The Microbial Community in a Professional Coral Aquaculture System

The Microbial Community in a Professional Coral Aquaculture System
A discussion with Adam Derickson of BattleCorals


Eli Meyer, AquaBiomics​

EM: Ever since I started trying to grow corals, I’ve been awed by some reef-keepers’ abilities to duplicate a coral reef ecosystem in their living rooms. You know the reef tanks I’m talking about, the ones filled with bushy colonies of Acropora growing so fast the tips are almost sticking out of the water. After years of reading and comparing notes with other hobbyists I couldn’t escape the conclusion there was something different about the water their tanks… something not measured in all our water quality testing. So I embarked on a new project to study the microbial communities that support aquarium ecosystems.

We’ve already learned a lot by comparing hobbyist’s tanks. But I still wondered what the microbiome of a dedicated coral aquaculture facility would look like. Are the professionals doing something different? So when I had the opportunity to test the microbiome in the main system at BattleCorals I jumped at it. We’ve all drooled over pictures of the corals grown in this tank… see for example the random selection of recently posted images from BattleCorals that I compiled for Figure 1.

bc compilation.jpg

Figure 1: Examples of Acropora grown at BattleCorals in the tank tested for this article. Photo credit: Adam Derickson.

Here’s a chance to learn something new about the system where those corals grew.

In this article, I’ll discuss these results with Adam Derickson of BattleCorals, who has been kind enough to share these findings with the community and answer some of our questions. Adam, thanks for your time and willingness to share these data with the community!


AD: My pleasure. I am truly impressed with this whole concept and humbled to be a part of your research.


EM: DNA sequencing is easy compared with growing corals that look like that!

But in hopes of learning a little about how you do it, lets talk about your test results. I’ve summarized some key findings in Figure 2 so the reader can easily find the numbers we’ll be discussing.

Let’s start with diversity. The diversity in this tank is similar to the average diversity in other tanks I’ve sampled. Between your biofilm and water samples we found just over 200 different types in your sample (212). This is right in the middle of the pack: half the tanks I’ve surveyed had higher diversity, and half had lower.

Experiments have shown that diverse communities like this don’t just happen on their own. Can you share any details about how you established the microbial community in this tank?

bc infographic.jpg

Figure 2: An infographic summarizing key findings from microbiome testing of the BattleCorals aquarium. Image and testing provided by AquaBiomics.

AD: Great question. The system tested is not that old. I set it up in the spring of 2017, after construction of my new facility was completed. While I actually didn't use any of the rock from my older system, I did use a lot of the water. I transferred a few hundred gallons from the old, to the new when I initially set it up. Some of the rock in my older system had been in saltwater tanks dating back 20+ years, most of the rock over 15 at least. So it's been long established, built from many different sources, and through a great deal of ups and downs over the years.


EM
: Really interesting that you used old water but not old rock. I sometimes encounter the view that “most of the microbes are in the rock, what’s in the water doesn’t matter”. Of course, direct counts show tens of thousands of bacteria per ml of aquarium water, and DNA evidence shows these include many of the ones hobbyists care about.

Your experience shows that this water can also be used to establish a healthy microbiome in a new aquarium. At least if you add enough of it!

Next lets talk about the levels of microbes in your results. The balance of different bacterial families in your tank was very different from the average aquarium I’ve sampled. In other words, the families that are typically present at high levels (Flavobacteriaceae and Pelagibacteraceae) were low in your sample. In their place, a few families typically present at low levels were much higher in your sample (Vibrionaceae, Verrucomicrobiaceae, and Fusobacteriaceae).

Researchers studying microbial “blooms” in the ocean (when one group of microbes rises to high levels) have found these are driven by environmental conditions, especially the kinds and amounts of nutrients available. So when I see an unusual balance of microbial families, I start by looking for possible explanations in the water chemistry.

I notice that you’re running at a higher salinity than many reefers which may play a role here since many microbes are really sensitive to salt levels. I’m guessing this is to maximize growth rates, right? I’d be curious to hear about your experience when you increased salinity.


AD: Its was a fluke actually that it happened in the first place. Here's the story (excerpt from write up). One day many years ago, and it really was one of those "well one day" type instances, I couldn't help but notice that my SPS were looking good, and I mean really good, like that thick powdery looking flesh that I had never quite been able to achieve, in all my years. I saw deep coloration and bursting new growth at every node. It was remarkable! Overall things were just doing much better than I was generally used too. After simple rundown of some basic params, the only real blaring change from my norm of many years, was that rather than seeing 1.025 on my refracto it was closer to 1.027.

So what happened was that over time, my rogue water replacement methods had crept my salinity up. And seeing the apparent effects on my own tank inhabitants, I have been keeping it high ever since. Really, it's just that simple. I stumbled upon something that seemed to be a good thing, and I have been riding high ever since.


0D714D73-837E-4ED0-AB53-92F7757AB020.jpeg

Figure 3: A view of the BattleCorals tanks tested for this article. Photo credit: Adam Derickson.

