This is what I've dreamed of for so long! Testing for microbes in our tanks!

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AquaBiomics

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Turnaround time is about 1 month (which is ambitious - other microbiome companies cite 1-3 months!) because samples have to be processed in a batch. I can turn around a batch a month at this stage.

I finished processing this batch of samples last week and sent to the sequencing facility. I see that they started the run on Thursday so I will probably be able to send out results within a couple days. Lots of very interesting tanks in this run, I'm looking forward to seeing this batch!
 
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lexinverts

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I just noticed Black Friday sales at aquabiomics.com. 25% off! The other news is that our data should be available very soon. I can't wait to see mine!
 

AquaBiomics

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So happy with the new sequencing center I'm using. I have sequencing data today, one week after sending them the finished batch of samples. I hope to push reports to clients within 24 hours. Lots of interesting stuff in this batch!

The real notifications will come by email, just thought I'd chime in here in case anyone was watching the thread.
 

Scubabum

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Ok as promised here are the results of my AquaBiomics test on my 26 year old 58 gallon Reef tank. Received my results on week 5.. This data provides detailed information on the community of microbes living in my aquarium. Each type of microbe in my sample was identified by comparing DNA sequences from my sample with a database of DNA sequences from known types. The relative abundance of each sequence can be used to compare the relative abundance of each type across samples. Looks like the diversity of my tanks Microbiome is lower than than typical range. I'll be the first to admit I don't know what most of this information means but looking forward to hearing comments of those that do.

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Scott Campbell

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Here are my results! I apparently have perhaps the most atypical tank possible with minimal diversity. Looks like one strain of bacteria accounts for roughly half the bacteria in my tank. o_O My tank is roughly 32 years old and I have never done anything to increase bacterial diversity. And the tank is completely overgrown so I rarely add anything new outside of the occasional snail or hermit crab. I do spend a lot of effort trying to maintain microfauna diversity (growing my own copepods, maintaining a refugium, growing various macroalgae, etc.) but that apparently has no significant effect on bacterial diversity.

My guess is that my tank has simply become less diverse as a function of age. I don't have any problems however. Fish are all healthy and have been with me for years. One for a couple decades. Corals grow quickly. I have a complete hodgepodge of corals that I have acquired over the years. Without some compelling reason, I can't imagine I will do anything to try to change the bacterial make-up of my tank. Not even sure how possible it is at this point to displace the mighty Rhodobacteria that rule my reef.

I plan on testing again in 6 months to see if anything changes. I will not be doing anything to try to affect a change however. This will simply be a second test to see if my diversity is staying the same or dropping further over time.

My expectation was that a high degree of bacterial diversity was probably desirable. Perhaps even critically important. Now I am not sure. My tank obviously seems fine with one dominant bacterial strain. Very interesting stuff! Excited to see other tank results!!


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AquaBiomics

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I'll come back later with specific answers. But for now I wanted to say that almost every sample in the batch behaved really well, the sequence quality was basically perfect and yields were reasonably good.

A small number of samples had issues (e.g. a swab sample that didnt work well), and I've emailed those clients to discuss the caveats for their samples.

But the data from this batch were generally very high quality so even if we see unexpected results... they are based on thousands of high quality DNA sequences... enough that I'm confident they reflect the communities sampled.

The questions of what that means... and what drives these communities to look similar or different.. remain wide open and endlessly interesting.
 

Mortie31

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It will be interesting to see how all this unfolds, if any theories develop or if there are just to many variables and lots of different biome balances that lead to a successful tank, I do do find looking at the results interesting, but I‘m not a biologist so the various strains and there importance are lost on me for now...
 

Randy Holmes-Farley

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It will be interesting to see how all this unfolds, if any theories develop or if there are just to many variables and lots of different biome balances that lead to a successful tank, I do do find looking at the results interesting, but I‘m not a biologist so the various strains and there importance are lost on me for now...
Like the human microbiome, I would expect it will require a lot of research to say what is desirable and what may be undesirable with respect to microbes in reef tanks of widely varying organisms and husbandry practices.
 

