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Bioprospecting for new medicine – full Audio

Bioprospecting in the lab. Photo by Sevie Kenyon, UW-Madison CALS

Caitlin Carlson, Associate Research Specialist
Department of Bacteriology
UW-Madison College of Agricultural and Life Sciences
cmcarlson5@wisc.edu

10:56 – Total Time

0:14 – What is bioprospecting
0:48 – Looking under rocks
1:11 – Many insects to collect
1:36- The search for new antibiotics/antifungal compounds
1:53 – Baking for microbes
2:28 – The adventure
2:48 – Products to market
3:09 – Patents to apply for
3:23 – Crushing bugs for science
5:03 – Thousands of microbes
5:38 – Creepy crawlies
6:22 – How to bioprospect
7:07 – Bioprospecting the new gold mine
7:41 – Surprises along the way
8:21 – How to get to the end result
9:52 – Novel discoveries
10:15 – The best insects
10:47 – Lead out

TRANSCRIPT

Sevie Kenyon: Prospecting for biology we’re visiting today with Caitlin Carlson, Department of Bacteriology University of Wisconsin – Madison in the College of Agricultural and Life Sciences and I’m Sevie Kenyon. Caitlin, what is bioprospecting?

Caitlin Carlson: We are on the front line of the process of discovering a new antibiotic or a new antifungal. Bioprospecting is the search for plant, animal, and bacterial species from which medicinal drugs and commercially valuable compounds can be obtained. Bioprospecting to me is traveling to different locations throughout the United States and looking for insects that I can bring back to the lab.

Sevie Kenyon: Caitlin can you describe what it looks like when you’re prospecting for an insect?

Caitlin Carlson: Well it’s pretty simple, I basically decide which area to go to an area that I think will be interesting environmentally and then I see if there’s areas where I can turn over rocks or take some bark or if there’s a river bed. Just anything that looks interesting where I think there’ going to be a lot of insects that I can collect.

Sevie Kenyon: And what kind of insects are you looking for?

Caitlin Carlson: So, we’re really interested in grasshoppers, centipedes, we love ants, social insects such as bees or dragonflies. We trend towards exotic as well as the mundane. So, anything from a little housefly to something as exotic as a scorpion or a slug or a honey bee.

Sevie Kenyon: What is it about these insects that you are looking for?

Caitlin Carlson: We’re looking at specifically for their microbes, and we’re looking to culture them for those microbes as many different species as we can to see if they could possibly produce antimicrobial compounds.

Sevie Kenyon: Caitlin can you describe how you find these microbes on the insects?

Caitlin Carlson:  So we have special recipes, I kind of think of it as baking for my microbes. We have a media that’s made out of chitin that is basically the exoskeleton of insects, so the microbes grow really well on that. As well as, we have a media that is specifically for soil. We’re looking for actinobacteria specifically which is a type of bacteria that is known for producing antimicrobial compounds.

Sevie Kenyon: And Caitlin, what kind of luck has your prospecting brought to you so far?

Caitlin Carlson: I’ve been very lucky. I’ve been able to travel to multiple places in the United States, I’ve transected all of Alaska, as well as New Mexico. We’ve also been to Florida, Hawaii, all over Wisconsin and we’re adding more places as we can.

Sevie Kenyon: And what do you hope to gain from these microbes?

Caitlin Carlson: We’re looking for new and novel natural products. That’s where the bioprospecting comes in. These are products that could be commercially viable at some point. They could be turned into an antibiotic or some sort of antifungal that could be used in a clinical setting.

Sevie Kenyon: And have you been able to produce any of these compounds yet?

Caitlin Carlson: We have, we have been able to produce a couple. The project is only in the third year but we’ve already been able to produce and move forward in patenting of three.

Sevie Kenyon: Caitlin can you describe for us your work?

Caitlin Carlson: Well we like to tell a story about the insects that we collect. So, when I’m going an traveling to a location I’ll collect an insect maybe from under a rock or a riverbed. And then from there, we’ll bring it back to the lab where we will crush it kind of like an elementary school kid crushes a bug, crush it and we’ll plate it onto that special media. Media that really makes the bacteria want to grow and then from there we will test those bacteria against a suite of human pathogenic bacteria. So, let’s say MRSA or Pseudomonas aeruginosa or any sort of clinical isolate. Something that has been known to be resistant to current antibiotics. We like to test these strains, we want to test them and see if they can battle with the human pathogens and beat them and inhibit them. If we do see a really interesting inhibition profile then we hand it to the chemists and the chemists job is then to determine what is active in that bacteria that is causing that inhibition. So, we’re seeing that’s inhibiting the growth. So, we’re just step one in a really long process of you know, I’m the one in the field collecting the insect but then culturing the bacteria and then someday if might be an antibiotic or an antifungal that ends up in your hospital room.