EM: I’ll add that while your salinity isn’t that much higher than a natural reef, many of the tanks I’ve sampled run at substantially lower levels (33 ppt or below). This makes me wonder whether differences in salinity within this range affect the microbial community… I think an experiment may be needed!

Dissolved nutrients are also likely to affect these levels. Based on the phosphate levels logged for your sample I would guess this system gets fed pretty generously. Can you share any details about what you feed this tank, and how frequently?


AD: Yeah, I have never been one to shy away from nutrients in the system. I like to see some measurable amount of phosphate and nitrate in my systems. I have a lot of fish and feed them well. Some of the only times I've really seen a definite noticeable reduction in polyp extension was when my phosphate levels bottomed out.


EM: Your description of a lot of well fed fish is interesting. Your tank has more Fusobacteriaceae than most, and in your case they’re almost all in the genus Cetobacterium, which is a well-known member of the fish gut microbiome. In other words, your tank’s microbiome shows evidence of a lot of fish poop!

I also notice you dose Iodide. While this is not uncommon in the hobby, few of the tanks I’ve sampled dose Iodide regularly, and this is known to affect the composition of marine microbial communities. I’d be curious to hear about your Iodide dosing practices and your experience with its effects.


AD: Another great question. This is something that came out of ICP testing. I have never paid much attention to iodine. When Triton first hit the scene I had my tank tested and at one point early on I had extremely low, undetectable iodine. And at the same time was seeing some abnormalities in a lot of my sps colonies. Mainly thinned tissue and minor tissue recession around bases. I went ahead and boosted my iodine levels and things did seem to perk up. Many of the symptoms I was seeing did subside after the iodine was brought up, so I've been supplementing lightly ever since.


EM: One of the things that really stood out about your tank for me is the high levels of nutrient-processing microbes. Ammonia-oxidizing microbes made up almost 8% of your sample, which is higher than about 85% of aquariums I’ve tested, about twice as high as the average sample. Your sample also had high levels of nitrite-oxidizing bacteria (0.9%), which is among the highest of any tanks tested (higher than 96% of samples), and over 3-times higher than the average sample.

This may not come as a surprise, since we expect to find these in a tank with a functional biofilter. But in fact, many established tanks have very low levels of these microbes. In some cases, nitrite-oxidizing bacteria aren’t even detected (although they’re likely still present at low levels).

As I review these surveys from different tanks, lately I’ve been thinking about competition between microbes and other organisms for ammonia. I’m considering the hypothesis that some tanks process most of the ammonia through nitrification, some through assimilation by invertebrates or heterotrophic bacteria, and some through assimilation by algae. In this framework, your tank appears to process most of its ammonia through nitrification, the classic pathway we all learn about when cycling a new tank.

To evaluate this interpretation of your system as “nitrification-dominated” I’d like to ask, do you deliberately grow any macroalgae in this system (e.g. in a reactor?) Similarly, would you say your tank has a large biomass of sponges or very little?


B24E2203-3A6A-467D-8FE9-F5A2B15D501E.jpeg

Figure 4: A view showing some of the live rock housed in the system tested for this article. Photo credit: Adam Derickson.

AD: I dont run algae or any means to keep macro in my systems any more but I do have a lot of different sponges in “cryptic” zones.


EM: So it sounds like no major algal populations to compete for ammonia, but perhaps some competition by sponges. Since I believe you don’t carbon dose, heterotrophic bacterial uptake is also likely pretty low in this system. This seems consistent with a system processing most of its ammonia through nitrification rather than heterotrophic or photoautotrophic assimilation.

Another factor that’s likely to influence these communities is the total amount of ammonia processed through the system. In principle an aquarium can maintain stable levels by matching high nutrient export to high nutrient import, or by matching low export to low import. But the former would be expected to support higher populations of ammonia-oxidizing microbes.

Based on your tank’s bioload and nutrient export, would you say your tank falls closer to the high-export, high-import end of the range, or the low-import, low-export end?


AD: I think I'm on the higher end for sure.


EM: So lots of ammonia moving through the system, and high levels of nitrifying microbes but very little competition by algae. Sounds like a very different situation from my display tanks, all of which process a lot of nitrogen through macroalgae, and have very low levels of nitrifying microbes. Interesting…

Another piece of good news in your results was the absence of known bacterial pathogens of fish or corals. I screened for almost 50 different pathogens and found none in your sample. Meanwhile, 1 out of 10 tanks I’ve tested has a coral pathogen, and 1 out of 8 has a fish pathogen.

I’m especially interested in wild imported corals, since a recent study shows that about 1 out of 3 corals sampled in nature has a parasitic bacterium that can behave as a pathogen under some conditions. I’ve found this bug (Aquarickettsia rohweri) in other tanks, but not your system!

As a profession coral grower I imagine you add new corals to the tank regularly. The absence of any detectable pathogens in your tank suggests you’ve come up with some successful practices for avoiding introducing pathogens or pests into your system. Are there any secrets you can share about how you treat and introduce new corals to keep your system?


