Chapter 28 - High-throughput sequencing technologies in metagenomics

Abstract

Microbes are a distinct and dynamic group of organisms that require a diverse set of nutritional requirements and environmental conditions to thrive. To culture the desired microorganism a chemically defined media can be prepared based on the nutritional requirements of the specific species. However, all microbes cannot be cultured under similar laboratory conditions since specific microorganisms require unique growing conditions and therefore, the existence of the significant members (nearly 99.99%) of microbiota remains undiscovered. This cultivation constraint has limited our understanding of microbial diversity and restricted our appreciation for the microbial world and thereby suggests the need for a detailed metagenomic analysis. Metagenomics is the study of the genome sequences of a community of organisms sharing a common environment. In contrast, genomics involves the complete decoding of the genetic material of an organism by high-throughput sequencing. Metagenomics has the potential to highlight the community structure and functional potential of a microbial community in an unprejudiced manner. Any species can be subjected to metagenomic analysis bearing either DNA or RNA as the genetic material. Metagenomic techniques have been used to define a wide range of niches, from coastal environments to hazardous soils to vectors causing arthropod diseases as well as microbiome of humans. These methods are also being used to detect infections in the anthropological remains and uncover new pathogenic viruses and characterize the human microbiome in disease and health conditions as well as for forensic purposes. Metagenomic studies have been revolutionized since 2005 when the NGS technologies were developed. The introduction of next-generation sequencing (NGS) technologies in 2005 sparked the metagenomics revolution. A variety of novel sequencing technologies and platforms like Roche 454 sequencing, sanger sequencing, Illumina sequencing, and ion torrent Personal Genome Machine (PGM) have emerged in recent years, increasing the practicality of metagenomic research. The current chapter aims to explore the potential high throughput sequencing technologies for metagenomic analysis of species from diverse environmental backgrounds. In addition, the challenges faced and future perspectives will also be discussed.