of the Pacific yews on the planet in a year, if you just wanted, if your only source for Taxol was that tree. Fortunately there are other routes to produce it. There are plant cell cultures where they've taken a piece of the Pacific yew and they grow that plant cell culture in, in tanks. And now we have a project going in to try to take the genes out of the Pacific. You put them into yeast and get yeast to produce it. We're still quite a few years away from that, because it's such a complicated molecule, but you can do all of these things.

Jay (11:43):

And, and what's more, once you built the chemical factory that contains the tanks that these microbes grow in, you can produce many different products in those tanks. You know, today you might grow up a yeast that produces mint oil, and then tomorrow you might put a different yeast in it that that produces Taxol. And the following day, you might put a yeast in it that will produce a new polymer material that you could put, you know, on the screen of your cell phone or something like that. So it gives you a lot of flexibility, and yet the inputs to that are the same. You just need sugar to feed your yeast.

Deepika (12:29):

So Jay what do you think would be limiting, you know, in the kind of products that we are not making that could be looked into in the future?

Jay (12:38):

Yeah, so I think materials is a really interesting area because, you know, the materials that we use largely are either based on things like wood and concrete, or they're based on petroleum, and many of those materials like plastics and, and, and things like nylon were kind of afterthoughts. They had molecules in the, the petroleum industry from refining petroleum to make fuels, and they looked at what they could do with those. And, you know, nylon is super important discovery, and some of these plastics are super important discoveries, but that doesn't mean that those materials are great. They're not great necessarily for the environment because they're not easily recyclable, many of them, and they accumulate in the environment. And maybe we can make materials using biology that will have more functionality, different functionality, especially for, you know, this economy we have that's based on electronics and batteries and all kinds of new materials.

Aliyah (13:56):

So I wanted to kind of talk about the interim, between the early days and looking toward the future, Jay, you mentioned that it's been more of a slow evolution. Have there been sort of big breakthrough moments that have pushed through, like the punctuated equilibrium? And if so, what were those breakthroughs and what did they enable?

Jay (14:18):

Oh, sure. There've been, there've been lots of breakthroughs. I mean CRISPR would be a breakthrough, I think that has enabled the engineering of a lot more organisms than was possible before and facile engineering of those. You know, if we go back in history, the ability to cut DNA to put pieces of DNA together, that was a breakthrough allowed genetic engineering just to exist. But yeah, there've been, there've been lots of breakthroughs that have, have helped accelerate the evolution of the field.

Deepika (15:06):

Yeah. I, I remember when I was in college and doing experiments I realized later somebody got a Nobel Prize on that was how the, the use of these polymerases to amplify a DNA sequence. And as an undergrad student, that was so amazing to me that, you know, you can do a Xerox copy and that makes it so [much] easier for us to, you know, with just very small amount of DNA or that you have, you can make a million copies and your efficiency of, you know genetic manipulations and all increases. Because you can assemble that all somewhere else and then put it together in a different host. And another thing was, that I really, that fascinated me was DNA sequencing and how quick it is -- coming to the U.S., it's like overnight, and you get sequences back! So to, to be able to read the genetic code, I mean the genetic code was I think deciphered like maybe in the 60s or 70s, but now the, the way we can like just sequence it so fast. And then, like in a classroom, we can do these experiments. It was like writing alphabets, and now we are making words and then sentences.

Jay (16:21):

And, and the ability to write DNA and not just any old DNA, but know exactly what you want to write and how it's going to impact the cell. And we're still at a very early stage on that. The ability to design biology is, is at its infancy, but it's so incredibly powerful and will be so incredibly powerful in the future.

Deepika (16:49):

Yeah. Like there are so many, these say that we are only able to bring to lab just 1% of microbes, which are out there still 99% are not, we don't have the ability to culture them, but with this genomic sequencing facility right now, we can like get the whole population and sequence it and just pick out what we need and, you know, clone it through PCR and then put it in the host we require. So that is, that is something like now we are not waiting on every microbiologist going out there and isolating [a new microbe] and figuring out a media and how to culture it. We can just pick what we want from the DNA

Jay (17:28):

It's a very good point. There's, there's this ability to sequence and sequence an entire population. And then when you think about all the people and all of the sequencing centers that have been doing that now over decades, we have an enormous library at our fingertips, a library of biology that we can use to write new stories.