AD
: Hmm well this is a topic that may deserve its own discussion actually. But in short, over the years I've developed definitely a pretty good routine to prevent unwanted organisms from getting into my systems. Patience, a keen eye, and a “no exceptions” policy are at the heart of this routine.


EM: I would definitely be interested in reading more about this! I’ve encountered lots of variation in how different reefers treat new corals before adding them to the tank. Since you’re doing it on a larger scale without introducing pathogens or parasites it would be great to hear more about what you’re looking for as you decide whether a coral is ready to be added to the main system.

It’s been really interesting for me check out the microbial community in your tank - it turns out that there is something different in your water. It’s providing a lot of food for thought about how to adjust the microbial communities in my own aquariums.

The science of aquarium microbiomes has not yet reached a stage where anyone can offer guaranteed prescriptions. This is the era of study and experiments. I believe that studying the microbiomes of successful tanks, and identifying the practices that led to the development of these communities will help the hobbyist community to develop evidence-based practices for establishing a healthy microbiome. So thank you again, Adam, for your contribution toward this effort! I hope this discussion was interesting for readers of Reef2Reef and inspires further experiments to understand the complex ecosystems in our aquariums.


AD: It has been my pleasure completely! I am in awe of what you are doing here and am honored to be included in your studies. I think this is a really exciting time for reef aquarists and it’s amazing to see testing of this sort made available to hobbyists. I see it as a new frontier of exploration and understanding of our reefs and the data you collect will greatly benefit the entire community in years to come. Thanks again for the consideration. I really look forward to what’s in store.

[edit - sorry for issues with images in the first version of this post. I think I have them fixed now!]
 
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sixty_reefer

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This have always fascinating me - it seems to be a trend world wide. In Swedish forum and Facebook groups people always advise not to use used water even if it comes from known healthy aquariums. When people buy working aquariums and ask if they should keep the water or some of it - 95 % of the advises sound like - no - no - no. Give it a fresh start - change 100 % of the water. In such cases - I always ask - if the original owner change his/her mind and decide not to sell - should you still advise - change 100 % of the water - otherwise you run in problems? I always advise - if you move it - clean the sand from most organic matter but keep the water.

Sincerely Lasse

In freshwater they used to say to keep the water it’s interesting how from salt to fresh the ideology it’s different
 

Chefwheredyougo

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It was a fleeting notion that faded with a slight smirk then a sigh, but I have to confess I did imagine see some dystopian future wherein we started selling our......... water. No coral in that bag, just water lol.
Apparently we should all be using it!
 

Ranjib

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Thank you so much for sharing this . Very very informative . I would love to know how this differs in a tank that’s struggling to grow sps. And if commonality exists among struggling tanks .
This is absolutely awesome article. Thank you again @Battlecorals and @AquaBiomics , I learned a lot reading through this .
 

John Biddle

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The Microbial Community in a Professional Coral Aquaculture System
A discussion with Adam Derickson of BattleCorals


Eli Meyer, AquaBiomics​

EM: Ever since I started trying to grow corals, I’ve been awed by some reef-keepers’ abilities to duplicate a coral reef ecosystem in their living rooms. You know the reef tanks I’m talking about, the ones filled with bushy colonies of Acropora growing so fast the tips are almost sticking out of the water. After years of reading and comparing notes with other hobbyists I couldn’t escape the conclusion there was something different about the water their tanks… something not measured in all our water quality testing. So I embarked on a new project to study the microbial communities that support aquarium ecosystems.

We’ve already learned a lot by comparing hobbyist’s tanks. But I still wondered what the microbiome of a dedicated coral aquaculture facility would look like. Are the professionals doing something different? So when I had the opportunity to test the microbiome in the main system at BattleCorals I jumped at it. We’ve all drooled over pictures of the corals grown in this tank… see for example the random selection of recently posted images from BattleCorals that I compiled for Figure 1.

bc compilation.jpg

Figure 1: Examples of Acropora grown at BattleCorals in the tank tested for this article. Photo credit: Adam Derickson.
Here’s a chance to learn something new about the system where those corals grew.


In this article, I’ll discuss these results with Adam Derickson of BattleCorals, who has been kind enough to share these findings with the community and answer some of our questions. Adam, thanks for your time and willingness to share these data with the community!


AD: My pleasure. I am truly impressed with this whole concept and humbled to be a part of your research.


EM: DNA sequencing is easy compared with growing corals that look like that!

But in hopes of learning a little about how you do it, lets talk about your test results. I’ve summarized some key findings in Figure 2 so the reader can easily find the numbers we’ll be discussing.

Let’s start with diversity. The diversity in this tank is similar to the average diversity in other tanks I’ve sampled. Between your biofilm and water samples we found just over 200 different types in your sample (212). This is right in the middle of the pack: half the tanks I’ve surveyed had higher diversity, and half had lower.

