Metagenomics: A Step into the Future!?

Is it a bird or a plane… Oh, it is just a step into the future. It is Metagenomics!

What if we could identify each and every microorganism on earth.
Oh my!
It would be the best thing that could ever happen to mankind! I mean, microorganisms can practically do every thing.
Just in case you are not aware, these tiny little organisms actually run the world, not ladies sadly (sorry Beyonce). They do not only run the world, without their activities, there would be no us.
They play key role in the nitrogen cycle, the carbon cycle and all other chemical cycles essential to our very existence. They are also present working in the fermentation, production and even cleanup of our environment.

Ranging from making food, production of drugs, enhancing the growth of our crops...you name it, microbes can do that for you. Sadly, we have been able to harness only about less than 1% of this wonderful population. So much left unknown!
With the little researchers have been able to identify, a lot of good have been done.

But then, you might wonder, how come with so much innovations and all the breakthroughs in science, how come only less than 1% have been harnessed?

This is because of something my lecturer likes to call VNBC. This translates to Viable But Not Culturable or better known as The Plate Count Anomaly Principle.
In simple terms, this means all the times we have been collecting samples from the environment, and culturing them, we have only been able to isolate about 1/10 of microbes present in that sample.
This means, those unidentified microbes were either;

• Viable but not culturable
• Dormant but viable
• Non-viable.

But then there is a new, well not so new, development. This is Metagenomics. Metagenomics presents a way out of this ignorance.

What is it exactly?

Metagenomics is the science of studying a collection of the genome or DNA fragment directly from a sample of environmental origin.
It is a technique that is culture-independent and it is able to provide information about..

• The structure of microbes
• Their genetic analysis
• Their functionality
• And even new genetic materials.

Metagenomics presents a scenario where microorganisms will be characterized based on their genetic material in order to be able to understand their functions, and most importantly how they can be applied.
This is a great advancement from the usual culturing technique which allows only the culturable ones to be sequenced

What does it entail?

Metagenomics, as the name suggests, is a step further from our usual genome sequencing or Genomics. Genomics refer to the study of components of a genome, that is, the nucleotides, DNA and genes. With studies of genomes dating way back to 1858 during the time of Darwin, lots of advancement have been made so far.
Such include, the shotgun and Sanger sequencing, recombination of bacteria and having a gene bank/database where genetic material is stored. In summary, Genomes can now be rapidly sequenced.

Process Involved

How then is the whole Metagenomics process carried out?
There are different processes involved in metagenomics. The first step is obviously getting the sample from the environment. This sample could be soil, water or any other. It usually contains hundreds of microorganisms. The DNA firstly has to be set free from the cells of the organisms in the sample. This is achieved through the use of either Chemical or Physical process. The chemical process involves dissolving in an alkaline solution while an example of the physical process is Sonification.

Either of the above processes enables DNA to be separated from the sample.
Now that we have the DNA, it has to be cut into smaller fragments because of its large size just so it can be manipulated. This is done by the Restriction Endonuclease enzyme.
Our new fragments are now combined with some carriers, also known as vectors that help in transporting the DNA fragments into cells to facilitate replication and protein production.
The next stage involves adding the vectors to a model organism. Now this is where the specialty of the whole Metagenomics process comes in. This process allows the DNA of those VNBC organisms to be grown and identified.
At this stage, each DNA fragment that is isolated is differentiated which allows for easy identification of each and every DNA material in our sample.
Next is culturing on selective media which allows the growth of the microbes you want to see.
Finally, the isolated DNA fragments are taken to the Metagenomics Library in order to be analyzed for its chemical and physical properties.

Why is this important?

Some of the relevance of microorganisms to our very existence have already been highlighted above. But then, that is only for the ones we have been able to identify.

How about the others?

Metagenomics seeks at providing answers to the following questions…

Who is present there?
Since we have barely been able to scratch the surface when it comes to identifying the microbes in our environment, Metagenomics seeks to discover more.

What is it doing there?
If a new organism is discovered, knowing its function is the next step. No organism just happens to be anywhere, there is always a role it is playing and that is another quest Metagenomics is on the path to uncovering.

How is it doing what it is doing?
If the function of a microbe in a particular environment is known, the next need-to-know is how it is performing that function. This helps to be able to replicate such functions and probably apply them in other areas that would be beneficial to mankind.
For example, when the first antibiotic was discovered, although by accident. Further studies followed the trail of answering such questions

In conclusion, Metagenomics holds so much promise and it is definitely exciting just thinking about it. It is definitely the breakthrough we have all been waiting for in the microbial world.

The secret of this invisible world is about to be unveiled!!!

It will probably take some time, but soon, we would graduate from just scratching the surface of the microbial world to gaining control.
Especially when Metagenomics is applied to different fields including Medicine, Environmental cleanup, Food production, Agriculture and so much more.

Thanks for reading!

References
Why Metagenomics
Metagenomics Process