What Shotgun Sequencing has uncovered about the Human Microbiome

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Introduction

The human microbiota consists of microorganisms that live inside as well as on humans and they outnumber the human germ cells and somatic cells ten times (Turnbaugh et al. 2007). The collection of genes of these microbial organisms (the microbiome) provides the characteristics that human beings lack (Zimmer 2010). There are two major techniques that are currently used to characterize the microbiome, namely; the (rRNA) small-subunit ribosomal RNA, and the metagenomic study, wherein shotgun sequencing is used to characterize community DNA of these microorganisms.

Shotgun sequencing of the human microbiome

Shotgun sequencing, also called shotgun cloning in genetics, is a process used for sequencing long strands of DNA. Shotgun sequencing was referred so by resemblance with the quasi-random shotgun firing pattern. The shotgun sequencing method was developed by Fredrick Sanger in the 1970s. The chain termination sequencing process is only be used to sequence relatively short DNA strands. Longer sequences of DNA must be sub-divided into shorter fragments, and then subsequently reassembled to give the entire sequence (Venter et al. 2004). Shotgun sequencing process, which uses random fragments, is used to sequence shorter fragments of longer DNA strands. The process is faster but more complex process.

The DNA strand is randomly broken up into many small fragments, in shotgun sequencing, which are then sequenced using the process of chain termination to obtain reads. The multiple target DNA overlapping reads are obtained through performing many rounds of DNA fragmentation and sequencing. The overlapping ends of many reads are then used by the computer programs to assemble the reads into a continuous DNA sequence.

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