(Back To The Forum) I run an Aquarium DNA testing company, AMA

[AquaBiomics]

My university does research on the urchin problem in caribbean, seems to be a certain type of ciliate that causes the urchins to die off, have you ever encountered something similar in your research?

We find a wide range of diverse ciliates in aquarium samples, including some associated with sea urchins (e.g. Entodiscus sp). I wonder which type you're referring to? I'm always interested in functions of the other ciliates.

 

[Hats_]

We find a wide range of diverse ciliates in aquarium samples, including some associated with sea urchins (e.g. Entodiscus sp). I wonder which type you're referring to? I'm always interested in functions of the other ciliates.

I believe it was Philaster apodigitiformis that caused the die off of D. antillarum in the Caribbean

 

[AquaBiomics]

I believe it was Philaster apodigitiformis that caused the die off of D. antillarum in the Caribbean

Yeah we have not seen that one yet in aquaria. Lots of P. sinensis, and a variety of other unclassified members of the genus.

 

[ackshee]

Hi, just wanted to chime in and say this is really cool.

I live in Portland, always nice to see other members in the area. I wanted to ask, are you using an eDNA metabarcoding approach for this work?

 

[AquaBiomics]

Hi, just wanted to chime in and say this is really cool.

I live in Portland, always nice to see other members in the area. I wanted to ask, are you using an eDNA metabarcoding approach for this work?

Exactly right.

Since it sounds like you're familiar with the approach I'll add details, we sequence a part of the 16s gene from microbial DNA for the microbiome test, and sequence a part of the eukaryotic 18s gene from eDNA for the tankDNA test.

Even after years of looking at this stuff I still find interesting surprises in some of these samples

 

[ackshee]

Exactly right.

Since it sounds like you're familiar with the approach I'll add details, we sequence a part of the 16s gene from microbial DNA for the microbiome test, and sequence a part of the eukaryotic 18s gene from eDNA for the tankDNA test.

Even after years of looking at this stuff I still find interesting surprises in some of these samples

Thanks for the quick response! That's awesome. Are you working as a fully commercial operation, or do you publish any research?

 

[56longroof]

Welcome back.

 

[ryanjohn1]

Keep up the good work. Recently had one of your tests done.

 

[AquaBiomics]

Thanks for the quick response! That's awesome. Are you working as a fully commercial operation, or do you publish any research?

At this point I have negative levels of interest in writing any more scientific papers myself. But if there are researchers interested in publishing from our database I'm open to collaboration.

 

[ryanjohn1]

At this point I have negative levels of interest in writing any more scientific papers myself. But if there are researchers interested in publishing from our database I'm open to collaboration.

Then just pop in and say hi once in a while. It’s really interesting stuff you’re doing. I just wish I understood more of it.

 

[Dburr1014]

Hmmm, never got my answer to my question....

Welcome back Dr.
I have read some pros and cons to the work you are doing. But that is how a lot of changes in the reef hobby get going. Thank you for your contributions!

I'm this response you noted fish gut bac was high in carbon dosed tanks and members of Vibrionaceae and Rhodobacteraceae were low.
Are you saying some bacteria are out competing others altering the numbers? Or you can't do a count, your just not seeing much in the samples.

Hmmm, never did get an answer....

 

[Camaro Show Corals]

Welcome!

 

[Goaway]

Welcome to r2r!

 

[Dan_P]

When I came back to the forums I came across a few pretty negative comments about various aspects of this technology or our service. Its a new technology for reef keeping, and skepticism can be natural and appropriate when something new comes up. I would be happy to answer any questions and attempt to relieve any concerns.

Hi Eli, welcome back. Looking forwards to reading about what you have learned after years of testing so many diverse systems.

I want to provide a slightly different flavor about the skepticism towards the testing that you provide. I believe newness of the testing was not a top reason for skepticism. Rather, the information your testing provided lacked a clear cut benefit for maintaining a reef aquarium. There was nothing we could do with the information your testing provided to up our game. But maybe that has changed and your future articles will shine some light on why I should care about my aquarium microbiome.

Dan

 

[ackshee]

Then just pop in and say hi once in a while. It’s really interesting stuff you’re doing. I just wish I understood more of it.

Here's some manageable reading if you're interested.

1. Environmental DNA (eDNA)
2. Metabarcoding

 

[ryanjohn1]

Here's some manageable reading if you're interested.

1. Environmental DNA (eDNA)
2. Metabarcoding

Thanks that’s great

 

[areefer01]

Hi Eli, welcome back. Looking forwards to reading about what you have learned after years of testing so many diverse systems.

I want to provide a slightly different flavor about the skepticism towards the testing that you provide. I believe newness of the testing was not a top reason for skepticism. Rather, the information your testing provided lacked a clear cut benefit for maintaining a reef aquarium. There was nothing we could do with the information your testing provided to up our game. But maybe that has changed and your future articles will shine some light on why I should care about my aquarium microbiome.

