The Aquabiomics talk todaj

[Chromis]

@IOnceWasLegend @Bolicks
Eli and a couple colleagues spoke to Humblefish group today and we learned they plan to purchase their own (PCR?) sequencer now that the price has come down from $500k to $1k. I know there was some thread on the possibility of a BAR sequencer that was at least 5% serious ha.

Another interesting tidbit was they found some corals might have a “deep” infection that needs a heavier antibiotic dip when the low-dose in-tank Aquabiomics Cipro treatment doesn’t work. I believe the example they have was an encrusting coral. @NanoCrazed I think this is what happened to that one yellow frammer that wouldn’t respond until you dipped it.

Also they never did a follow up study on their in-tank Cipro treatment to make sure they really eradicated the bacteria long term.

 

[Bolicks]

Very cool! Do you happen to know which device they want to buy? The "cheap" MinIon comes to mind - it does require some serious analysis know-how to use. Could be a great asset to fish doctors and curious aquarists.

 

[NanoCrazed]

@IOnceWasLegend[/

Another interesting tidbit was they found some corals might have a “deep” infection that needs a heavier antibiotic dip when the low-dose in-tank Aquabiomics Cipro treatment doesn’t work. I believe the example they have was an encrusting coral. [USER=14419]@NanoCrazed I think this is what happened to that one yellow frammer that wouldn’t respond until you dipped it.

Makes sense...

For me, i always thought of it as stubborn strains... but deep infection is plausible. I usually kill 2 birds with one stone...er, dose...as the case may be. I make a concentrated dip.. soak the pieces and then pour the mix into the QT. This way i get the benefit of a strong dip, and economic upside of not using more antibiotics than necessary.

I usually throw away the first dip though as that usually has a lot of gunk coming off pieces.

 

[Chromis]

Very cool! Do you happen to know which device they want to buy? The "cheap" MinIon comes to mind - it does require some serious analysis know-how to use. Could be a great asset to fish doctors and curious aquarists.

No, I don’t think he mentioned a particular model, but mentioned it would take a lot of work to port their software over.

 

[IOnceWasLegend]

So, regarding @Chromis comment about the sequencer: I think purchasing a dedicated sequencer for the club, while it would be SUPER cool, is unlikely feasible. Beyond the considerable financial cost, I think the technical aspects required to use it (processing samples into nucleic acids, processing nucleic acids into sequencing libraries, running the sequencer, bioinformatics, etc) make it a non-starter. Take this with a grain of salt since I have not kept up-to-date with the latest benchtop sequencers, but my understanding is that even things like the MinION 1) require some of those technical aspects, and 2) are one-time-use devices, so - while we might be able to get six or eight samples at a run - that'd be ~$1,000 for that run.

I was unable to make the talk (though I'm interested in watching it later), so I'm curious: why is Humblefish buying their own dedicated sequencer?

 

[Bolicks]

So, regarding @Chromis comment about the sequencer: I think purchasing a dedicated sequencer for the club, while it would be SUPER cool, is unlikely feasible. Beyond the considerable financial cost, I think the technical aspects required to use it (processing samples into nucleic acids, processing nucleic acids into sequencing libraries, running the sequencer, bioinformatics, etc) make it a non-starter. Take this with a grain of salt since I have not kept up-to-date with the latest benchtop sequencers, but my understanding is that even things like the MinION 1) require some of those technical aspects, and 2) are one-time-use devices, so - while we might be able to get six or eight samples at a run - that'd be ~$1,000 for that run.

I was unable to make the talk (though I'm interested in watching it later), so I'm curious: why is Humblefish buying their own dedicated sequencer?

I'll echo your statement - the tabletops I know still requires accessory devices, a lot of technical training and are very expensive per run!

 

[Chromis]

why is Humblefish buying their own dedicated sequencer?

Sorry that wasn’t totally clear. Aquabiomics is purchasing their own sequencer now that they’ve come down to $1k.

 

[IOnceWasLegend]

Sorry that wasn’t totally clear. Aquabiomics is purchasing their own sequencer now that they’ve come down to $1k.

Ah; understood. That makes a LOT more sense.

The tech is cool, and there's a lot of questions it could answer that I'd be curious about. I don't think we could beat Aquabiomics' pricing/ease-of-use, though, even if the club were willing to buy everything I (and the other lab rats) would need to do this in-house.

I think the best thing to do might be to see - if Aquabiomics is willing - to do a 'bulk' discount if there were a lot of us interested in doing it. Potentially give them longevity data (e.g. more datapoints to "is the tank more diverse the longer it's been up"), anecdotal microbiomics data (X coral does well in this person's tank; is there a similar 'signature' in other tanks?), etc.

Another cool thing to do (and that might be mutually beneficial, given it would be directly hobby-related) would be to see if they'd be interested in a microbiomics "before" and "after" of tanks following a frag swap. This might be a little more challenging (since interested parties would have to keep close track of who they received frags from), but could be pretty cool to see how new additions might change the biomes of our tanks.

Alternately, we (or, I, if there's interest) could reach out and see if there's specific area(s) they're looking to generate more data in, or want to run a pilot experiment on, and see if anyone in the club could provide a mutually beneficial arrangement.