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

[AquaBiomics]

if indeed the proportions in the water are the same, for example as on rock or in the sump vs the tank, etc.

This idea has popped up a couple of times which makes me think I've miscommunicated something. Usually when multiple people have the same mistaken idea it means I have misspoken

I'm not suggesting that the quantities of biofilm bacteria are the same in the water as in the biofilm. Or that their ratios are even the same. I expect that each microhabitat has its own, characteristic microbiome, based on what we see in marine microbial ecology.

Fortunately, our goals don't rely on inferring those levels. We're using the water + biofilm data themselves to compare tanks, not trying to infer the levels in other parts of these tanks. I think of this like sampling the blood to learn about the liver. Sure you could take a liver biopsy, but it would be costly and difficult while blood chemistry is relatively easy; draw blood and send it off to the lab.

Does that make any more sense?

 

[MnFish1]

Sorry but you seems to have no idea about statistics or data analysis!

Hmmm - apology accepted. I do have a graduate degree in microbiology - and several years designing and performing clinical trials - but its possible that I have 'no idea about statistics or data analysis!' (I appreciated the ! in your post). My guess is that you're misreading my post somehow - or not understanding it. My post that you quoted didnt mention anything about statistics or data analysis. The point was:

If the testing (which he said hadn't been completed yet) showed major differences in various parts of the tank/sump - as compared to the general water column - that it would be difficult to correlate which 'microbiome' should be altered with a 'bacterial product' of some sort. Ie is it the live rock biome thats important or the sump biome or the water biome.

 

[AquaBiomics]

I have two tanks on my system, they are 40 feet apart. I would like to see how their biomes compare. Does that make sense with what you are testing?

Are they physically connected by a sump, or separate?

I have tanks half an inch apart (six pairs of them) that show very different microbiomes. So if your question is about the distance between them... as far as I can tell, half an inch is enough to establish a very different community - depending what you put in the tanks.

 

[MnFish1]

This idea has popped up a couple of times which makes me think I've miscommunicated something. Usually when multiple people have the same mistaken idea it means I have misspoken

I'm not suggesting that the quantities of biofilm bacteria are the same in the water as in the biofilm. Or that their ratios are even the same. I expect that each microhabitat has its own, characteristic microbiome, based on what we see in marine microbial ecology.

Fortunately, our goals don't rely on inferring those levels. We're using the water + biofilm data themselves to compare tanks, not trying to infer the levels in other parts of these tanks. I think of this like sampling the blood to learn about the liver. Sure you could take a liver biopsy, but it would be costly and difficult while blood chemistry is relatively easy; draw blood and send it off to the lab.

Does that make any more sense?

Yes thanks - it makes a lot of sense. My question related more to the end result than the goal - i.e. in the end (when you are taking the results of the testing and recommending actions) - do you think it will really be possible to decide 'which bacteria to add' based on a water sample in Tank A as compared to Tank B - when the, for example, live rock biome in Tank A and Tank B may be completely different?

The questions btw are not designed to criticize what you're doing - but rather im curious at the multiple different variables that can affect this..... Like - time of day the sample is taken, the water flow in tank 1 vs tank 2, the reproducibility of the test (i.e. do you find if you take 3 samples that you get relatively the same results over a short time, does the location of where the sample is taken - relative to the return/etc - make a difference. Note - I'm not expecting answers to these questions - they were just things as I was thinking about the research end of your project

 

[AquaBiomics]

Would this be consistent with greater organisms destruction in some tanks than others, such as constant messy herbivores grazing algae? (Herbivores generally needing to consume more material per day than carnivores)

I think this is a very good explanation, grazers are messy. Including zooplankton and micro crustaceans like the tiny amphipods that live all over many aquariums.

Now you've got me curious to ID those mitochondria. One more for the to-do list!

 

[Thales]

Are they physically connected by a sump, or separate?

I have tanks half an inch apart (six pairs of them) that show very different microbiomes. So if your question is about the distance between them... as far as I can tell, half an inch is enough to establish a very different community - depending what you put in the tanks.

Connected by a sump. I'll be sending samples soon.

 

[stacksoner]

I really hope that they sell chloramphenicol for Vibrio and whatever else is needed to solve the problems that they make customers aware of.

 

[rkpetersen]

Which one did you disclude?
If you don't want to name at least give us a hint!

The US one, unfortunately.

 

[AquaBiomics]

I really hope that they sell chloramphenicol for Vibrio and whatever else is needed to solve the problems that they make customers aware of.