Dan

The report is not user friendly. I do not mean that disrespectful to Eli or anyone here. There is a lot of data in the report some of which includes links to external sites. This isn't something a new hobbyist would easily digest and can be difficult to a seasoned alike.

Early on when this first started Eli was able to provide a summary to the hobbyist. This, in my opinion, was the value add. Due to time constraints, volume, this isn't a thing anymore so it is left to the hobbyist. Results come in, post asking for help (again no disrespect), and the wheel turns.

There are a couple good videos on the web with Eli and Lexiverts going into detail and I'd recommend anyone considering the service to watch those first. Not directed at you Dan_P just a general comment to anyone considering it.

 

[Badblackdog]

Hi again Reef2Reef,

I used to post here a lot but have been away from forums for a couple years. I thought I'd re-introduce myself here since the community has probably grown a lot since I was here last.

I'm a professional biologist and recovering academic. I live in Oregon's beautiful Willamette Valley with my wife, 3 kids, a bunch of farm animals, and more reef tanks than I'd care to admit in polite company. (only one display tank in the house, but theres that whole greenhouse I built to house coral tanks too...)

After a couple decades in the research world using DNA sequencing to study corals and a variety of other odd creatures, I started a DNA testing company a few years aiming to bring these same methods to the aquarium hobby. We've been running samples for the reefkeeping community ever since, and this has grown into my full time job and primary source of support.

Over the past 4 years we've gathered lots of data on the microbial community in reef tanks. We've also built a database of eukaryotic parasites including those that cause some of the most common fish diseases. Some of our earliest findings I wrote up on these forums, but as we grew I ran out of time for these writeups. I hope to change that in the near future. A few teasers to share:

• The bacteria associated with the coral disease SCTLD appear to be causing disease in Acropora and other SPS in the hobby, but some of our clients have promising data on a possible treatment
• We're finding Myxozoans, an unexpected group of fish parasites that hadnt previously been discussed much in the hobby - the jury's still out on whether they're causing fish mortality in the hobby, but they're a nasty parasite in fish aquaculture...
• We've come across a variety of other interesting parasites like the Amoeba that cause Amoebic Gill Disease, or the toxic dinoflagellates Pfiesteria

In some ways our findings contradict a theory many had suggested before DNA sequencing was available, that all tanks probably contain parasites like Cryptocaryon (Ich). On the other hand, we find a variety of other, sometimes unexpected parasites. There's a lot more than just Ich out there! (of course, we do find plenty of Cryptocaryon too. Especially since over the past few months we've improved the sensitivity of our tankDNA test; I suspect our estimate of ~10% prevalence will continue to climb).

When I came back to the forums I came across a few pretty negative comments about various aspects of this technology or our service. Its a new technology for reef keeping, and skepticism can be natural and appropriate when something new comes up. I would be happy to answer any questions and attempt to relieve any concerns.

We test reef tank DNA for a living. Ask me anything!

-Eli

Can you tell if my reef tank is part Labrador? I keep finding dog hair in it.

JK. Sounds like we can learn a lot from your service.

 

[crazyfishmom]

Prior to jumping ship to industry my work as an academic focused on human population genetics. Even in this field where a lot is known and we have lots of access to dataset after dataset after dataset it is incredibly difficult to establish causal relationships for example between the microbiome and human disease or between even our own genes and disease. I think this speaks to how difficult it is for anyone of us with a tank to try to derive relationships between the species present in our tanks and beneficial or negative outcomes being tied to the presence or absence of certain bacterial species.

I think your work is incredibly exciting and I will likely try to compare between my tanks at some point as I’ve purposefully established them in very different ways because why not but I would love to see your data quality control and data quality control. After years of staring at sequencing reads I wouldn’t be able to stop thinking about it until I saw the data in full. Would this be something you might be willing to share if an NDA were signed?

 

[Dan_P]

The report is not user friendly. I do not mean that disrespectful to Eli or anyone here. There is a lot of data in the report some of which includes links to external sites. This isn't something a new hobbyist would easily digest and can be difficult to a seasoned alike.

Early on when this first started Eli was able to provide a summary to the hobbyist. This, in my opinion, was the value add. Due to time constraints, volume, this isn't a thing anymore so it is left to the hobbyist. Results come in, post asking for help (again no disrespect), and the wheel turns.

There are a couple good videos on the web with Eli and Lexiverts going into detail and I'd recommend anyone considering the service to watch those first. Not directed at you Dan_P just a general comment to anyone considering it.

I have seen the reports and when Eli was starting up the business, saw the narrative he put together to put the results into perspective. I still have the feeling it is a solution looking for a problem. Maybe Eli’s future reports will clarify things.