Probing Poop For Cellulose-Chomping Microbes

In the search for ways to break down tough plant material like cellulose into biofuel, researchers are looking in odd places—like the feces of pandas, zebras and giraffes. Biochemist Ashli Brown and microbiologist David Mullin discuss the microbes that inhabit the guts of herbivores.

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IRA FLATOW, host: This is SCIENCE FRIDAY from NPR. I'm Ira Flatow.

Well, I'm going to bring up a topic that I never thought I'd really talk much about. I'll tell you why. You already know how we make biofuels, like ethanol, from raw materials like we eat - corn, starch, cane sugar - and how we compete for those things, right? Do you want food? Do you want fuel? Well, that's the easier thing to do. That's why we do it, because it's easy. But there is a harder thing to do, and the harder to figure out is an economical way to squeeze energy out of tough woody plant matter full of stringy cellulose, like wood chips and switchgrass and even newspapers, things that we don't eat.

My next guests are both looking for the answer in an unusual place: poop. If you think about it, it actually makes a lot of sense. Animals that dine on fibrous things like - animals like pandas and zebras and giraffes - they extract energy from this hard-to-digest stuff. And how do they do it? The secret is hiding in their poop.

David Mullin is an associate professor in the Department of Cell and Molecular Biology at Tulane University in New Orleans. Welcome back to SCIENCE FRIDAY, Dr. Mullin.

Dr. DAVID MULLIN: Thank you.

FLATOW: You're welcome. Ashli Brown is an assistant professor in the Department of Biochemistry at Mississippi State University in Starkville. Welcome to the show, Dr. Brown.

Dr. ASHLI BROWN: Thank you very much.

FLATOW: Let's talk about this. Why are you looking through animal poop? Why is that a good place to begin to look? Either one of you can jump in if you'd like. Go ahead, Dave.

MULLIN: I can tell you why we started looking...

FLATOW: Go ahead.

MULLIN: ...years ago, is that we knew they were daring.

(SOUNDBITE OF LAUGHTER)

FLATOW: There you have it. It's like Mount Everest, right?

MULLIN: That's right.

FLATOW: And if there are so many, you know, microbes in the guts of animals - and we know from doing the program that there are lots and lots of different bugs running around there - how do you single out the ones that you want and know that they used - break down the cellulose?

MULLIN: Yeah, that's really the trick. And it turns out, we wanted to look specifically for biofuels-producing bacteria, and we developed a very simple method for isolating them. And we now have, you know, a pretty good size collection of different bacteria that produce biofuels. But I think beyond getting them out of poop, one of the interesting things is just to sort them so that you can find those that both make biofuels, plus have other really desirable features beyond just making biofuels from cellulose.

FLATOW: I see. Ashli, how did you get the idea to look at panda poop, in particular?

BROWN: Well, I think one of the unique aspects of the giant panda is the fact that its digestive tract itself is the same as any other carnivore. So unlike looking at microbes that come from ruminant animals or animals that have multi-chambered stomachs, the digestive tract of the panda bear is exactly the same as any other bear. And so it lacks any of those adaptations to digest that woody plant material, the bamboo. And so they rely, much more heavily, on the microbes that reside in their gastrointestinal tract to break that material down.

FLATOW: Mm-hmm. And where do you get your study material, shall I call it that?

BROWN: We have a partnership with the Memphis Zoo. Memphis...

FLATOW: Aha.

BROWN: The Memphis Zoo is about two hours - a little over two hours from Mississippi State University. And so we collaborate with them, and we get our fecal material from Le Le and Ya Ya at the Memphis Zoo.

FLATOW: And when you say that pandas are good to study, there are other animals that break down cellulose, but a lot of them are ruminants, right? They have multiple stomachs and things and large process they go through.

BROWN: Correct, correct. And so we're looking at some of those maybe minute differences within the bacteria itself that allow them to be able to do this.

FLATOW: And, David, can you - you actually turned newspapers into butanol, did you not?

MULLIN: Yes. You know, we've tried all sorts of different types of cellulose, and cotton fibers work great. Paper of different types, works great. And so we're - and we started, you know, looking at agricultural products like sugarcane bagasse, which is, you know, just the stuff left up - over after sugarcane has been pressed to remove the, you know, the sugar.

FLATOW: Mm-hmm. Ash - I'm sorry? You said?

MULLIN: No, no.

FLATOW: Ashli, can you give us the process of what you do? I mean...

BROWN: Sure. Our process is a little bit different. We're not so much focused on the microbes that would directly produce gas that could be used as a biofuel or an oil. We're looking to take these cellulolytic bacteria from the giant panda and incorporate them into a consortium that would help some of our other bacteria or yeast that produce oil and use that as a platform. So they would aid in these other microbes that would then produce the fuel.

FLATOW: Mm-hmm. So you'd be creating biofuel with their aid.

BROWN: Correct. Correct.

FLATOW: Is it possible to genetically change those once you've discovered those bacteria and make them better and more efficient at what they do naturally?

BROWN: Sure. That's one of the things that we're looking at now, is we're really going in and trying to figure out all the nuances for those cellulolytic enzymes within our panda microbes. And once we have the genes, our idea then would be to genetically engineer or insert those genes into our yeast, into our oleaginous microorganism so that they would then have those very specific proteins that can help break down the woody material and then make the fuel from it.

FLATOW: 800-989-8255 is our number. And you can also tweet us @scifri, @-S-C-I-F-R-I. Go to our Facebook page, /scifri. What kind of possible commercial applications are down the road for this? Let me ask Ashli and David. First, Ashli.