Aliyah (17:55):

I see. So one thing that I definitely wanted to ask you both about, and I'm so excited to hear are surprises in your career, moments where you discovered something that worked incredibly well, like perhaps even way better than you expected. And then also the moments where something that you were trying sort of fell flat, but in both cases how you might've learned something really great from those.

Deepika (18:18):

Jay, please you start! [Laughs]

Jay (18:23):

I've had a fair number of successes and lots of, of failures. And I've always tried to learn from the failures. I've always liked to have the failures occur as quickly as possible. [Laughing].

Jay (18:39):

And the successes sometimes take longer for them to play out. A good example of I think a success and a surprise in the laboratory was when we were engineering yeast to produce artemisinin, the anti-malarial drug. And we had discovered the enzyme that was the key step to produce artemisinic acid, the precursor to artemisinin, and the first candidate that we put into yeast worked; it did more of the chemistry than we thought it would do. It did essentially three steps in one step which saved us a huge amount of time. And it occurred very early on in the project, which was also really nice. And I attribute this to team members in my laboratory who, who were thinking very deeply about the problem and working on all aspects of it and, and planning for, you know, the possibility that it would work, but also the possibility that it would work. And so I fully attributed to those very smart and hardworking people.

Aliyah (19:49):

And is that, anti-malarial, the strain that you developed is that still currently being used to make supplies of medicine?

Jay (19:57):

So, the goal of that project was to produce artemisinin and to give another source besides the plant version. And ever since that process, based on the microbe has been introduced, the price of artemisinin has been low and stable. It was used early on a few years ago, now it's, it's idled because the artemisinin that's produced by the plant is so inexpensive right now, there's so much being produced. But that will change with time. The prices will go back up, and that organism, the great thing about synthetic biology and about engineering microbes to produce these things, is we can just pull it out of the freezer, we can grow it. And, and in a matter of days or weeks, you can have a supply on hand, but that same organism has been re-engineered by Amyris. And they have cosmetics that are being produced using this engineered yeast that was first engineered for producing artemisinin, and that's saving sharks because there's a key molecule that would normally be derived from shark livers, [it's also being used to] produce a sugar substitute that is a low-calorie, very good sweetener. So there's a variety of products that are now being produced and on the market, in the hands of consumers from that original yeast that was engineered for producing artemisinin.

Aliyah (21:26):

Wow. And what is that yeast like, what is that yeast up to in the wild? What does it do if it's not genetically engineered?

Jay (21:33):

Producing ethanol and bread.

Aliyah (21:36):

All right. So great. It's like mankind's favorite microbe! Wonderful. [Laughs]

Deepika (21:44):

So yeah, I think my experience has been with my PhD work and my postdoc work here so far. And I think one of the projects when I came to JBEI was on methanotroph engineering.

Aliyah (21:57):

So what is a methanotroph?

Deepika (21:58):

So a methanotroph is a microbe that exclusively grows on methane. Methane is a single carbon gas, you know, it's it's a component of natural gas that we burn, and it's a co-product made by the chemical processes or microbial processes that made crude oil. So we were looking at this technology of, you know, how we can make use of natural gas to make some value added chemicals, but these methantrophs, the problem with these gas utilizing hosts is they grow very slow.

Deepika (22:35):

And it's very difficult to, if you cannot grow them well, the next challenge is how you engineer them. So there were initially some challenges of, you know like working on establishing a facility, how to grow methantrophs and all, but what I've learned in that science is a very collaborative field. You cannot do things alone. You need guidance and, or at least, you know, it's, it's always [necessary] to talk to people who have expertise. So by the duration of the project, I was able to produce a small amount of the bio-surfactant that we wanted to produce. So that is going to be a replacement for petrochemical industry-based produced, you know, surfactants and detergents. Right now, it is a proof of concept, but it can be further engineered to do that. So, I mean, whenever anything for me, as Jay was saying that failures will be a part of, you know, the work. But I think for science doing synthetic biology and metabolic engineering for some time, I, to me no is not the answer. I always have to find out why there is this "No," you know, then you can make the "No" into something. [Laughs] Because if it is not working, I'm always curious to find out like, why? Why is this is not working. And if I do not answer the why, like why this is not growing, I will never. Like my methanotroph was not growing. And if I did not answer why it was not growing, I would never go back and fix the issue of why it was not growing. So, yeah. So my way of approaching would be, would have been that.

