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Metagenomics: An overview

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Metagenomics: An overview

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Metagenomics: An overview

  1. 1. Metagenomics : an overview Jerome A (c) JEROME
  2. 2. METAGENOMICS  Metagenomics: analysis of metagenomes, sequences from environmental samples  The "metagenomics" Handelsman in 1998. was first used by  Study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species (c) JEROME
  3. 3.  Identification of microbes in a complex community by exploiting universal and conserved targets  Amplifying selected target regions within 16S rRNA genes for microbial genus and species identification (Petrosino et al., 2009)  Microbes are ubiquitous – they are extremely adaptable to conditions and survive everywhere  99% microbes cultivate (c) JEROME are uncultivable/ difficult to
  4. 4.  Metagenomics bypasses the requirement of clonal cultures.  Metagenomics novel tool for studying uncultivable microbes (Bacteria, Archaea and viruses).  Responsible for substantial advances microbial ecology, evolution, and diversity (c) JEROME in
  5. 5. Rumen – Complex microbial community  Anaerobically digest complex components of feedstuffs  Microbial ecosystem of the rumen : importance of ruminants as a source of meat and milk  Bacteria –Upto 1011 : Hydrolysis of substrates  Fungi – 106 : Penetrates the substrate and Breaks down into small pieces  Protozoa -105 : Hydrolyses substrates and excretes monomeric sugars  Archaea- 108 : Mainly methanogens : help in continuity of sugar fermentation and acts as a hydrogen sink (c) JEROME
  6. 6. Importance of rumen metagenomics  Culture-based methods is difficult  Link analysis of the community structure to ruminal functions  To manipulate feeding systems efficiency of digestion in the rumen. (c) JEROME and improve
  7. 7. Steps in metagenomic study Metagenomic DNA Isolation andSequencing Library Preparation and e-PCR Data acquisition and extraction Sequencing reads and Assembly Bioinformatics Analysis Using appropriate softwares Genome reconstruction Sequence based binning , Annotation Predict Function Validation and Step towards media designing (c) JEROME
  8. 8. Scope of metagenomics  Milk metagenomics  Viral metagenomics  Soil metagenomics  Sewage/sea metagenomics  Extraterrestial metagenomics …… (c) JEROME
  9. 9. Use of NGS in metagenomics Allow access to largely unexplored microbial system: Leading to a steep increase in metagenomics. Various platforms for NGS  ABI SOLiD  Illumina Hiseq/MiSeq  Roche 454  Ion Torrent PGM/PROTON (c) JEROME
  10. 10. Bioinformatic tools for Metagenomics CLC Workbench Assembly, mapping BLAST Similarity based alignment MG-RAST Annotation RAST MEGAN Analysis Prodigal Vegan Community ecology study Cytoscape Visualization tools (c) JEROME
  11. 11. THANKS (c) JEROME

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