I had my water tested my AquaBiomics and need an explanation.

Paul B

Well-known member
Long Island NY
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I don't know but this is what he wrote to me:

Hi Paul,

Here are my thoughts on the microbiome of your famous aquarium, the most mature reef tank I've yet had the privilege of testing. Both your water and biofilm samples contained plenty of DNA so these conclusions are based on analysis of thousands of high quality DNA sequences from your sample.

First the diversity (which is simply the number of different kinds of microbes found in your sample). Your tank was more diverse than 2/3 of those I sampled. This is even more impressive when you consider its age. Older tanks tend to have lower diversity ... tanks <5 years old ranged from about 100 to over 600. Aside from yours, every tank older than 10 years had a diversity ≤ 155.

These results suggest that your efforts to replenish diversity have made a big difference. Your diversity is almost double that of other >10 year old tanks.

Next the balance. Balance scores tell you how similar your sample was to other reef tanks. It probably won't surprise you to learn that your microbiome is quite different from others'. A score of 1 would mean your microbiome was identical to the average... your score (0.12) means that the major families of microbes found in aquariums are present at very different levels in your tank than in the average tank.

This doesnt mean your microbiome is unhealthy. It means its very different from the average. Considering the health of your tank and the differences in your reef keeping practices, I see no reason to consider this profile a problem. On the other hand, if there is something about your tank's behavior that consistently differs from others, this could provide a clue as to why.

You can see the basis for this score in part 2. Your tank has an unusually high level of Helicobacteraceae (the big red chunk in part 2), which is normally a very small fraction of the community. You may recognize the name from the bacterium that causes ulcers and other GI diseases in humans (Helicobacter pylori). Many members of this family are associated with animal surfaces, colonizing the GI tracts of various animals. Other members are associated with deep sea sediments and other sulfide rich environments.

That has me thinking... I believe you use an reverse under gravel filter, is that right? I would love to test the sediments from your filter and see if Helicobacteraceae are especially abundant there. I speculate that the high levels of Helicobacteraceae may result from this filtering method.

(again, no reason to consider this a problem. Its a big difference, and I'd like to understand differences like this)

Your tank is also very low in the families that typically make up a large fraction of the community, including Pelagibacteraceae and Flavobacteriaceae. These are often the most abundant types in natural ocean water samples, and also in aquariums. You have these groups, just at lower levels than is typical.

In the oceans, the relative levels of different heterotrophic bacteria are mostly driven by the kind of DOC available. I suspect the same is true in our tanks. Both of these groups have particular nutritional requirements that may be different from conditions in your tank. Flavobacteriaceae is specialized for taking up polysaccharides and proteins. Pelagibacteraceae is specialized for life in low-nutrient waters, and needs reduced sulfur compounds like DMSP as well as glycine for growth.

I suspect these differences result from the balance of nutrient important and export in your system. I know you've long been an advocate of natural foods. I'd love to hear more about your feeding practices to think about how this may be affecting the microbial community.

Like a surprising fraction of tanks, yours was relatively low on nutrient processing microbes. I want to be clear this wasnt universal, its not that we can't detect them. Some tanks just have bigger populations than others, we've seen this over and over now.

This doesnt mean they are absent in yours, of course, it means the populations are relatively small. I would like to explore this further. I suspect that some tanks rely more on other export processes, leading to lower populations of ammonia-oxidizing or nitrite oxiding microbes. I also suspect bioload and feeding play a role. I'd love to hear more about your bioload, feeding practices, and whether you have any macro algae (e.g. a refugium) in your system.

(Sorry for all the questions, as you recall we had some technical issues getting these details logged on the sample registration page)

You tank was completely free of known bacterial fish pathogens and known bacterial coral pathogens. I need to emphasize this does not address eukaryotic parasites like those that cause Ich; just the prokaryotic pathogens (Bacteria or Archaea). Still, given your advocacy of a no QT approach, this is a noteworthy finding. While 1 out of 8 tanks had a known fish pathogen (Photobacterium damselae), and 1 out of 10 tanks in my first batch had a known coral pathogen (Aquarickettsia rohweri), yours had no evidence of any known pathogens.


I suspect this is long enough and will stop there for now, but I'll be curious to continue discussing your interesting sample. Thanks again for participating!


Dr. Fish
HF Vendor
Navarre, FL
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From a disease standpoint, harmful bacteria in the water are typically least concerning. It is something a healthy fish can fight off because they are usually low in number, especially in a DT environment. Although, gram-negative bacteria can wreak havoc in a small QT, or if the fish already has a pre-existing parasitic infestation.

It is interesting that your tank only has a small population of nutrient processing microbes. Do you run an algae scrubber or something? Like the report suggested, a nutrient export system probably limits nitrifying bacteria propagation.

Were the samples only taken from the water or did you also include a small rock/sand sample?

Paul B

Well-known member
Long Island NY
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Bobby, I do use an algae scrubber. I don't know how efficient it is. The water samples were taken from the water and a scraping from the glass in the dark. Maybe all my nitrifying bacteria are in my reverse undergravel filter where I did not take a sample from.
The water sample is drawn into a large baster looking thing then pushed out through a small (quarter size) paper filter which is put into a solution and sent to them.
The other sample is on like a Q tip and put into a solution in a small container to send in.
I do take mud from here but this year, just a little. Maybe a few tablespoons.

Tamberav. Thank you. I know, I am about as famous as Brad Pitt and maybe a little better looking. :rolleyes:


20 Year Noob
Metairie, LA
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You can see the basis for this score in part 2. Your tank has an unusually high level of Helicobacteraceae (the big red chunk in part 2), which is normally a very small fraction of the community. You may recognize the name from the bacterium that causes ulcers and other GI diseases in humans (Helicobacter pylori).
I also don't recommend eating any fish from Paul's tank. Fish from Bobby's tank will be safer to consume.