MnFish1

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Ok as promised here are the results of my AquaBiomics test on my 26 year old 58 gallon Reef tank. Received my results on week 5.. This data provides detailed information on the community of microbes living in my aquarium. Each type of microbe in my sample was identified by comparing DNA sequences from my sample with a database of DNA sequences from known types. The relative abundance of each sequence can be used to compare the relative abundance of each type across samples. Looks like the diversity of my tanks Microbiome is lower than than typical range. I'll be the first to admit I don't know what most of this information means but looking forward to hearing comments of those that do.

Screenshot 2019-11-27 11.46.25.png

Screenshot 2019-11-27 11.46.46.png


Screenshot 2019-11-27 11.47.03.png


Screenshot 2019-11-27 11.47.28.png


Screenshot 2019-11-27 11.47.45.png
My comment would be that your aquarium (at that age) - assuming its doing well - the bacteria that do best in whatever environment you're providing are the ones that are there. Point is - there is no proven level of 'diversity' that is 'good or bad'. Everyone assumes a more diverse bacterial population is 'good'. I have a different thought - Maybe there are certain types of bacteria that are 'best' or 'better' for a tank - and if those are 'more present' than the bacteria that are harmful that COULD be far more beneficial than having a more diverse bacterial population. As a microbiologist - to me - this is a solution in search of a problem. It would be interesting if you tried to add diversity - mud, sand, etc etc - and rechecked in 6 months - my strong hunch would be that it will be relatively the same.
 
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MnFish1

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The questions of what that means... and what drives these communities to look similar or different.. remain wide open and endlessly interesting.
Curious - are you collecting data - or are you actually charging for samples. I agree with you that 'its interesting endlessly' - but if you're charging for this testing at this point - I would hope you would have more answers - and before people call me a naysayer - No - I'm not - and if you want a sample of my tank (especially now - because its doing horribly) - I'd happy to send it in - but - pay for it ? Not so much:)
 

AquaBiomics

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Curious - are you collecting data - or are you actually charging for samples. I agree with you that 'its interesting endlessly' - but if you're charging for this testing at this point - I would hope you would have more answers - and before people call me a naysayer - No - I'm not - and if you want a sample of my tank (especially now - because its doing horribly) - I'd happy to send it in - but - pay for it ? Not so much:)
Salesmen pretend to have concrete answers, while scientists use data to ask questions.

DNA sequencing isn't free, but like ICP, its also not mandatory :)
 

Scott Campbell

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My comment would be that your aquarium (at that age) - assuming its doing well - the bacteria that do best in whatever environment you're providing are the ones that are there. Point is - there is no proven level of 'diversity' that is 'good or bad'. Everyone assumes a more diverse bacterial population is 'good'. I have a different thought - Maybe there are certain types of bacteria that are 'best' or 'better' for a tank - and if those are 'more present' than the bacteria that are harmful that COULD be far more beneficial than having a more diverse bacterial population. As a microbiologist - to me - this is a solution in search of a problem. It would be interesting if you tried to add diversity - mud, sand, etc etc - and rechecked in 6 months - my strong hunch would be that it will be relatively the same.
Perhaps noteworthy that Scubabum's tank and my tank are both old tanks dominated by a single strain of bacteria - even though the dominant strains are different. That might just be what happens as a tank ages.

I was very pleased to see I had no fish or coral pathogens. So perhaps you are correct - a bunch of "good" bacteria regardless of the overall diversity of that good bacteria and a minimal amount of "bad" bacteria might be all that matters.
 

Scott Campbell

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Curious - are you collecting data - or are you actually charging for samples. I agree with you that 'its interesting endlessly' - but if you're charging for this testing at this point - I would hope you would have more answers - and before people call me a naysayer - No - I'm not - and if you want a sample of my tank (especially now - because its doing horribly) - I'd happy to send it in - but - pay for it ? Not so much:)
I would honestly be skeptical if AquaBiomics actually did claim to have "answers". Certainly this early on.

I am more than happy to pay for the test. The results obviously have no practical benefit for me at present - but I am hopeful trends will emerge over time that can be of help to everyone.
 

taricha

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Some reading that may or may not be relevant. It's never a sure thing that "these" bacteria in your system are like "those" bacteria we can read about. But here's maybe interesting associations.

