Metagenomics: An overview

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Metagenomics: An overview

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  • The absorption of fermentation products, mainly VFA, from the rumen into the blood, and outflow of microbial cells to the abomasum and small intestine provide the animal energy and protein, respectively. The rumen environment, created by interactions between the animal and the microbes, operates as an efficient continuous culture system with optimal physical and chemical conditions for microbial growth and activities, more or less continuous availability of substrate (atleast in grazing cattle), removal of end products (by absorption, eructation or passage), and passage of undigested feed.
  • 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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