Experiments have shown that diverse communities like this don’t just happen on their own. Can you share any details about how you established the microbial community in this tank?

bc infographic.jpg

Figure 2: An infographic summarizing key findings from microbiome testing of the BattleCorals aquarium. Image and testing provided by AquaBiomics.
AD: Great question. The system tested is not that old. I set it up in the spring of 2017, after construction of my new facility was completed. While I actually didn't use any of the rock from my older system, I did use a lot of the water. I transferred a few hundred gallons from the old, to the new when I initially set it up. Some of the rock in my older system had been in saltwater tanks dating back 20+ years, most of the rock over 15 at least. So it's been long established, built from many different sources, and through a great deal of ups and downs over the years.



EM
: Really interesting that you used old water but not old rock. I sometimes encounter the view that “most of the microbes are in the rock, what’s in the water doesn’t matter”. Of course, direct counts show tens of thousands of bacteria per ml of aquarium water, and DNA evidence shows these include many of the ones hobbyists care about.

Your experience shows that this water can also be used to establish a healthy microbiome in a new aquarium. At least if you add enough of it!

Next lets talk about the levels of microbes in your results. The balance of different bacterial families in your tank was very different from the average aquarium I’ve sampled. In other words, the families that are typically present at high levels (Flavobacteriaceae and Pelagibacteraceae) were low in your sample. In their place, a few families typically present at low levels were much higher in your sample (Vibrionaceae, Verrucomicrobiaceae, and Fusobacteriaceae).

Researchers studying microbial “blooms” in the ocean (when one group of microbes rises to high levels) have found these are driven by environmental conditions, especially the kinds and amounts of nutrients available. So when I see an unusual balance of microbial families, I start by looking for possible explanations in the water chemistry.

I notice that you’re running at a higher salinity than many reefers which may play a role here since many microbes are really sensitive to salt levels. I’m guessing this is to maximize growth rates, right? I’d be curious to hear about your experience when you increased salinity.


AD: Its was a fluke actually that it happened in the first place. Here's the story (excerpt from write up). One day many years ago, and it really was one of those "well one day" type instances, I couldn't help but notice that my SPS were looking good, and I mean really good, like that thick powdery looking flesh that I had never quite been able to achieve, in all my years. I saw deep coloration and bursting new growth at every node. It was remarkable! Overall things were just doing much better than I was generally used too. After simple rundown of some basic params, the only real blaring change from my norm of many years, was that rather than seeing 1.025 on my refracto it was closer to 1.027.

So what happened was that over time, my rogue water replacement methods had crept my salinity up. And seeing the apparent effects on my own tank inhabitants, I have been keeping it high ever since. Really, it's just that simple. I stumbled upon something that seemed to be a good thing, and I have been riding high ever since.


0D714D73-837E-4ED0-AB53-92F7757AB020.jpeg

Figure 3: A view of the BattleCorals tanks tested for this article. Photo credit: Adam Derickson.
EM: I’ll add that while your salinity isn’t that much higher than a natural reef, many of the tanks I’ve sampled run at substantially lower levels (33 ppt or below). This makes me wonder whether differences in salinity within this range affect the microbial community… I think an experiment may be needed!


Dissolved nutrients are also likely to affect these levels. Based on the phosphate levels logged for your sample I would guess this system gets fed pretty generously. Can you share any details about what you feed this tank, and how frequently?


AD: Yeah, I have never been one to shy away from nutrients in the system. I like to see some measurable amount of phosphate and nitrate in my systems. I have a lot of fish and feed them well. Some of the only times I've really seen a definite noticeable reduction in polyp extension was when my phosphate levels bottomed out.


EM: Your description of a lot of well fed fish is interesting. Your tank has more Fusobacteriaceae than most, and in your case they’re almost all in the genus Cetobacterium, which is a well-known member of the fish gut microbiome. In other words, your tank’s microbiome shows evidence of a lot of fish poop!

I also notice you dose Iodide. While this is not uncommon in the hobby, few of the tanks I’ve sampled dose Iodide regularly, and this is known to affect the composition of marine microbial communities. I’d be curious to hear about your Iodide dosing practices and your experience with its effects.


AD: Another great question. This is something that came out of ICP testing. I have never paid much attention to iodine. When Triton first hit the scene I had my tank tested and at one point early on I had extremely low, undetectable iodine. And at the same time was seeing some abnormalities in a lot of my sps colonies. Mainly thinned tissue and minor tissue recession around bases. I went ahead and boosted my iodine levels and things did seem to perk up. Many of the symptoms I was seeing did subside after the iodine was brought up, so I've been supplementing lightly ever since.


EM: One of the things that really stood out about your tank for me is the high levels of nutrient-processing microbes. Ammonia-oxidizing microbes made up almost 8% of your sample, which is higher than about 85% of aquariums I’ve tested, about twice as high as the average sample. Your sample also had high levels of nitrite-oxidizing bacteria (0.9%), which is among the highest of any tanks tested (higher than 96% of samples), and over 3-times higher than the average sample.

This may not come as a surprise, since we expect to find these in a tank with a functional biofilter. But in fact, many established tanks have very low levels of these microbes. In some cases, nitrite-oxidizing bacteria aren’t even detected (although they’re likely still present at low levels).

