Will It Sequence: a mystery fish

08 November 2019

Interview with 

Tony Sapsford, Frog End Aquatics; Louise Fraser, Illumina

MYSTERY_FISH.png

Fish with a question mark overlaid.

Share

Supposedly geneticists can use the water from a fishtank to determine the species of fish it used to contain. Is it true? To put it to the test, Phil Sansom went to meet Tony Sapsford, owner of Frog End Aquatics - where our mystery fish resides...

Tony: My name's Tony and I am the owner of Frog End Aquatics.

Phil - And Frog End Aquatics, in case you can’t hear it in the background, is chock full of bubbling fish tanks.

Tony: Basically it's a large tropical aquarium set up, if you like. There's 86 tanks in total.

Phil: 86?

Tony: 86 tropical tanks, 10 cold water tanks, 2 big koi ponds and 4 marine tanks.

Phil: How many fish are in here?

Tony: Christ almighty, Got to be probably five or six thousand.

Phil - I was there for one type of fish in particular. But as Tony led me past tank after colourful tank, I couldn’t help getting distracted.

Phil: Wow.

Tony: Well as you can see there are seahorses, shrimps. This is saltwater.

Phil: God, I forget how beautiful seahorses are. They're tiny and jet black.

Tony: They are, yep.

Phil: Now Tony, have you got a favourite fish?

Tony: Yes. I mean to be honest with you, these days my favourites are puffers. When I started in the hobby thirty odd years ago that was one of the first things I had, was a giant puffer fish.

Phil: Really?

Tony: That is sort of what got me into it. I had a big one - he was nearly fifteen inches long. He would literally fill up with water and when he wants to go down he would go to the surface and spit the water out.

Phil: Really?

Tony: Yeah, yeah, they are cool.

Phil - Enough distractions. I was there with a job to do.

Tony: Right, we are just heading over here.

Phil - We went over to a tank with a very special type of fish. I had a rinsed-out jam jar, and I handed it to Tony to collect a water sample.

Phil: Oh my god you are putting your hand in!

Tony: It’s not going to hurt me, trust me.

Phil: Are you sure?

Tony: Yep.

Phil: You’re just leaving your hand in there!

Tony: Yeah, literally they are so shy, they will just go and hide behind the up-lift.

Phil: I thought they’d absolutely go for you.

Tony: No, not at all they are very, very shy things.

Phil - I had my sample of water from the tank of my mystery fish.

Phil: What do you expect to find in there?

Tony: Probably fish poo. They should find fish poo and probably any remnants of whatever they have been eating today - I mean they are quite messy feeders.

Now that the sample of water is ready, Phil Sansom took it over to the lab at gene sequencing company Illumina, where Louise Fraser works...

Louise: Hi, I'm Louise Fraser. I work at Illumina and I have a team who focus on extracting DNA from human blood samples, saliva samples.

Phil: Louise, I've got a present for you.

Louise: Wow, this is very different to what we would normally receive. Normally we would receive a sample in a sterile container. So what I'm looking at is a jam jar which appears to be full of water.

Phil: Are you going to have to turn down my sample?

Louise: No, we're always very happy to receive all kinds of samples

Phil: Very diplomatic of you, I am going to give this to you.

Louise: Thank you. It does just look like tap water with a few bits in it.

Phil: Now I'm not going to tell you what kind of fish was in that tank, but just off the bat - any guesses?

Louise: I don't know, goldfish, or some of those very large koi/carp type fish? I don't know. You just can't tell from the water.

Phil: Tell me what exactly you're going to do with the sample first.

Louise: What we have here is about half a litre of water and that volume is too big to easily process in the lab. So we would concentrate any of the DNA that's in that sample by flowing the water through a filter. We would then lyse any of the cellular material in the sample which means to break open or pop open the cells to release the DNA into the solution and we would then be able to isolate the DNA by binding the DNA to a magnetic bead so we can easily pull out the DNA.

Phil: Apart from the fish that was in that water, are you expecting to find any DNA from anything else?

Louise: Yes we would. You would expect to find the microbiome of the fish tank so that bacteria, for example, that may like to live in those fish tanks, and knowing the sequences of those bacteria might help us to identify what the fish was and we might find traces of what was originally in your jam jar.

Phil: Oh no.

Louise: That depends how well it's been washed out.

Phil: If you can get to the jam and figure out what kind of jam that was. I'll be so impressed.

Louise: No promises, we will aim for the fish and we'll see what else we get.

Phil: Now what about the food that the fish was eating. Are you expecting to find that as well?

Louise: We might find DNA sequences from that. I'm not quite sure what goes into fish food.

Phil: Are you excited?

Louise: I'm very excited. I'll be very interested to see the result, see what we can find. Before, we were able to do high depth sequencing on samples like this, you would only look for things that you knew were there, but with sequencing we can look for everything and then try and figure out what was there in the first place.

Phil: Good luck!

Louise: Alright, thank-you very much!

Comments

Add a comment