This is the #1 question that experienced reefers ask me. "What can I do about it?"

To specifically answer your question about Vibrio, I am not currently testing chloramphenicol because my reading suggests it is not specific enough. I am testing another more specific medication for Vibrio, but it is early in R&D. I can make no promises until I have data to support them.

My vision is not to repackage and sell chloramphenicol, or other simple treatments or additives like this. If that turned out to be the key medication, it could be readily bought in the internet age. After recently setting up a molecular biology lab independently, I will say Its amazing what you can buy on amazon these days

My vision is instead to enable the experiments that will teach us which additives or practices establish a beneficial community, or correct problems in an unhealthy community. I'm running some of these experiments, but I also know that there are experiments underway across the community. Now that the measurements are available, I don't think it'll be long before we all learn collectively what makes a healthy microbiome, and how to establish one.

 

[rushbattle]

This is the #1 question that experienced reefers ask me. "What can I do about it?"

To specifically answer your question about Vibrio, I am not currently testing chloramphenicol because my reading suggests it is not specific enough. I am testing another more specific medication for Vibrio, but it is early in R&D. I can make no promises until I have data to support them.

My vision is not to repackage and sell chloramphenicol, or other simple treatments or additives like this. If that turned out to be the key medication, it could be readily bought in the internet age. After recently setting up a molecular biology lab independently, I will say Its amazing what you can buy on amazon these days

My vision is instead to enable the experiments that will teach us which additives or practices establish a beneficial community, or correct problems in an unhealthy community. I'm running some of these experiments, but I also know that there are experiments underway across the community. Now that the measurements are available, I don't think it'll be long before we all learn collectively what makes a healthy microbiome, and how to establish one.

I just want to say that this effort is so rad. I started with RNA gene chips back in 2002, doing nutrition work. What can be done now for 100 dollars blows my mind completely. Its like the jetsons, but real. Hopefully we can get to that point soon!

 

[AquaBiomics]

Yes thanks - it makes a lot of sense. My question related more to the end result than the goal - i.e. in the end (when you are taking the results of the testing and recommending actions) - do you think it will really be possible to decide 'which bacteria to add' based on a water sample in Tank A as compared to Tank B - when the, for example, live rock biome in Tank A and Tank B may be completely different?

The questions btw are not designed to criticize what you're doing - but rather im curious at the multiple different variables that can affect this..... Like - time of day the sample is taken, the water flow in tank 1 vs tank 2, the reproducibility of the test (i.e. do you find if you take 3 samples that you get relatively the same results over a short time, does the location of where the sample is taken - relative to the return/etc - make a difference. Note - I'm not expecting answers to these questions - they were just things as I was thinking about the research end of your project

I think your questions make a lot of sense. I bet all these factors (time of day, flow, microhabitat etc. ) affect the microbiome, honestly. Biology is messy and complex, thats what makes it so interesting. I have addressed reproducibility and will continue to do so in probably every run - see the graph in post # [I will fill this in] for an example.

Some of these factors (e.g. time of day) also affect aspects of water chemistry (e.g. alkalinity, pH). I figure the best we can do is standardize what we can, and make a note about other details so we can learn which of these have a large effect on the community.

As far as, "what does the water really tell you about the important communities in the rock?" Another good question. I havent shown you the evidence yet so this point naturally remains an unknown.

I've just finished the second of two articles that I considered essential background (posted today on the AquaBiomics homepage). With those completed, next I'll describe a months-long experiment in which I established replicate tanks in different ways.

To your question - these data show that the microbial communities associated with live rock (i.e. the kinds of microbes used to establish different tanks) absolutely determines the community in the water. The effects are not subtle - some treatments (good live rock) promoted microbial communities very similar to mature reef tanks. Other treatments did not, and instead promoted low-diversity communities that processed ammonia and nitrite but looked nothing like a mature reef tank.

So I am convinced the water samples tell us a lot about the surface-associated communities, and think the upcoming article will help make that case. More soon!

 

[AquaBiomics]

I just want to say that this effort is so rad. I started with RNA gene chips back in 2002, doing nutrition work. What can be done now for 100 dollars blows my mind completely. Its like the jetsons, but real. Hopefully we can get to that point soon!

My PhD dissertation relied heavily on a set of about 200 DNA sequences, and consumed many years of my life.

Here, we're sequencing 10,000 DNA sequences at a time for a hobby.