As I review these surveys from different tanks, lately I’ve been thinking about competition between microbes and other organisms for ammonia. I’m considering the hypothesis that some tanks process most of the ammonia through nitrification, some through assimilation by invertebrates or heterotrophic bacteria, and some through assimilation by algae. In this framework, your tank appears to process most of its ammonia through nitrification, the classic pathway we all learn about when cycling a new tank.

To evaluate this interpretation of your system as “nitrification-dominated” I’d like to ask, do you deliberately grow any macroalgae in this system (e.g. in a reactor?) Similarly, would you say your tank has a large biomass of sponges or very little?


B24E2203-3A6A-467D-8FE9-F5A2B15D501E.jpeg

Figure 4: A view showing some of the live rock housed in the system tested for this article. Photo credit: Adam Derickson.
AD: I dont run algae or any means to keep macro in my systems any more but I do have a lot of different sponges in “cryptic” zones.



EM: So it sounds like no major algal populations to compete for ammonia, but perhaps some competition by sponges. Since I believe you don’t carbon dose, heterotrophic bacterial uptake is also likely pretty low in this system. This seems consistent with a system processing most of its ammonia through nitrification rather than heterotrophic or photoautotrophic assimilation.

Another factor that’s likely to influence these communities is the total amount of ammonia processed through the system. In principle an aquarium can maintain stable levels by matching high nutrient export to high nutrient import, or by matching low export to low import. But the former would be expected to support higher populations of ammonia-oxidizing microbes.

Based on your tank’s bioload and nutrient export, would you say your tank falls closer to the high-export, high-import end of the range, or the low-import, low-export end?


AD: I think I'm on the higher end for sure.


EM: So lots of ammonia moving through the system, and high levels of nitrifying microbes but very little competition by algae. Sounds like a very different situation from my display tanks, all of which process a lot of nitrogen through macroalgae, and have very low levels of nitrifying microbes. Interesting…

Another piece of good news in your results was the absence of known bacterial pathogens of fish or corals. I screened for almost 50 different pathogens and found none in your sample. Meanwhile, 1 out of 10 tanks I’ve tested has a coral pathogen, and 1 out of 8 has a fish pathogen.

I’m especially interested in wild imported corals, since a recent study shows that about 1 out of 3 corals sampled in nature has a parasitic bacterium that can behave as a pathogen under some conditions. I’ve found this bug (Aquarickettsia rohweri) in other tanks, but not your system!

As a profession coral grower I imagine you add new corals to the tank regularly. The absence of any detectable pathogens in your tank suggests you’ve come up with some successful practices for avoiding introducing pathogens or pests into your system. Are there any secrets you can share about how you treat and introduce new corals to keep your system?


AD
: Hmm well this is a topic that may deserve its own discussion actually. But in short, over the years I've developed definitely a pretty good routine to prevent unwanted organisms from getting into my systems. Patience, a keen eye, and a “no exceptions” policy are at the heart of this routine.


EM: I would definitely be interested in reading more about this! I’ve encountered lots of variation in how different reefers treat new corals before adding them to the tank. Since you’re doing it on a larger scale without introducing pathogens or parasites it would be great to hear more about what you’re looking for as you decide whether a coral is ready to be added to the main system.

It’s been really interesting for me check out the microbial community in your tank - it turns out that there is something different in your water. It’s providing a lot of food for thought about how to adjust the microbial communities in my own aquariums.

The science of aquarium microbiomes has not yet reached a stage where anyone can offer guaranteed prescriptions. This is the era of study and experiments. I believe that studying the microbiomes of successful tanks, and identifying the practices that led to the development of these communities will help the hobbyist community to develop evidence-based practices for establishing a healthy microbiome. So thank you again, Adam, for your contribution toward this effort! I hope this discussion was interesting for readers of Reef2Reef and inspires further experiments to understand the complex ecosystems in our aquariums.


AD: It has been my pleasure completely! I am in awe of what you are doing here and am honored to be included in your studies. I think this is a really exciting time for reef aquarists and it’s amazing to see testing of this sort made available to hobbyists. I see it as a new frontier of exploration and understanding of our reefs and the data you collect will greatly benefit the entire community in years to come. Thanks again for the consideration. I really look forward to what’s in store.

[edit - sorry for issues with images in the first version of this post. I think I have them fixed now!]
The science of human gut microbiomes has not yet reached a stage where anyone can offer guaranteed prescriptions either, and it's getting a whole lot more research. I'm not sure which of the two biomes would be expected to be more varied and complicated. Humans areonly one species but are very complex animals with widely varying diets and environments. Reefs have far more animal diversity. My guess is this interesting work on't yield much in the way of useful results for many many years. Sad, seems ripe for a breakthrough.
 

Skynyrd Fish

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I have always been a fan of adding some good water from an awesome tank. I added a bunch of frags this year and dipped and replugged. My nice wife and kids got me two wwc frags. They went straight In The tank and so did all the water. I did not replug them. Since then I have noticed a couple corals have perked up and have been on the move. A red, blue and green Millie I’ve had for 7 months that has done not much went into go mode. It has sprouted new branches and colored up deeper within 3 to 4 weeks of adding the water. Coincidence? Maybe, maybe not. My tank has been set up running for 19 years. I got a new tank to set up, when I do I’ll be ordering a battle box with that good water. You got some old Detroit favorites I’d like. Especially sunnyx sunset Milli. I can’t find any at the swaps around here. Thanx guys for the write up. Makes sense to me.
 

