What is Shotgun Metagenome Sequencing?

What is Shotgun Metagenome Sequencing? How is shotgun metagenome sequencing different from 16s metagenome sequencing? These are valid questions and questions that can be resolved with a quick breakdown of metagenome sequencing methods.


What is the difference between Metagenomics and Metagenome Sequencing?


Metagenomics is the study of microbial populations sampled directly from the environment such as soil from crop fields, pond water, an open wound etc. Metagenomic studies can be completed with a variety of metagenome sequencing methods including:


Metageonome Sequencing Sample


  • Shotgun metagenome sequencing
  • 16s rRNA sequencing
  •  Whole-genome sequencing
  • Transcriptome sequencing


Is there a difference between 16s rRNA sequencing and Shotgun metagenome sequencing?


The short answer is yes! But how so?... The answer is simple really, 16s rRNA sequencing is strictly focused on sequencing the 16s rRNA gene found in all bacteria and archaea. This is why 16s rRNA sequencing is often referred to as targeted resequencing, this method targets the 16s rRNA gene only (For more information on 16s rRNA sequencing). On the other hand, shotgun metagenome sequencing targets all genes from all microbial organisms. This sequencing method is aptly named "Shotgun" due to its widespread of targets, whereas targeted resequencing methods could by the same logic be named "Rifle" metagenome sequencing.


Shotgun metagenome sequencing is able to provide scientists a more full picture of the microbial diversity present in their environmental samples. This is made possible by the process of DNA fragmentation. DNA fragmentation is the process by which DNA is randomly sheared into shorter sequences that are able to then be sequenced. This process of random shearing is one of the reasons shotgun metagenomics is able to provide a more in-depth look into the microbial diversity of the sampled environments. In the past, microbiologists would have to rely on traditional culturing and cloning techniques in order to complete shotgun sequencing studies. Today, with the popularization of next-generation sequencing platforms, these traditional microbiology techniques are no longer necessary, and as a result there is less bias involved in shotgun metagenome studies. The biases introduced through the use of cloning and culturing techniques would in large-part limit the opportunity for scientists to identify those microorganisms that were less abundant. However, NGS has brought the power of high-throughput sequencing to researchers around the globe who are now able to detect those members of the environment that were in such low-abundance would have been previously undetected.


Not only does Shotgun metagenome sequencing provide the ability for researchers to gain insight into the taxonomic makeup of their environmental samples, but because this method is not limited to the 16s rRNA gene, researchers are also able to gain insight into the functional genes present as well as the metabolic pathways.


It is clear to see that Shotgun metagenome sequencing provides the most complete picture of microbial diversity and function in a specified environment.


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