Metagenomic Analysis and its Applications

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Abstract

Metagenomics is a molecular tool used to analyse DNA acquired from environmental samples, in order to study the community of microorganisms present, without the necessity of obtaining pure cultures. Functional metagenomics allows high resolution genomic analysis of unculturable microbes and correlation of the genomes with particular functions in the environment. Metatranscriptomics and metaproteomics are relatively recent sub-areas of metagenomics, which allow further functional analysis of microbial communities. Metaproteomics is emerging as a complementary approach to metagenomics, which aims to characterize the proteins from the microbiota. The integrative omics approach leads to a comprehensive information describing the community from genes to RNA to proteins and metabolites. In this chapter, we discuss types of metagenomics analysis such as 16S (for bacteria), whole metagenomics and 18S/ITS (for fungus), and limitations associated with each type of analysis, and their applications.

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Arpita Ghosh is a Manager of Bioinformatics at Eurofins Genomics India Pvt Ltd/ Eurofins Clinical Genetics India Pvt. Ltd. She is also a PhD student at Perdana University, Malaysia. She has a rich research experience of more than seven years in various fields of genomics and clinical genetics data analysis using Next Generation Sequencing technology. She has published more than 15 international publications in different areas of genomics and clinical genetics. She has been working on cutting edge applications of genomics like amplicon based metagenomics (16S, ITS), whole metagenome, WGS, RNASeq, small RNA, GBS and Tilling, among others. Her current research is on virus metagenomics and to identify novel genes from viral genomes. Her primary research interest is in the field of genomics, application heat of which can be felt invarious fields such as molecular diagnostics and the study of the environment.

Aditya Mehta has more than five years of Industrial research experience in various fields of applied genomicsand translational genomics data analysis using various next generation sequencing platforms. He has worked on large scale data analysis projects like RNASeq, whole genome, Metagenomicsand 16S/18S analysis using high throughput sequencing data. He has extensive experience in analysing metagenomics and 16S rRNA data generated on Illumina platform. He has carried out large scale data analysis of various metagenomics samples like soil, water and the human gut and identified microbial diversity, their relative abundance in sample and also deciphering the gene functions. He has in depth knowledge of various metagenomics tools, software and databases that are widely used for microbial data analysis and taxonomical identification from experimental sample. He has designed new strategic approaches and workflow steps for microbial data analysis, including further downstream analysis.

Dr. Mohammad Asif Khan is currently appointed as the Director of the Perdana University Center for Bioinformatics (PU-CBi), Malaysia, and a Visiting Scientist for the Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine (JHUSOM), USA. His research interests are in the area of biological data warehousing and applications of bioinformatics to the study of immune responses, vaccines, venom toxins, drug design, and disease biomarkers. He has contributed in the development of several novel bioinformatics methodologies, tools, and specialized databases, and currently has three patent applications granted.

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