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Interesting idea. I would be curious to see how my system compares to @Battlecorals as we have exchanged a lot of coral over the years, though not a lot of water :) I think we have a track record that we can both agree varies between what has done well for one of us or the other!

My system is much older, based on about 30 lbs of cultured Fiji live rock from 2006 that has really shaped the fauna in the tank. Ridiculous quantity and diversity of life were on that rock, unlike anything I've ever seen before or since...2 sea hares, 2" predatory flatworm, 3 spp. of Xenia, a Tubipora, colonial tunicates, half a dozen urchins, crabs, etc. just to name the big stuff. Though sadly not much of that persisted, the sponge diversity is still pretty robust 14 years later, and is quick to colonize the couple hundred pounds of dry rock I've seeded since. If I had a time machine I would go back in a heartbeat and buy a lot more than 30 lbs of it!

Up for a comparison test @AquaBiomics ? I'm also curious about your methods and more detailed results if you can share them. I dabbled in genetics for my M.S. but it was before the days of next gen.
 

therman

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The science of human gut microbiomes has not yet reached a stage where anyone can offer guaranteed prescriptions either, and it's getting a whole lot more research. I'm not sure which of the two biomes would be expected to be more varied and complicated. Humans areonly one species but are very complex animals with widely varying diets and environments. Reefs have far more animal diversity. My guess is this interesting work on't yield much in the way of useful results for many many years. Sad, seems ripe for a breakthrough.

A good friend of mine, Steve Robbins, who was actually a volunteer from my zoo days went on to study coral/sponge microbiomes in Australia. He recently published the results of a heap of work in this paper, with a load of interesting insights into what is going on in a species of SPS (Porites lutea). So dont despair, things are happening!

 
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Interesting idea. I would be curious to see how my system compares to @Battlecorals as we have exchanged a lot of coral over the years, though not a lot of water :) I think we have a track record that we can both agree varies between what has done well for one of us or the other!

My system is much older, based on about 30 lbs of cultured Fiji live rock from 2006 that has really shaped the fauna in the tank. Ridiculous quantity and diversity of life were on that rock, unlike anything I've ever seen before or since...2 sea hares, 2" predatory flatworm, 3 spp. of Xenia, a Tubipora, colonial tunicates, half a dozen urchins, crabs, etc. just to name the big stuff. Though sadly not much of that persisted, the sponge diversity is still pretty robust 14 years later, and is quick to colonize the couple hundred pounds of dry rock I've seeded since. If I had a time machine I would go back in a heartbeat and buy a lot more than 30 lbs of it!

Up for a comparison test @AquaBiomics ? I'm also curious about your methods and more detailed results if you can share them. I dabbled in genetics for my M.S. but it was before the days of next gen.
Hi, I'm happy to share details about methods and output. None of these details are proprietary - I'm using standard approaches used by the genomics and microbiology community.

Briefly, I amplify a region of the 16S marker from each sample, and sequence the resulting amplicon library on Illumina MiSeq. I produce about 10,000 paired reads (DNA sequences) from each amplicon. After filtering these to remove low-quality or uninformative reads, I identify and count the sequence variants in each sample using the dada2 package in R. Finally I compare each sequence variant to the GreenGenes database to identify the type or microbe (Bacteria or Archaea) each sequence came from. This produces a list of microbial types and their abundance, which I use to produce the report. Thats a very short overview, I'd be happy to go into more details.

I've attached an example report. These are results from one of my tanks (this is *not* an ideal microbiome; just a report I am free to share since it came from one of my own tanks!) I've slightly updated the report format since making this one, but this gives you some idea what the user gets.

If a user wanted more details (e.g. a complete list of the hundreds of different microbes in their sample, with their abundances), I can easily produce this and send it on request. My sense was that most users would prefer a summarized version so thats what I include by default.

Does that help?
 

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therman

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Hi, I'm happy to share details about methods and output. None of these details are proprietary - I'm using standard approaches used by the genomics and microbiology community.

Briefly, I amplify a region of the 16S marker from each sample, and sequence the resulting amplicon library on Illumina MiSeq. I produce about 10,000 paired reads (DNA sequences) from each amplicon. After filtering these to remove low-quality or uninformative reads, I identify and count the sequence variants in each sample using the dada2 package in R. Finally I compare each sequence variant to the GreenGenes database to identify the type or microbe (Bacteria or Archaea) each sequence came from. This produces a list of microbial types and their abundance, which I use to produce the report. Thats a very short overview, I'd be happy to go into more details.

I've attached an example report. These are results from one of my tanks (this is *not* an ideal microbiome; just a report I am free to share since it came from one of my own tanks!) I've slightly updated the report format since making this one, but this gives you some idea what the user gets.