The future is funny. No flying cars yet but still crazy how fast things have moved!

 

[Reesj]

Hmmm - apology accepted. I do have a graduate degree in microbiology - and several years designing and performing clinical trials - but its possible that I have 'no idea about statistics or data analysis!' (I appreciated the ! in your post). My guess is that you're misreading my post somehow - or not understanding it. My post that you quoted didnt mention anything about statistics or data analysis. The point was:

If the testing (which he said hadn't been completed yet) showed major differences in various parts of the tank/sump - as compared to the general water column - that it would be difficult to correlate which 'microbiome' should be altered with a 'bacterial product' of some sort. Ie is it the live rock biome thats important or the sump biome or the water biome.

I'm stuned to learn that some one with your education lack the knowledge how water coloum and surface bacteria levels can help undestand a tanks chemistry. You seriously think that you need to have the same exact amount of bateria in every part of the tank for us to understand about the test results ? You should be able to easily make statistical analysis with a set of data.

Anyway It seems @AquaBiomics already replied as well about this.

 

[stacksoner]

This is the #1 question that experienced reefers ask me. "What can I do about it?"

To specifically answer your question about Vibrio, I am not currently testing chloramphenicol because my reading suggests it is not specific enough. I am testing another more specific medication for Vibrio, but it is early in R&D. I can make no promises until I have data to support them.

My vision is not to repackage and sell chloramphenicol, or other simple treatments or additives like this. If that turned out to be the key medication, it could be readily bought in the internet age. After recently setting up a molecular biology lab independently, I will say Its amazing what you can buy on amazon these days

My vision is instead to enable the experiments that will teach us which additives or practices establish a beneficial community, or correct problems in an unhealthy community. I'm running some of these experiments, but I also know that there are experiments underway across the community. Now that the measurements are available, I don't think it'll be long before we all learn collectively what makes a healthy microbiome, and how to establish one.

A Reef Immunity System of sorts... I tried to purchase antibiotics as a bio lab and got shutdown.

Think about going to a Doctor. You pay for expertise and get a diagnosis and a prescription to fix it. You don't have to buy the meds from the doctor, but s/he will make sure that whatever they prescribe is easily accessible.

 

[MnFish1]

I think your questions make a lot of sense. I bet all these factors (time of day, flow, microhabitat etc. ) affect the microbiome, honestly. Biology is messy and complex, thats what makes it so interesting. I have addressed reproducibility and will continue to do so in probably every run - see the graph in post # [I will fill this in] for an example.

Some of these factors (e.g. time of day) also affect aspects of water chemistry (e.g. alkalinity, pH). I figure the best we can do is standardize what we can, and make a note about other details so we can learn which of these have a large effect on the community.

As far as, "what does the water really tell you about the important communities in the rock?" Another good question. I havent shown you the evidence yet so this point naturally remains an unknown.

I've just finished the second of two articles that I considered essential background (posted today on the AquaBiomics homepage). With those completed, next I'll describe a months-long experiment in which I established replicate tanks in different ways.

To your question - these data show that the microbial communities associated with live rock (i.e. the kinds of microbes used to establish different tanks) absolutely determines the community in the water. The effects are not subtle - some treatments (good live rock) promoted microbial communities very similar to mature reef tanks. Other treatments did not, and instead promoted low-diversity communities that processed ammonia and nitrite but looked nothing like a mature reef tank.

So I am convinced the water samples tell us a lot about the surface-associated communities, and think the upcoming article will help make that case. More soon!

Thanks alot for the explanation -I would not treat any vibrio with chloramphenicol ( ps - it will kill a lot more than vibrio)

 

[taricha]

I've just finished the second of two articles that I considered essential background (posted today on the AquaBiomics homepage). With those completed, next I'll describe a months-long experiment in which I established replicate tanks in different ways.

Loved the finished article (on microbiome differences)!
Can't wait to read next installment.

Two things I'm most looking forward to eventually in this project.
One: Eventual comparisons of microbiome shifts before/after bacteria-directed nutrition interventions (carbon dosing, aminos, coral polyp foods etc.)
Two: possibility of detecting bacterial families that partner with nuisances: cyano, dinos etc.

