Metagenomics: An overview

1. Metagenomics : an overview
Jerome A
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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
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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
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are
uncultivable/
difficult
to

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
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in

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
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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.
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and
improve

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
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8. Scope of metagenomics
 Milk metagenomics
 Viral metagenomics
 Soil metagenomics
 Sewage/sea metagenomics
 Extraterrestial metagenomics ……
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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
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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
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11. THANKS
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