If a user wanted more details (e.g. a complete list of the hundreds of different microbes in their sample, with their abundances), I can easily produce this and send it on request. My sense was that most users would prefer a summarized version so thats what I include by default.

Does that help?


Very cool! Have you done any baseline testing for wild reefs? Any microbial trends you see correlated with types of corals (hard vs. soft, SPS vs. LPS, etc)? Differences if tanks were started with Indo Pacific rock vs Caribbean rock? So many questions...
 
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The science of human gut microbiomes has not yet reached a stage where anyone can offer guaranteed prescriptions either, and it's getting a whole lot more research. I'm not sure which of the two biomes would be expected to be more varied and complicated. Humans areonly one species but are very complex animals with widely varying diets and environments. Reefs have far more animal diversity. My guess is this interesting work on't yield much in the way of useful results for many many years. Sad, seems ripe for a breakthrough.
Yeah, most researchers I know in the field are pretty skeptical (for example) of the many unregulated "probiotics" sold to benefit the human gut microbiome.

On the other hand, its clear that adjusting the human gut microbiome can have important benefits for human health. Fecal microbiota transplantation (FMT) has been widely used to treat Clostridium difficile infections (Kelley et al. 2015). The same approach shows promising results for a growing number of other conditions, including obesity / metabolic syndrome (Marotz & Zarrinpar 2016) and inflammatory bowel diseases (Narula et al 2017)

It's clear that the microbiome can be adjusted, whether through diet, environmental effects, or FMT. But most treatments marketed to adjust the human gut microbiome are based on little to no clinical evidence.

The same is true in the aquarium hobby... so many products claiming to affect the microbial community, but how many of these claims are supported by evidence? I wish there was as much evidence available for any of these products as there is for live rock from my little study.

I share your sense that this area is ripe for a breakthrough, but am perhaps more optimistic about how quickly we can answer some of these questions. We don't have the funding or numbers of medical research, but we also don't have the FDA standing in the way! As a researcher I'm interested in answering some of these questions anyway, but as a reef keeper I am optimistic that we'll be able to freely experiment with any new treatments suggested by these tests.
 
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Very cool! Have you done any baseline testing for wild reefs? Any microbial trends you see correlated with types of corals (hard vs. soft, SPS vs. LPS, etc)? Differences if tanks were started with Indo Pacific rock vs Caribbean rock? So many questions...
I havent done the comparison yet, but there are lots of publicly available data from natural reefs. I will write up a comparison at some point. Since the raw data are available, I don't see any need for new samples -- I'll just analyze those data alongside my data from aquariums.

I chose not to make natural reefs the baseline for aquariums, though, because it was clear just from comparing existing data in the literature that these were quite different communities. Try as we might to simulate the conditions on the reef, our little glass boxes differ in important ways from the reef. For example, one thing that I think affects this a lot is the surface area to volume ratio. We know these house different communities. In a natural reef, there is a HUGE volume of water, relative to the surfaces. In our tanks, there is a tiny volume of water relative to the surfaces. Not to mention differences in flow, etc.

Not to say at all that I consider these comparisons unimportant - I just didnt think the test would be useful if it concluded "100% of aquariums have abnormal microbiomes". I chose instead to compare reef tanks with reef tanks, using the "typical reef tank" as my baseline. (This is simply the average of all tanks sampled so far, excluding my experimental tanks and any tanks specifically flagged as unhealthy by the owner).

Early comparisons showed that about half the aquariums sampled converged on a similar pattern, while the others differed in a few characteristic ways. This observation of a characteristic "normal" reef tank community, shared by half the tanks in the comparison, from multiple owners, supports the use of a "typical reef tank" profile as a meaningful baseline for comparison.

But I always have to emphasize that deviations from the typical community aren't necessarily a problem, maybe they are the secret to the success of that tank. See Adam's result in this thread as a possible example.

So many questions, I agree! I'll get data back soon from a carbon dosing experiment that I recently ran... today I start my bottled bacterial supplement test... there are far more questions than I can test alone, but I'm excited to see what the reefing community can do with this tool at their disposal.
 

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Yeah, most researchers I know in the field are pretty skeptical (for example) of the many unregulated "probiotics" sold to benefit the human gut microbiome.

On the other hand, its clear that adjusting the human gut microbiome can have important benefits for human health. Fecal microbiota transplantation (FMT) has been widely used to treat Clostridium difficile infections (Kelley et al. 2015). The same approach shows promising results for a growing number of other conditions, including obesity / metabolic syndrome (Marotz & Zarrinpar 2016) and inflammatory bowel diseases (Narula et al 2017)

It's clear that the microbiome can be adjusted, whether through diet, environmental effects, or FMT. But most treatments marketed to adjust the human gut microbiome are based on little to no clinical evidence.

The same is true in the aquarium hobby... so many products claiming to affect the microbial community, but how many of these claims are supported by evidence? I wish there was as much evidence available for any of these products as there is for live rock from my little study.