Deepika (24:07):

And so I have fallen flat, but I have picked up myself up. And yeah, I was able to engineer them.

Aliyah (24:15):

Nice hearing you both talk about the different strains you've worked with, it sounds a little bit like you're discussing unruly pets at some times. [Laughs].

Deepika (24:24):

Yeah that's the right word. [Laughs]

Aliyah (24:25):

So I of course wanted to talk a little bit about with biomanufacturing, a lot of the applications that I think of at least, are, are medicine. But there's also so many materials that can be developed using biomanufacturing and so many possibilities for sustainable technologies. So, Jay, I know that you have a lot of expertise in synthetic biology and biomanufacturing as it pertains to sustainable fuels. And I was hoping you could give us a little bit of a highlight about what's going on with that now?

Jay (24:57):

Yeah. So so great question. We can engineer microbes to produce fuels that are great replacements for petroleum-based fuels, the kinds of, similar to the kinds of hydrocarbons that you would derive from petroleum. And the microbe can produce those from sugar. And, and the beauty of that process is that sugar might come from a plant, and that plant grows on carbon dioxide from the atmosphere. So you have a plant that takes up sunlight, carbon dioxide, fixes it, makes it into sugar. You extract the sugar from the plant, feed it to the microbes. The microbe produces a fuel. And when you burn that fuel in a car or a truck or a plane, then that carbon is renewed returned to the atmosphere. So you have this possibility of having carbon neutral fuels, where you don't add additional carbon to the atmosphere from producing those transportation fuels.

Jay (25:54):

We see a lot of automobiles and trucks moving to electrification, and this is a great thing. As long as the electricity is made from sunlight or wind or some renewable source, then you're not adding carbon to the atmosphere when you drive those electric vehicles. But for planes, it's going to be more challenging because batteries don't have, yet have the energy density that that petroleum fuels do, and, and these liquid hydrocarbons. And that density is critical because if you want to get a plane off the ground, you can't have all of the weight of the plane being in that storage material, it's gotta be in something really dense. So with biology, we can make fuels that are, are great replacements for the petroleum-based fuels. And there'll be carbon neutral. The challenge right now is price, and, and making them in a way that will compete with, with petroleum-based fuels, because these are incredibly inexpensive molecules.

Jay (27:07):

Even, even when our gas price, the price of the pump goes up to, you know, $4 a gallon. When you think about the energy that you're getting for $4, it's, it's a trivial amount of money. And replicating that using biology where you're growing plants in the field that's, that's, that's pretty challenging, but the promise is there. And, you know, with some, some policy or regulation on the amount of carbon, put it into the atmosphere, or a price on the carbon, you put into the atmosphere that isn't renewable carbon, then that could make change everything and make those fuels realistic.

Aliyah (27:50):

Would also an investment in some scientific infrastructure lower the cost? Is there also just a lack of facilities that can make it [biofuels] on the scale needed?

Jay (27:59):

Certainly those, those fuel manufacturing plants, those bio-refineries that are going to take in all of that sugar or the plant material that's made in, in farms across the planet and then transform that carbon source into a fuel. Those are expensive undertakings building those factories, you know, those, those costs you know, on the order of 200 million to a billion dollars, or more. And if you look at the big petroleum refineries, those are many billions of dollars. So, so to outfit the planet with these refineries, these bio-refineries that are going to transform agriculture waste into fuels is going to be an expensive undertaking. And in order to get that money, you have to be sure that the people who loaned the money for, for building those have to be sure that they're going to get their money back. And, and so that's why we have to have the, the biofuel production process be economically viable.

Deepika (29:03):

There is an added advantage to the process, definitely. Like these will be drop-in fuels. We don't have to switch over cars and all transportation industry to EV. We can just use our current running the vehicles and cars, right? So I think that is one very big advantage of using the biomass to biofuel pipeline.

