Published on February 27, 2014
PRESENTED BY RAHUL SAHU
INTRODUCTION Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The term "metagenomics" was first used by Jo Handelsman, Jon Clardy, Robert M. Goodman, and first appeared in publication in 1998. This relatively new field of genetic research enables studies of organisms that are not easily cultured in a laboratory as well as studies of organisms in their natural environment.
The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. The term metagenome referenced the idea that a collection of genes sequenced from the environment could be analyzed in a way analogous to the study of a single genome. The human microbiome project (HMP) will require metagenomic sample sequencing data as a primary resource for analysis of the relationship between microbial communities and the individuals they inhabit.
Metagenomic approaches • 3 broad types of metagenomic approaches are: – Biochemical approach – Whole genome shotgun (WGS) methods• WGS approaches have been used mainly in environmental studies from various sites (e.g., sea water, abandoned mines). – 16s-RNA sequencing (ribotyping) • Most widely studied approach for microbiological point of view.
Methodological Advances Natural samples contain DNA in Natural samples contain DNA in several forms like free DNA, virus particles, cells, etc. These samples can be suspended in water, bound to the soil or other solid particles, or contained within an aggregate of microorganisms (biofilm). Now the above 3 approaches can be used.
Shotgun sequencing WGS sequencing is performed by sequencing the ends of clone libraries created as small plasmids or occasionally cosmids. The individual sequences are compared to sequence databases to identify species and genes.
Applications • Metagenomics can improve strategies for monitoring the impact of pollutants on ecosystems and for cleaning up contaminated environments. Increased understanding of bioaugmentation or biostimulation trials to succeed. • Recent progress in mining the rich genetic resource of non-culturable microbes has led to the discovery of new genes, enzymes, and natural products. The impact of metagenomics is witnessed in the development of commodity and fine chemicals, agrochemicals and pharmaceuticals where the benefit of enzymecatalyzed chiral synthesis is increasingly recognized.
• Metagenomic sequencing is being used to characterize the microbial communities. This is part of the Human Microbiome initiative with primary goals to determine if there is a core human microbiome, to understand the changes in the human microbiome that can be correlated with human health, and to develop new technological and bioinformatics tools to support these goals. • It is well known that the vast majority of microbes have not been cultivated. Functional metagenomics strategies are being used to explore the interactions between plants and microbes through cultivationindependent study of the microbial communities.
Future Directions • New enzymes, antibiotics, and other reagents identified • More exotic habitats can be intently studied • Can only progress as library technology progresses, including sequencing technology • Improved bioinformatics will quicken analysis for library profiling.
• Investigating ancient DNA remnants • Discoveries such as phylogenic tags (rRNA genes, etc) will give momentum to the growing field • Learning novel pathways will lead to knowledge about the current nonculturable bacteria to then culture these systems Culture these organism Information on why certain microbes are uncultured Discover novel pathways
References • Presentation by Susannah Green, Tringe and Edward M. Rubin - Department of Energy Joint Genome Institute • Metagenomics-Current Innovations and Future Trends: Diana Marco • www.genomviron.com • www.Rothamsted.ac.uk
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