I share your sense that this area is ripe for a breakthrough, but am perhaps more optimistic about how quickly we can answer some of these questions. We don't have the funding or numbers of medical research, but we also don't have the FDA standing in the way! As a researcher I'm interested in answering some of these questions anyway, but as a reef keeper I am optimistic that we'll be able to freely experiment with any new treatments suggested by these tests.
I agree completely with all of the wonderful prospects for making adjustments in the human microbiome, but except for C Diff (actually saving lives so I don't mean in any way to diminish the value of this) it's all still promises. I hope it turns out to be a lot better than all those promises made about human stem cells. I think both will be huge, but sadly biology is so much more complicated than everything else and progress is slow. But steady, so I remain hopeful.

I'm familiar with several "experiments" where a single sample of human gut microbiome was divided into pieces and simultaneously sent to several different labs for analysis and the results were quite far apart. It's most disheartening that even the lowest level details can't seem to be gotten right so it isn't very easy to be optimistic about the projections, diagnoses, treatments etc made based on this low quality info.

Please understand, I'm not casting aspersions on you or any of the other researchers in these fields. This is immensely hard work which I believe holds tremendous value (at least the work on the human microbiome). I suspect progress will be intermittent at best for quite awhile, but eventually be huge.

I am glad that we all retain the freedom to experiment with our own tanks and I suspect the cumulative value of these experiments, written up in places like this forum, will help to point researchers in useful directions. I like to experiment and someday hope to add a little value of my own, but I'm not quite there yet.
 
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I agree completely with all of the wonderful prospects for making adjustments in the human microbiome, but except for C Diff (actually saving lives so I don't mean in any way to diminish the value of this) it's all still promises. I hope it turns out to be a lot better than all those promises made about human stem cells. I think both will be huge, but sadly biology is so much more complicated than everything else and progress is slow. But steady, so I remain hopeful.

I'm familiar with several "experiments" where a single sample of human gut microbiome was divided into pieces and simultaneously sent to several different labs for analysis and the results were quite far apart. It's most disheartening that even the lowest level details can't seem to be gotten right so it isn't very easy to be optimistic about the projections, diagnoses, treatments etc made based on this low quality info.

Please understand, I'm not casting aspersions on you or any of the other researchers in these fields. This is immensely hard work which I believe holds tremendous value (at least the work on the human microbiome). I suspect progress will be intermittent at best for quite awhile, but eventually be huge.

I am glad that we all retain the freedom to experiment with our own tanks and I suspect the cumulative value of these experiments, written up in places like this forum, will help to point researchers in useful directions. I like to experiment and someday hope to add a little value of my own, but I'm not quite there yet.
All fair points. Its always especially concerning to read about inconsistency in testing e.g. with human genetic tests or aquarium ICP tests.

In my own lab, variation between replicate samples is very low, but I imagine that is the case for most or all testing services. For variation between labs, I'm not aware of another service I can compare with directly but have been thinking about reaching out to some academic colleagues who do similar work to arrange a comparison of results. It'd be nice to confirm that we get very similar or identical answers, as we should.
 

Terri Caton

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Yeah, most researchers I know in the field are pretty skeptical (for example) of the many unregulated "probiotics" sold to benefit the human gut microbiome.

On the other hand, its clear that adjusting the human gut microbiome can have important benefits for human health. Fecal microbiota transplantation (FMT) has been widely used to treat Clostridium difficile infections (Kelley et al. 2015). The same approach shows promising results for a growing number of other conditions, including obesity / metabolic syndrome (Marotz & Zarrinpar 2016) and inflammatory bowel diseases (Narula et al 2017)

It's clear that the microbiome can be adjusted, whether through diet, environmental effects, or FMT. But most treatments marketed to adjust the human gut microbiome are based on little to no clinical evidence.

The same is true in the aquarium hobby... so many products claiming to affect the microbial community, but how many of these claims are supported by evidence? I wish there was as much evidence available for any of these products as there is for live rock from my little study.

I share your sense that this area is ripe for a breakthrough, but am perhaps more optimistic about how quickly we can answer some of these questions. We don't have the funding or numbers of medical research, but we also don't have the FDA standing in the way! As a researcher I'm interested in answering some of these questions anyway, but as a reef keeper I am optimistic that we'll be able to freely experiment with any new treatments suggested by these tests.

Thank you so much for referencing recent studies! I see so many practices in this hobby based on extremely old studies that have never been replicated. (Cough, cough...fallow tank time for Ich)

I do give credence to practices that work even without concrete evidence. But there is no doubt we would find that evidence if time and money allowed sufficient studies.

And I definitely think I won’t be throwing out that water from my next Battlebox!
 

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Thank you so much for referencing recent studies! I see so many practices in this hobby based on extremely old studies that have never been replicated. (Cough, cough...fallow tank time for Ich)

I do give credence to practices that work even without concrete evidence. But there is no doubt we would find that evidence if time and money allowed sufficient studies.

And I definitely think I won’t be throwing out that water from my next Battlebox!


Very good points thanks for the post. I'm really excited to see where some of this research leads us all actually.
 

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