Aliyah (29:23):

And a lot of, for a lot of people, I mean, when I hear the term biomass, I don't necessarily know where that's coming from. But a lot of this plant material that could be used for fuel is in fact currently just waste product or otherwise unused, correct?

Jay (29:40):

Yeah. There's a lot of this out there. So, so let's just take California, for instance, we have all of these wildfires in, in forested land. And part of the reason that those burns so hot right now is because they haven't, because we've prevented them from burning more regularly as they would if, if they weren't tended by humans. And so they accumulate all of this plant material: fallen down trees, leaves, all those things. If we had a way to collect that and transform it into transportation fuels, not only could we reduce the occurrence of wildfires but we would produce these carbon neutral fuels that could fuel our automobiles or trucks or planes. And there are other examples in, in agriculture, for instance, when you grow a crop, a food crop, you might take, you know, for instance the rice from growing rice and, and collect that. Decades ago, they used to burn the rice fields to burn off the biomass. They don't do that anymore because that's adding pollution to the atmosphere. But imagine that you collect that rice straw you, you grow the rice, you have the food in the rice, but then you collect the rice straw and you haul that off and you have that made into biofuels. So, you can have your food and your fuel all in one potential crop.

Aliyah (31:09):

So are the microbial strains that are needed for this process, do they already exist? I mean, I know obviously scale and investment and policy need to change as well, but are the microbes that would be needed sort of already at the point of engineering where they could be doing this on a bigger scale?

Deepika (31:27):

So, yeah, I think if you look about, if you talk about drop-in biofuels and all, you know, these are toxic chemicals, a lot of cells do not naturally survive [exposure to] them. Otherwise we could have isolated those hosts right now, right in our lab, which can grow on petrochemicals. So, through engineering, we are giving capabilities and immunities to these hosts, and there is also a substitute biofuel which is ethanol. I think 10% ethanol is added to gasoline, but as Jay was mentioning earlier, that there is an energy density gap between, you know, that biofuel, which is there, which comes from sugar fermentation, and what we are trying to develop so that, you know, we can use them in planes and all. So those microbial strains, which can actually make that the next generation biofuel, that we are developing, they're in the, I think they are in the developmental stage to meet that target of you know, to be able to produce that amount of fuel from sugar fermentation, that can be commercialized. But yeah, it's, it's on the path.

Aliyah (32:30):

It's on the path, OK.

Jay (32:32):

You know, one of the challenges is, we're, we're robbing the cells of materials and energy that they would normally use to make themselves. So cells will take in sugar and they use that then to, to replicate, to make more cells. And we're pulling a lot of that off and turning it into a fuel or forcing the cell to turn it into a fuel. The cells would rather not do that. So biology has this great thing called evolution, and those cells will evolve away from producing your product. And so there's always this tension between what the cells would like to do and what we would like them to do. And eventually the cells win out, they always win out. Biology always moves toward evolution, and they evolve away from wanting to produce your fuel. And then you have to go back and clean out the tanks, and start with, you know, a new generation of those microbes where, you know, the majority of them are producing your, your product.

Aliyah (33:43):

Wow, I did, I did not know that, that you're kind of always forcing the needle a little bit back all the time.

Deepika (33:51):


Aliyah (33:51):

That's fascinating, Jay, earlier, you mentioned that there is a huge interest in making materials through biomanufacturing. What's the advantage of biomanufacturing for this application?

Jay (34:04):

Yeah, so you know, I think the, the motivation for making materials is, is multifold. One is, is to make materials that we currently don't have available because chemistry and petroleum precursors are limiting. And by using biology, we can make materials with completely new properties that, that might have some advantage. Another reason to make materials is maybe it's, it's toxic to the environment to make those materials in that, in that particular way, using chemistry and using petroleum. And maybe we can make them in a more environmentally friendly way, with less inputs of energy or less harmful side products being produced in the process. And then, you know, there's a whole range of, of products like plastics that have accumulated in our environment. And if we could produce plastics that were biodegradable, for instance, and compostable, we have a few of these available, but not many because they don't necessarily have the properties of the petroleum-based plastics. And just like petroleum-based fuels, petroleum-based plastics are really cheap. And so again, here's that, here's an area where the science, the biology dovetails with regulation. If we had a regulation on plastics that don't degrade and that all plastics must be either compostable or readily recyclable, then that would encourage and, and allow for these slightly more expensive plastics to come to market easier.