Oceanospirillaceae from @Scubabum
"Widespread Oceanospirillaceae Bacteria in Porites spp." and associated with other massive stony corals.


Rhodobacteraceae from @Scott Campbell
Often these are associates of algae
"They are highly abundant in the pelagic zone ...and in algae-associated biofilms ... The authors report that Rhodobacteraceae can comprise up to 30% of the pelagic Alphaproteobacteria within a coastal lagoon and up to 25% of the total bacterial community in a biofilm at the Mediterranean coast,"

And they provide vitamin b12 that most algae has an absolute need for
"marine Rhodobacteraceae are major vitamin suppliers for B12-auxotrophic prokaryotes and eukaryotic primary producers, such as chlorophytes, diatoms, dinoflagellates, coccolithophores and brown algae"

Or again, maybe "these" bacteria are nothing like "those" bacteria. Even within families, bacteria are endlessly diverse.
 

Scott Campbell

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Some reading that may or may not be relevant. It's never a sure thing that "these" bacteria in your system are like "those" bacteria we can read about. But here's maybe interesting associations.

Oceanospirillaceae from @Scubabum
"Widespread Oceanospirillaceae Bacteria in Porites spp." and associated with other massive stony corals.


Rhodobacteraceae from @Scott Campbell
Often these are associates of algae
"They are highly abundant in the pelagic zone ...and in algae-associated biofilms ... The authors report that Rhodobacteraceae can comprise up to 30% of the pelagic Alphaproteobacteria within a coastal lagoon and up to 25% of the total bacterial community in a biofilm at the Mediterranean coast,"

And they provide vitamin b12 that most algae has an absolute need for
"marine Rhodobacteraceae are major vitamin suppliers for B12-auxotrophic prokaryotes and eukaryotic primary producers, such as chlorophytes, diatoms, dinoflagellates, coccolithophores and brown algae"

Or again, maybe "these" bacteria are nothing like "those" bacteria. Even within families, bacteria are endlessly diverse.
Makes sense - over the years I have often been more focused on growing macroalgae than corals.
 

taricha

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Makes sense - over the years I have often been more focused on growing macroalgae than corals.
Ha!
Now if we find out @Scubabum has a tank full of porites, montastrea and other stony corals from hawaii I'm gonna go buy a lottery ticket.

Scott, would love to hear details on your macroalgae and system?
 

MnFish1

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Salesmen pretend to have concrete answers, while scientists use data to ask questions.

DNA sequencing isn't free, but like ICP, its also not mandatory :)
Which are you - a salesman or a scientist. There is at least data behind ICP testing (though perhaps not behind individual testing companies)? I mean - it was a snappy reply - but it didnt answer what I asked - which was - along the lines of - one of my tanks is having a problem - Is there a charge for sending in a sample. It seems to (me) that a scientist would consider this a valuable piece of data.
 

Scott Campbell

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Ha!
Now if we find out @Scubabum has a tank full of porites, montastrea and other stony corals from hawaii I'm gonna go buy a lottery ticket.

Scott, would love to hear details on your macroalgae and system?
Long ago I got the idea in my head that I could go without water changes by harvesting macroalgae. I would put a certain amount of food in the tank and offset that by pulling out diverse macroalgae. So for about 10+ years I tried to grow a huge variety of macroalgae in my main tank. But it just wasn't a very practical solution. It was too difficult to pull macroalgae out of my main tank - so I eventually added a side tank for most of the algae growth. And trying to keep a diversity of macroalgae types proved challenging. One type or another would invariably take over. And a small amount of food added to a tank becomes a rather enormous amount of macroalgae - so I ended up with just one fish (my yellow tang) with very limited feedings. And even then it was just too difficult to offset the food by growing macroalgae. It was a good learning experience. Life is much easier now harvesting Chaeto out of my side tank, relying more on carbon dosing as my primary export mechanism and filling the main tank with critters that eat algae (urchin, tang, rabbitfish, etc.) Like now I can have more than one fish! <lol>

Bottom line - my tank has always grown a lot of different algae types. Still does. So it makes sense that the bacterial make-up of my tank would reflect that.
 
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