Introducing Microbiome 2.0

About 6 years ago we introduced our original Microbiome Test for aquariums. For the first time, this allowed reef keepers to identify specific bacteria growing in their tanks. In that time we’ve all learned a lot about the microbial communities in our tanks, the pathogens affecting our corals, and the composition of those bottled bacterial products.

Today we’re introducing an upgraded version of the test thats providing important new insights into previously unidentifiable Vibrio pathogens in reef tanks.

In this article I’ll describe how the technology works, what we’re learning from the new test, and how we’re handling the transition from the original to the upgraded version.

How it works

To classify microbes with DNA sequencing, we read the DNA bases (A,C,G, or T) in a specific part of the genome – like reading a single page from every book on a shelf to identify which books you have.

The original microbiome test focuses on a ribosomal gene called 16S. We use this region because its widely used by environmental microbiologists studying coral reefs, and they had a number of good reasons for using it. Features of the DNA sequence in this region makes it “universal” – it can be used to detect and sequence DNA from bacteria of any kind. This allows us to study the whole community at once, a powerful benefit that has revolutionized our understanding of microbial communities from coral reefs to humans to terrestrial soils to the human gut.

But this benefit comes with a tradeoff: some groups cannot be identified to the species level using this approach. In many cases its useful enough to know the genus, but in others its important to identify bacteria to the species level.

In reef aquariums, 16S sequencing finds bacteria from the Vibrio genus in most tanks. And a few of these can be identified to the species level. But unfortunately most of the ones in reef tanks turn out to be impossible to tell apart using just this marker.

Figure 1. Left: Sequencing the 16S marker produces identical DNA sequences from many Vibrio species, making it impossible to tell them apart. Right: sequencing the new HSP marker produces unique sequences for each Vibrio species, providing species-level ID for Vibrio in your sample.

Since sequencing the 16S marker can’t tell these apart, we turned to a different marker (HSP) developed by scientists studying Vibrio in oyster diseases. This marker has the opposite tradeoffs of 16S – it’s not universal at all, only capturing DNA from Vibrio and a few other groups. But it provides species-level resolution within the Vibrio genus.

So for our new Microbiome 2.0 Test we use both markers. Effectively this doubles the work on our end, but its clearly worth it. With Microbiome 2.0 you get the best of both worlds – a broad description of all groups down to at least the genus level, and a deep dive into the important Vibrio group with species-level resolution.

(The reader may already be thinking, what about other groups? Can you use a similar approach for other important pathogen groups? Absolutely – in fact we’re putting the finishing touches on a similar test for Mycobacterium sp. that we’ll be releasing as a free upgrade sometime in 2026. Stay tuned!)

What we’ve learned

The new species-level Vibrio data has revealed something striking: pathogenic Vibrio bacteria are far more common in reef aquariums than we previously knew. After analyzing our first 114 tanks with the upgraded test, we found that nearly half of all reef tanks (48-49%) harbor either a Vibrio coral pathogen or fish pathogen. We’ve now identified 7 different coral-pathogenic species and 10 fish-pathogenic species across our sample set, though fortunately most occur at relatively low levels when present.

The most common pathogen we’re detecting is Vibrio owensii, a well-established coral pathogen that causes Montipora White Syndrome. It’s showing up in over a third of the tanks we’ve tested. We’re also finding V. campbellii and V. fortis (both fish pathogens) in about 25% of tanks each, and V. coralliilyticus – one of the best-studied coral pathogens – in 12% of samples. What’s particularly important here is that while these pathogens are common, about 58% of the Vibrio species we’re finding in reef tanks are actually non-pathogenic environmental bacteria. You can read more about our findings here.

This really underscores why species-level identification matters so much – it’s the difference between identifying a genuine threat and a harmless member of the reef microbiome.

The transition to microbiome 2.0

Sequencing this additional marker produces such an improvement in the original purpose of the Microbiome Test that we chose to upgrade the test rather than include it as an optional feature.

So from now on, every Microbiome Test we sell will be version 2.0.

Running this additional marker means additional costs on our end. While we’re talking about costs, our operating expenses have risen by more than 50% since we opened in 2019. (Other business owners can probably relate – this isn’t specific to our industry). But despite these increases, we stubbornly resisted raising our prices. We havent raised them once in 6 years – how many services can say that? But something had to give, and the costs aren’t going down. For these reasons the upgraded Microbiome 2.0 Test will sell at a slightly higher price ($120).

But we think you’ll agree that the enhanced power to detect Vibrio pathogens is worth it.

What about the kit you already bought? How do you upgrade to a Microbiome 2.0?

Simple: you don’t have to do anything. Every sample we receive from now on, we will process as a Microbiome 2.0 test (with the additional marker to resolve Vibrio pathogens). So you, our existing clients, get the new upgraded test at the old price.

So send in those samples, no matter when you bought the test, and let’s see what kind of Vibrio is growing in your tank!