In depth microbiome water testing for Hewbie!

[AydenLincoln]

So in case anyone was wondering how Hewbie is still doing he is still losing weight but is eating so the question remains what is causing him to be in a continued deficit state? I decided to send his water out for shotgun metagenomic sequencing and targeted 16S/ITS/18S testing. What is this you may ask? It is deep analysis of the water to identify all the species of bacteria, algae, fungi, and viruses and put together a picture of what is in his microbiome as a whole. It is run through scientific instruments, raw data is pulled out, and then a scientist interprets the data and puts it into an easily readable format that I the average person can understand and comprehend. How will this help me? From there I can see what bacteria and other organisms are in the water, how much, and narrow it down to what could be causing illness and go back to his vet. I still need to send a stool sample out again for bacterial culture but I have yet to catch him popping in front of me after where I could collect it. What company am I using Zymo Research a large biotechnology firm able to support a wide range of studies and testing. They offered a $350 code and it turned out to be the cost of around two ICP-OES tests which I did and it did not reveal anything extraordinary or unusual.
For anyone interested you can see more here! https://www.zymoresearch.com/

Little buddy says hi!

 

[BryanM]

Hewbie!!! Good luck buddy, you make me want to start another tank :)

 

[Decamicron Labs Verified Sponsor]

Awesome! How many GB/number of reads are you getting?

 

[AydenLincoln]

Awesome! How many GB/number of reads are you getting?

20 million paired-end 2x150

 

[AydenLincoln]

Hewbie!!! Good luck buddy, you make me want to start another tank :)

He says you totally should and he would be honored to have inspired you to get a puffer!

 

[Decamicron Labs Verified Sponsor]

Awesome! How many GB/number of reads are you getting?

Nice, sounds like you are using their illumina platform. That’s about 6GB in total. I assume the $300-$400 figure is for two 20M samples, one for shotgun and one for PCR? Are they doing extraction for you?

I am just curious because the price is very sensitive to number of reads, and there may be other places that can do better.

 

[Decamicron Labs Verified Sponsor]

20 million paired-end 2x150

Nice, sounds like you are using their illumina platform. That’s about 6GB in total. I assume the $300-$400 figure is for two 20M samples, one for shotgun and one for PCR? Are they doing extraction for you?

I am just curious because the price is very sensitive to number of reads, and there may be other places that can do better.

 

[AydenLincoln]

Nice, sounds like you are using their illumina platform. That’s about 6GB in total. I assume the $300-$400 figure is for two 20M samples, one for shotgun and one for PCR? Are they doing extraction for you?

I am just curious because the price is very sensitive to number of reads, and there may be other places that can do better.

It is more like over $500 retail but I used a coupon so I only spent around $200 for it all.

 

[Decamicron Labs Verified Sponsor]

It is more like over $500 retail but I used a coupon so I only spent around $200 for it all.

$500 is a lot even for retail. I don't know what they charge for extraction and bioinformatics these days, but there are other places that can probably do cheaper than $200 with more reads if you're paying for 1 6GB sample using Illumina. Shotgun is something different to targeted 16S, ITS, and 18S testing, and which of the three you pick matters as well, unless they are pooling all three.

I would skip the stool culture sample, a large percentage of bacteria are unculturable and there are a lot of culturable cells in seawater that probably aren't causing Hewbie's issues. My doctor friends have all been saying that human diagnostics will move towards these sequencing technologies instead of petri dish cultures over the next decade.

Anyways, best of luck! I hope you find out whats wrong with Hewbie. He is very cute.

 

[AydenLincoln]

$500 is a lot even for retail. I don't know what they charge for extraction and bioinformatics these days, but there are other places that can probably do cheaper than $200 with more reads if you're paying for 1 6GB sample using Illumina. Shotgun is something different to targeted 16S, ITS, and 18S testing, and which of the three you pick matters as well, unless they are pooling all three.

I would skip the stool culture sample, a large percentage of bacteria are unculturable and there are a lot of culturable cells in seawater that probably aren't causing Hewbie's issues. My doctor friends have all been saying that human diagnostics will move towards these sequencing technologies instead of petri dish cultures over the next decade.

