Will it sequence: a tube of flies

13 January 2020

Interview with 

Ed Farnell, Illumina

Ed_Farnell_Illumina.jpeg

Geneticist Ed Farnell being interviewed by Phil Sansom at Illumina.

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With the gauntlet thrown down, Phil Sansom went to visit gene company Illumina. He brought the tube full of dead flies to scientist Ed Farnell - someone who originally worked on a Naked Scientists project back in 2017...

Ed - I think it was during the middle of the horse lasagna crisis, I think we're going to call it. Wouldn't it be cool if we took a sausage, which is something that traditionally, you know, it's harder to tell what's gone into that because everything's minced up and we sequenced it and we had a look to see what species we could find in there.

Phil - Did you find horse?

Ed - We didn't find any horse. No, but we found all the things you might expect to find in a butcher shop. So we found some lamb, we found some chicken, we found some beef. And when we looked really, really hard, we even managed to find some human DNA as well, probably from the butcher who was preparing the sausages.

Phil - Well, let me present you with your new sequencing task. And I've got to say it is less nice than a sausage.

Ed - Yeah, go on.

Phil - Alright, here it comes.

Ed - Oh man. Okay. Yeah, no, that is actually quite disgusting. So I kind of made a bold statement that I might not find it that gross, but these are some really, really big flies.

Phil - Isn't it gross?

Ed - Yeah. They're pretty hairy. They look pretty, pretty grim.

Phil - Have you ever worked with anything like this before?

Ed - With whole flies? No. So to take it from the fly itself is really interesting.

Phil - Is it going to be tricky?

Ed - Yeah. So they're going to present a couple of challenges that we've been thinking about. One thing is how are we going to detect the bacteria and how are we going to detect the bacteria against the host? What most people will do is they will smear the flies all over some agar plates and they’ll grow the bacteria. The problem with that is this sort of culture can introduce a bias whereby only certain types of bacteria will grow on certain growth media and actually there's a smarter method we can use now with sequencing. So we're going to try two different experiments with these flies. I think with some of them, what we'll try doing is just mashing up the entire fly. Then we'll get all of the fly DNA and all of the bacteria that's in the fly: on the outside of the fly, on the inside of the fly, in its mouth parts, in its stomach.

Phil - You're going to get a lot of fly.

Ed - We're going to get an awful lot of fly and also bear in mind the fly and the bacteria will be mixed all up together. So this would be a whole metagenomic sequencing. And the way we combat having a lot of fly is by doing a lot of sequencing.

Phil - And what's metagenomic?

Ed - Metagenomic. So that's looking at the bacterial population, the whole bacterial population within the fly.

Phil - Oh, so not just the fly, the extra stuff there?

Ed - It's looking at the extra stuff. So what we can do is we can extract all that DNA,, say "Oh this matches to fly, we'll get rid of that. We're not interested in it." Everything that's left, we can take that and start aligning it to bacterial and viral genomes and see what we get.

Phil - What's the risk that you just get overwhelmed by fly, fly, fly, and you never get bacteria?

Ed - So there is some risk, but I say we can sequence very, very deeply and you'd be surprised how much bacteria there are in things. Even in humans, like for example, if you've ever done one of the tests like 23 and me or ancestry where you do a spit tube, those spit tubes can be almost 50% bacteria from the inside of your mouth.

Phil - Okay. You said first option was mash up the flies. Second option?

Ed - So the second option is just to dunk the flies in a special chemical that is normally part of the DNA extraction procedure and we're just going to leave them there and dissolve basically everything on the outside of them and hopefully not too much fly. So I'm not sure how that's going to work out. This is the bit where it gets a bit experimental because we don't really know how long we're going to have to leave them in there so we don't dissolve too much fly. But we do still collect everything that's on the outside of them and then we just proceed with the rest of our DNA extraction from there to get hopefully what is most of the things on the surface of the fly.

Phil - Perfect.

Ed - And if both of them work the nice thing here is we'll have a nice comparison. It's like is the bacteria population on the outside of the fly different to the bacterial population on the whole fly? So you know, we get an idea of maybe there's something different in the stomach to the outside.

Phil - Oh, that's interesting.

Ed - I just thought about it now, yeah, we will have a kind of differential. I mean it's not perfect. I'm sure those of you listening will be able to pick lots of holes in the idea, but I think we'll be able to do something a little bit more interesting with that. Maybe, depending on how it works out. I mean, it's science. We're trying this for the first time, so we'll see how it works out.

Phil - Other parts of the challenge that we were originally given by our contact at Addenbrooke's: these flies probably came from something that died in the eaves, some sort of horrible squirrel or possum or something...

Ed - That just got a magnitude more disgusting but carry on.

Phil - But do you think you could find that based on what's in the flies' stomachs?

Ed - That's a really good question. I don't know enough about fly biology to know how old these flies are, what might still be left in their stomachs, how recently the flies came from the eaves. I mean we can but look and see what happens.

Phil - I'd be really excited if you found squirrel in there. I mean, disgusted.

Ed - Disgusted and excited! Yeah, that would be a unique challenge, but we'll give it a go.

Phil - Before I left, Ed put the tube of flies in Illumina’s freezer. The one that looks like a bank safe, and keeps things inside around minus eighty degrees C. And that was it. For two very festive weeks I left them in Ed’s capable hands.

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