Sevie Kenyon: Caitlin, give us a sense of the scale of this project. How many insects are we talking about, how many samples, how many different bacteria samples?

Caitlin Carlson: We have collected well over one thousand insect hosts and from those over one thousand insect hosts we’ve cultured over 10 thousand bacterial isolates from these insect hosts. So, it’s pretty large and you’re sitting in a room full of petri plates right now and we’re just growing. We’re continually collecting and we’re continually growing our library of bacterial isolates to test.

Sevie Kenyon: Caitlin, I want too actually about collecting theses insects, isn’t that a little creepy?

Caitlin Carlson: I think it’s fun. I always like to say to people I have the job that my 7th grade self would love. I love traveling to places, kicking over rocks, hiking upsides of mountains, just being out in the field and the adventure of it. Yes, it can get a little creepy, I’m not a fan of the spiders or the centipedes especially the centipedes, but I know that it’s the work that I’m doing as fun as it is, it’s also very important and I love it.

Sevie Kenyon: Caitlin, let’s say you kick over a rock and there’s multiple insects there, what do you do?

Caitlin Carlson: First we celebrate by saying “Yay, lots of insects” and then we have sterile conical tubes we take and we sterilize forceps as well, tweezers, and we try to pick up as many as we can and put them in individual tubes where we then have an elaborate field notebook with barcodes to make sure that we can catalog them and try to identify them to Order level. And we throw them in a bag and we keep going and we keep collecting until we get as many as we can in that one area and then we move on. At the end of the day you’re pretty tired but that’s when the real work starts and cataloging and making sure everything is organized.

Sevie Kenyon: Caitlin is there any similarities to the gold prospectors of another century?

Caitlin Carlson: Well I think so, I like to think that when I go to a new area that I’m foraging except that instead of gold it’s insects. You probably get weirder stares from people when you enter into say a national forest and you have a ranger and they’re like “Oh you’re looking insects? OK” but yeah, I feel like I’m kind of paving the way forward. Exploring new worlds maybe of a smaller variety than a gold prospector.

Sevie Kenyon: So, Caitlin what’s the biggest surprise you’ve ever gotten looking for these insects?

Caitlin Carlson: I guess the biggest surprise that I’ve encountered on one of my trips would be turning over rocks just recently in Arizona and seeing a scorpion and realizing that yes, we have to collect that. It was quite scary but, you know when you have a tube in your hand I’m surprised at how confident I feel.  I know that it is not going to get me through the tube. So, I’m braver than I would be without one.

Sevie Kenyon: Can you draw us a picture between what you do and the end result?

Caitlin Carlson: We are on the frontline of the process of discovering a new antibiotic or a new antifungal. I’m just step one in let’s say hundreds and the lab that I work in is part of a collaborative project, it would be way too much work for one lab to handle and there’s many moving pieces in this puzzle, from the insect that I collect and the bacteria that I culture. Then we have to see if it’s going to be useful as a new antimicrobial. So, from here we have to test it against human associate bacteria, bacterial pathogens, so that’s going to be something like MRSA or the enterobacteria ACA, a wide array of bacteria associated with human disease. And then from there, I grow them together I like to call them my little cage matches, to see which one survives. If my experimental bacterial strain from the insect inhibits the human pathogen then there’s something interesting there that could possibly lead to an antimicrobial agent and then from there we have to figure out what this bacteria is producing that is inhibiting this growth of this clinical pathogen. We move it forward and then that’s where the chemists come in and the chemist’s job is to figure out what is being produced to inhibit that pathogen.

Sevie Kenyon: And Caitlin, has your lab discovered some novel new things?

Caitlin Carlson: We have, we’ve discovered about 15 novel natural products from insect associated bacteria and we have multiple moving forward in the process of patenting so we have about 5 moving into clinical applications currently.

Sevie Kenyon: So, Caitlin are there insects that are better yielders than others?

Caitlin Carlson: We really are interested in ants, grasshoppers, bees, butterflies, we’re actually really interested in maggots as well. Any sort of fly that is going to feast on decaying matter is also extremely interesting to us, remember we’re not interested in the actual host we’re interested in their microbes. So, if the microbes are exposed to decaying matter then they might be producing something really interesting.

Sevie Kenyon: We’ve visiting with Caitlin Carlson, Department of Bacteriology University of Wisconsin – Madison in the College of Agricultural and Life Sciences and I’m Sevie Kenyon.

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