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BioQuest | Vol. 1, No. 1 (July 2017) 36 Introduction Metagenomics is the study of the collective genomes recovered from environmental samples without prior cultivation. It enables the investigation of genome information on organisms. It is widely accepted that up to 99.8% of the microbes present in many environments are not readily culturable. ‘Metagenome technology’ tries to overcome this bottleneck by developing and using culture-independent approaches. From the outset, metagenome-based approaches have led to the accumulation of an increasing number of DNA sequences, but until this time the sequences retrieved have been those of uncultured microbes. These genomic sequences are currently exploited for novel biotechnological and pharmaceutical applications and to increase our knowledge on microbial ecology and physiology of these microbes. Using the metagenome sequences to fully understand how complex microbial communities function and how microbes interact within these niches represents a major challenge for microbiologists today (1). In plant pathology, the metagenome of disease- suppressive soils is of particular interest given the expected prevalence of antibiotic biosynthetic clusters. However, owing to the complexity of soil microbial communities, deciphering this key genetic information is challenging (2). There is a clear potential for metagenomics to contribute to the study of microbial communities of the rhizosphere, in particular PGPR. Possible contributions include the discovery of novel plant growth promoting genes and gene products, and the characterization of unculturable PGPRs (3). Metagenomics provides a new rationale and effective methodology for identification of potentially important genes, enzymes and biomolecules present in microbial community. It is based on studies of ecological diversity of uncultured and cultural microorganisms using molecular biology (4). Sampling and processing Sample processing is the first and most crucial step in any metagenomics project. The DNA extracted should be representative of all cells present in the sample and sufficient amounts of high-quality nucleic acids must be obtained for subsequent library production and sequencing. Processing requires specific protocols for each sample type, and various robust methods for DNA extraction are available (5,6). Initiatives are also under way to explore the microbial biodiversity from tens of thousands of ecosystems using a single DNA extraction technology to ensure comparability. Sequencing technology The metagenomic shotgun sequencing has gradually shifted from classical Sanger sequencing technology to next-generation sequencing (NGS). Sanger sequencing, however, is still considered the gold standard for sequencing, because of its low error rate, long read length (> 700 bp) and large insert sizes (e.g. > 30 Kb for fosmids or bacterial artificial chromosomes (BACs). All of these aspects will improve assembly outcomes for shotgun data, and hence Sanger sequencing might still be applicable if generating close- to-complete genomes in low-diversity environments is the objective (7). Genome assembly Genome assembly is a process wherein a large number of sequences are assembled together to generate a representation of the original chromosomes from which the DNA originated. If the research aims at recovering the genome of uncultured organisms or Metagenomics and its prospects in phytopathology Jeevan B 1 *, Rajal D, Subrahmanyam G, Veeranna D, Vijay N, Chutia M 1 Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, Assam (India) * Corresponding author email: [email protected]