Anyways, best of luck! I hope you find out whats wrong with Hewbie. He is very cute.

So I actually looked around and most places either couldn’t do exactly what I wanted or wanted to charge thousands of dollars. These instruments are very expensive so that is a driving factor and these scientists are filled with a ton of knowledge and it takes a tremendous amount of time to interpret the data and organize it. To further clarify this is everything that is included. Although I don’t directly work on these instruments as a scientist. I deal with the insurance side of them they are incredibly expensive and complex and easily in the hundreds a of thousands of dollars to buy and maintain….so $80-$190 per test really isn’t bad. I also could not find another company who could do any remotely similar work that I wanted on a direct consumer level. Most either only work directly with government, veterinarians, or research institutions and/or only focus on freshwater or wastewater. If you offered services to the public. What would you charge? I was reading you do some of your own internal NGS testing.

 

[Decamicron Labs Verified Sponsor]

This is quite literally where all of Decamicron Labs' profits go. I do this stuff essentially as a second unpaid job:
https://decamicronlabs.com/pages/research

I don't know what your relationship with Zymo is, but if you really value their data analysis and expertise I say go for it. Their DNA extraction kits are quite well known to molecular biologists.

I'm not sure where you got that $1000 figure from, but Aquabiomics is a very well known company to reefers that offers a ~$100 test that has more reefer oriented data analysis. They might not be as well known to people outside the community though.

The Aquabiomics service does offer very few reads, and the owner shot himself in the foot by buying quite literally one of the least cost efficient units, but nevertheless Eli used to reef. The bioinformatics Zymo provides look much more targeted for wastewater researchers and ecologists. Besides the virulence factors, there doesn't seem to be anything quite actionable.

What is wrong with Hewbie?

 

[AydenLincoln]

This is quite literally where all of Decamicron Labs' profits go. I do this stuff essentially as a second unpaid job:
https://decamicronlabs.com/pages/research

I don't know what your relationship with Zymo is, but if you really value their data analysis and expertise I say go for it. Their DNA extraction kits are quite well known to molecular biologists.

I'm not sure where you got that $1000 figure from, but Aquabiomics is a very well known company to reefers that offers a ~$100 test that has more reefer oriented data analysis. They might not be as well known to people outside the community though.

The Aquabiomics service does offer very few reads, and the owner shot himself in the foot by buying quite literally one of the least cost efficient units, but nevertheless Eli used to reef. The bioinformatics Zymo provides look much more targeted for wastewater researchers and ecologists. Besides the virulence factors, there doesn't seem to be anything quite actionable.

What is wrong with Hewbie?

Aquabiomics no longer exists/went out of business earlier this year or I would have gone with them. I looked at the pricing I got from someone else well known it was $2500 for NGS. The other quote I directly got was $300+ for NGS but only for a specific set/database comparison to freshwater fish farming which wouldn’t have helped me. I got a few other prices from different biotechnology companies and it was very expensive anywhere else lol. The other labs at research universities didn’t offer similar services like this for saltwater or direct to consumer and I looked at a more than a dozen across the country. Hewbie had an internal infection and went to the vet. https://www.reef2reef.com/threads/hewbie’s-official-diagnosis-and-images.1165980/

 

[AydenLincoln]

This is quite literally where all of Decamicron Labs' profits go. I do this stuff essentially as a second unpaid job:
https://decamicronlabs.com/pages/research

I don't know what your relationship with Zymo is, but if you really value their data analysis and expertise I say go for it. Their DNA extraction kits are quite well known to molecular biologists.

I'm not sure where you got that $1000 figure from, but Aquabiomics is a very well known company to reefers that offers a ~$100 test that has more reefer oriented data analysis. They might not be as well known to people outside the community though.

The Aquabiomics service does offer very few reads, and the owner shot himself in the foot by buying quite literally one of the least cost efficient units, but nevertheless Eli used to reef. The bioinformatics Zymo provides look much more targeted for wastewater researchers and ecologists. Besides the virulence factors, there doesn't seem to be anything quite actionable.

What is wrong with Hewbie?

I am intrigued to talk to you more about what you do. I am going to send you a message on Instagram from @HewbieThePufferfish much easier to message regularly for me on there.