Deepika (35:54):

I, I feel that it is, we should see that dependence on petroleum is not currently only on gasoline, but as you know, on all the materials. You know, like from your microphone's polymer, that is wrapping up the wire to the hair clips and the clothes we are wearing. And, you know, you see anything around your room. A lot of that material has come out, at some point of time, as a chemical from the gasoline or petroleum refining process. So if we are looking at a repressive replacement fuel we will still be digging out crude oil for every other need that we have. So it is very important, like the, not only think about fuels, but all these materials, replacement materials too.

Aliyah (36:36):

Interesting. Yeah. I don't think I, that's not something I really think about on a day-to-day basis is just how much around me is from petroleum. You know, I feel so good about myself cause I just got a hybrid and you know, but my dependency in other areas is not gone down at all!

Jay (36:52):

Can I, there's can I aspect of your hybrid though. And that is that companies like Toyota are, are really encouraging the development of new materials for those same hybrid cars. For instance, some of the plastics are, are now compostable plastics or are being produced using biology.

Deepika (37:18):


Jay (37:18):

So, so it's not just about efficiency of the automobile. It's also that many of the interior parts of that car are also environmentally friendly and renewable.

Deepika (37:34):

Yeah. I, when I go to the supermarket now, I see like the shampoo says it's organic and even the bottle is also made from, you know, biodegradable plastic. You buy organic milk and the carton is like, you know made from recycled or refurbished or repurposed plastics or something. So it's the same thing that Toyota, I think now they are thinking of, you know, it's not just the hybrid, but the overall impact should be hybrid.

Aliyah (37:59):

Yeah. It's, it's good to know that there are some avenues where consumer-driven, consumer preferences can help you know, really push these technologies, push people like, both of you, to get more funding for your work to advance this. Because a lot of it does seem, you know, with big industry, to sort of be out of our hands as consumers. So that is heartening to hear. Okay. So we've talked a lot about cool applications for biomanufacturing in materials and in fuels. But one area that I really wanted to talk about is in medicine, because that is an area where a lot of people are hoping for new improved technologies, Deepika, you told me that you're working on using microbes and microbiomes to develop new therapeutics. Can you tell me more about that?

Deepika (38:45):

Yeah, so I have recently, like with the onset of COVID, I started working on a probiotic vaccine technology, an idea that I had been thinking about for some time. So probiotics are the bacteria or microbes, which we take as oral supplements. Most of us, you know, and they are over-the- counter, you can buy them.

Aliyah (39:08):

Or they're in our yogurt!

Deepika (39:08):

In our yogurt, yeah, yogurt, right? So we normally eat them. They are not something which is toxic to us. They, they only help us in our digestion and producing some types of vitamins and all that. So, we always focus over synthetic biology efforts so far on identifying, you know, the molecules of interest and the pathways to produce them in alternate microbes getting them to be produced from microbes. But what we take for granted is the recovery and purification process that happens next.

Deepika (39:39):

And so it's very time consuming and expensive process., Coming to medicine and pharma, the product purification costs do add up because this is something which is getting injected to the blood or say, through nasal sprays or something, it has to come through to a very, you know, very purified form, like 99.9% purity at the time. And that made me think, like either I can overproduce that one molecule itself, or I think a certain category of molecules can be produced in probiotics that can directly, you know be absorbed through, our intestine. So our intestine, our gut is designed for absorption purposes because we eat food, right? [Laughs]. So we can, I think that our intestine and gut is a very good target for absorption of these medicinal or therapeutic molecules. And you will not have to purify them.

Aliyah (40:32):

Right. Because I think that that's a thing that I myself don't think about when you're taking a medicine, that's derived from a cell that had to be produced by a cell, which a lot of people do. Everything else about that cell, all the proteins, all the other things that are produced, all of that has to be taken away to get that one thing [one compound]. And so what you're doing is amazing because you don't have to worry about that.

