Application of fluorescence in situ hybridization (FISH) for analysis of the microbiome

What is FISH? FISH is an extremely powerful tool for the direct analysis of bacteria in the sample

FISH stands for Fluorescence in Situ Hybridization.

How it works? It works that at the beginning there are specifically programmed probes,

which target a bacteria species or a whole bacterial group.

These probes are labeled with a dye, which can be, for example, a fluorescence dye.

The probes are introduced into the sample and they penetrate all bacteria,

but bind only to these bacteria, for which they have been programmed for,

only to these bacteria they will bind and cannot be washed away.

At the end, this specific bacteria cells will start to shine because they have the fluorescence dye inside the cell.

When you apply the high, energetic light at the end, the bacteria are shining.

The whole cells are shining - It's a whole cell approach. And you can identify these bacteria.

What are the advantages of FISH?

The advantages of FISH are that you can identify, quantify and visualize the bacteria directly at their site of action

and you can detect only the living one. You can get a real look into the real biocenosis.

Because a biocenosis is a complex mixture of different populations, a dynamic mixture.

And with FISH, you can monitor this species or the whole populations.

I've been a part of the team which developed and applied this FISH technology in the early 90s

for the detection of bacteria directly in the samples. And later we transferred this powerful technology

into an industrial standard, which we have called VIT - vermicon identification technology.

When we look at microbiome research, we are looking at analysis of biocenoses

because inside the microbiome, there are different populations.

They're growing, they're dying, they're changing. It's a really dynamic, complex formation.

And so what's the methods for analysis of such a biocenosis?

Well, you can cultivate them. That's not a very good idea, because most of the bacteria cannot be cultivated.

You can sequence them. Yes, you get a lot of sequence data and very interesting and good sequence data,

but you have to analyze it and the sequence data give you not a real look inside the biocenoses.

But with the FISH technology you get a real insight,

because you really see what is happening, what is happening there, what is happening in the sample.

You get this answer.

So what do you get, when you apply the FISH technology to the analysis of your microbiome samples?

Well it's easy, you get an identification, quantification and visualization of the bacteria

inside the microbiome samples. We at vermicon, we are offering these type of FISH services

for the analysis of the microbiome samples. We can get all the exciting data lying inside when we visualize the interaction

and when we get the different populations.

We are also offering different types of kits for the analysis of bacteria in samples.

So at the end, when you are thinking about whether to give it a try or not,

I personal really can recommend you that you just try it. You will see that this technology is

powerful and that's the most important one - that it can really give you some answers

for your most important questions.