BROWN: I think for us, you know, being from Mississippi with an agricultural state, you know, if we can use this to take plant refuse, leftover agricultural material and then break it down and then convert it into something useful, I think that that's a really great focus. You know, one of the most expensive parts of the production of biofuels is the feedstock, and I think that, you know, most of the scientific community is now in agreement that we really need to get away from feedstocks that compete directly with food.

FLATOW: Mm-hmm. And, David, is there enough waste cellulose out there to make big quantities of biofuel?

MULLIN: Well, the USDA claims that there's around 1.3 billion tons per year that's produced in the United States. This would be cellulose biomass that's discarded right now. And we've looked into some of the possibilities for - you know, in the case we played with cotton fibers, for example. There's around two million tons of, you know, cotton gin waste that's not used for any other purpose. It's normally just - it costs money to dispose off. And so, you know, so that's just one possible source of cellulose. And the sugarcane - the gas that's produced near us could probably also be used to convert the cellulose, you know, the cellulose in it into biofuel.

FLATOW: Mm-hmm. And, of course, cellulosic ethanol has always been one of the holy grails of biofuel. You're not going the ethanol route, are you?

MULLIN: So - I would picture it happening like this, in - within this year: A piece of property is bought next to an oil refinery, and an ethanol plant is constructed. The feedstocks would roll down the Mississippi River so that the cost of transport would be low. And, initially, ethanol would be produced that could be sold directly to the adjacent, you know, refinery. Then, once the federal regulations are in place for butanol, which is what we're interested in, you know, the EPA and local and state sort of, you know, regulatory agencies say that it's OK to begin producing it, then the plant could be retrofitted.

It's easy to retrofit ethanol plants to make butanol. But once you make butanol, that's a drop-in fuel. It's - you know, you don't have to blend it with gasoline. You can put it directly into a car and then drive away. So we've been focusing on butanol.

FLATOW: And how difficult is it to get from that ethanol to the butanol stage?

MULLIN: There would be different bacterial strains used for producing the ethanol than the butanol. But basically, retrofitting an ethanol plant, that's a - that's - you know, the technology was developed in the 1940s, and it's easy to do.

FLATOW: Could you get - could you take Ashli's panda poop bacteria and do that for you?

MULLIN: I mean, her poop bacteria are absolutely fascinating. I've been following in that story since it first came out. But I'm not exactly sure of the details. You see, what we have been trying to do is what you would call consolidated bioprocessing. So we wanna have both steps in one, where you have, you know, the capability of digesting cellulose in combination, naturally, with the ability to produce butanol. So we have organisms that do that. And you mentioned earlier that, you know, features could be - I mean, that strains could be engineered.

We recently completed the genome of the - our best strain so that we can look at every single gene in there and begin the process of, you know, shifting them around and playing with them.

(SOUNDBITE OF LAUGHTER)

FLATOW: Right. So you're not - you're just still on the early research stages of playing with the genome there.

MULLIN: We've finished analyzing the genome, and I think these, you know, these biofuels are really going to be important for the United States. I think it's important for people to move forward rapidly and not, you know, delay. I think, you know, we discovered this bacterium we're working with about a year ago, but I can imagine it being used in the industry in probably in less than a year for making, you know, for making - actually making butanol.

FLATOW: In less than a year, and in...

MULLIN: Less than a year.

FLATOW: ...enough quantities to compete with natural gas? (unintelligible) is big now.

MULLIN: Well, I don't know about natural gas. I don't know about natural gas, but, you know, without mentioning the names, unless you want me to, there's three big players right now in the industry. And, you know, there are - they popped - they basically popped up. And these are small companies that can produce, you know, two million gallons per year just as startups. I think these could be shifted to, you know, much higher production just by, you know, building out the plants. These are just small, sort of, demonstration plants.

FLATOW: But don't you have all these vested interests working against you, people who are already, you know, vested?

MULLIN: Yeah. Yeah. So my view of this is that I'll get to work on this for a few more years, and then they'll hand me my hat and show me to the door.

(SOUNDBITE OF LAUGHTER)

MULLIN: Because you would be...

If you're talking about industry.

(SOUNDBITE OF LAUGHTER)

FLATOW: Yeah, because you'd be a big competitor for them.

MULLIN: Right. I couldn't compete with any sort of industry.

FLATOW: So you're looking for somebody to step in and say, hey, we're going to take over or help you do your project. Come join us.

MULLIN: I think for those of us that work in science, it could be an advantage to have a - maybe a useful, collaborative connection with an industry, and they could support graduate students maybe or provide some supplies for the lab to work with and, you know, work could be done at a company, as well as at, you know, your laboratory in complicity .

FLATOW: Ashli, do you think this is all possible?

BROWN: Yeah. I definitely think it's possible. I think, you know, that, you know, some things are very close to the near future of being done, and some of them are a ways off. But I definitely think that, you know, sort of a multiple approach to a common problem is definitely the way to go.

FLATOW: All right. Thank you both, and good luck to you. Ashli Brown, assistant professor in the department of biochemistry at Mississippi State University in Starkville. David Mullin, associate professor at the department of cell and molecular biology at Tulane University in New Orleans. Have a good weekend.

BROWN: Great. Thank you.

MULLIN: Thank you.

FLATOW: I'm Ira Flatow. This is SCIENCE FRIDAY, from NPR.

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