Deepika (40:54):

Worry about that, right. So, like Humulin, or human growth hormone, all these are produced with E. coli. So E. coli is an opportunistic pathogen, sometimes. Opportunistic means whenever your immunity is suppressed, then it might start [causing] infection or symptoms of infection or fever and things like that. In a healthy human, E. coli might not, not show any symptom. So that means E. coli carry certain proteins or certain molecules, which we call them endotoxins, that may start [causing] symptoms in people which are immunocompromised. And that's why when these Humulin and human growth hormone HGH was produced, it was purified out of E. coli. And that happens even today, like anything E. coli has become this protein and molecule production factory, but everything that is produced out of this factory has to be purified if it is being injected or given to us, because, you know, we don't know who's going to take this, right. It could be an immunocompromised patient too. With probiotics, we eliminate the risk of producing toxins, because we know that they do not.

Aliyah (42:03):

So how far along are you in this process and what are you currently working on?

Deepika (42:10):

So this was a CARES Act funding project that I actually got for probiotic vaccine for COVID-19 with the same concept, that we would be eliminating the cost of purification and recovery. Like if you look at the COVID vaccine now, which is from these pharmaceutical companies, they require cryogenic -- that means a very low temperature -- preservation of minus 80 to minus 20, but we never see over yogurt being stored at minus 20 degrees. So that is more approachable and accessible. If you have low temperature requirement of storage for these hosts that are expressing the vaccine,

Aliyah (42:52):

So this type of vaccine would eliminate the need for purification because you're taking the whole microbe. And then it would also cut down on the supply chain demands, like we saw being such an issue early on in the pandemic in 2020.

Deepika (43:07):


Aliyah (43:07):

And then it could also take the pressure off of clinics and hospitals as having to administer it.

Deepika (43:12):

Exactly. You don't need needles, you don't need to go to the hospitals and we don't even know, maybe Amazon will start selling it. You can just order it through app. [Laughing] Through Instacart, wherever it's available, you know, I should get so many doses for like, you know, at home.

Aliyah (43:27):

That would be great. [Laughing]

Deepika (43:27):

Like with your weekly groceries. [Laughing]

Aliyah (43:31):

That would be amazing. Yeah. And so many of us are eating yogurt or, or as you mentioned, taking probiotics anyways, that I think is really exciting. And, you know, I think it's also makes sense as a next step because so much of biology right now is, is realizing the importance of microbiomes. And I see, you know, medicine kind of going the way of microbial community based instead of the one isolated molecule. Looking at what communities of microbes can do.

Deepika (44:01):

Exactly. Yeah. How I see it as that as human beings, we have co-evolved with bacteria. We did not evolve in a very clean environment, microbes existed before us. So factually our body has less amount of cells, our cells, compared to the microbes that live upon or inside us. So they outnumber us in our own like count of cells. So they definitely do, they have a purpose in our body. So few years ago there was a human genome project, right. A very big genome project. And after that I still see that people say that these genes, they predict it may cause cancer, but there is no guarantee that if there is a deletion cancer will happen. And there's also not a guarantee that if gene is correct, the cancer will not happen. So what is like, what is the gap, which is making it just probable and not complete is I think, because again, we have co-evolved with these hosts and they have a role to play. So with the microbiome project, we may be, you know, moving into a future to where we bridge these our you know, knowledge gap into how these things how microbiome is interacting with our body. Then I think we can target the medicine, through gut.

Aliyah (45:19):

Since our interview, Deepika has gotten farther along in her phase one study of a probiotic vaccine for SARS-CoV-2. After engineering, a strain of probiotic microbe to produce the virus's, spike protein, she and her colleagues began testing how well the vaccine concept works when orally administered to a strain of mice. These mice were specially bred to produce the human version of the ACE two receptor, which is the cell surface receptor that the virus binds to so that it can enter the cell, begin replicating itself, and initiate the cycle of infection. The team is now almost ready to analyze whether the bacteria triggered an immune reaction in the mice and to assess if the response was strong enough to confer immune protection.

Aliyah (46:16):

Thanks for joining me. And I hope you tune in next time for more insider science stories.