 

[stacksoner]

Thanks alot for the explanation -I would not treat any vibrio with chloramphenicol ( ps - it will kill a lot more than vibrio)

Chloramphenicol is the only scientifically proven treatment for Brown Jelly Disease, White Band Disease, and RTN. What else is at risk of dying when all your corals are getting annihilated by such an aggressive bacteria that's resistant to every other antibiotic?

https://royalsocietypublishing.org/doi/full/10.1098/rspb.2014.0094

 

[MnFish1]

Chloramphenicol is the only scientifically proven treatment for Brown Jelly Disease, White Band Disease, and RTN. What else is at risk of dying when all your corals are getting annihilated by such an aggressive bacteria that's resistant to every other antibiotic?

https://royalsocietypublishing.org/doi/full/10.1098/rspb.2014.0094

There is probably vibrio in every tank. It does not always cause a problem - I was only saying that if it happens to be found - it doesnt need to be eliminated unless there is a disease

 

[sde1500]

So think of it this way, take a piece of coral that is RTNing and frag away the dieing tissue. Take that tissue and swish it in some water. Send that for analysis and get the results back now knowing what strains are in play.

LOL I can think of a company that thinks they wouldn't need that sample to scream from the hill tops EXACTLY what you'll find.

2. By building a large database of samples from hobbyist and aquaculture tanks, we will learn a lot. I already have some data in hand and am gathering more.

This will be very interesting to follow. I read much of this thread and understood far less, but it seems to be very fascinating project. For now maybe not much more than to say "neat" after the results. But data is wildly valuable these days.

I don’t want to be misinterpreted; I think this testing is awesome and provides a lot of data. I just hope such cultures are not immediately commercialized and sold based on the test results. For all we know, said tank with dinos could have a full microbial recovery if fed more— and just pouring in the absent microbes would do nothing, as it is not the “cause” of the issue. Just correlational.

Agreed, that was my initial thought as well. Too quick to commercialize an additive could be misconstrued as "snake oil". See above comment on screaming company.

I found this exert from Eli's analysis very interesting

"We screened for 9 different coral pathogens, and found no evidence of these in any tanks sampled for this study. "

*Prime corals has left the chat*

I can share my specific laboratory protocols if someone wants them -- there is no room for secrecy in science, and no need for it in a service like this.

Fantastic stance. For something this opaque, to provide all the info you can certainly serves to alleviate peoples concerns.

Neat service, I commend you for being so transparent!

Seconded

Briefly, here is part of my reports for two tanks; one doing well, and the other that was dealing with frequent dinoflagellate outbreaks.

First, here is the key that is provided by AquaBiomics to help you interpret your scores:

Here are the scores for one of my tanks that was doing well.

Here are the scores for the tank with dino outbreaks

The diversity score is in the red, and my microbial richness is in the yellow. Per the recommendations from this report, I added some live rock from the tank that was doing well. The dinoflagellate problems have subsided since. Soon, I will have a follow up report to see how the microbiome has changed, if at all, since the first snapshot.

That is where the data will be super interesting, I'd imagine the snapshot would improve. Post that analysis would be to determine if it remains diverse, and or what happened to cause the lack of diversity.

Sorry but you seems to have no idea about statistics or data analysis!

I'm stuned to learn that some one with your education lack the knowledge how water coloum and surface bacteria levels can help undestand a tanks chemistry. You seriously think that you need to have the same exact amount of bateria in every part of the tank for us to understand about the test results ? You should be able to easily make statistical analysis with a set of data.

Anyway It seems @AquaBiomics already replied as well about this.

Curious why you felt it necessary to resort quickly to insults? Nothing said was egregious. Had I levied the question you would have been correct in your assumption I am not well versed in those topics. However it would have been equally uncalled for to insult me. We all are here to ask questions, learn, and advance this hobby. What is in this thread is quite advanced, far beyond the understanding of many. Consider that prior to lobbing insults next time.

 

[MnFish1]

I'm stuned to learn that some one with your education lack the knowledge how water coloum and surface bacteria levels can help undestand a tanks chemistry. You seriously think that you need to have the same exact amount of bateria in every part of the tank for us to understand about the test results ? You should be able to easily make statistical analysis with a set of data.

Anyway It seems @AquaBiomics already replied as well about this.

I'm stunned that you don't know how to spell stunned...... JK. You're putting words in my mouth and implying something I never did. BTW - the reason he is STUDYING this whole thing is because No one knows exactly how water column and surface bacteria can help understand a tanks chemistry - so I don't get your perceived 'anger' - or whatever at my merely asking questions to the researcher.

My gut feeling is that (again unless he has data to the contrary) - and data as to how reproducible the tests are depending on the factors I already mentioned - I don't know what to make of a report based on a single test from a single water area.