Metagenomics is the study of microbial communities directly in their natural environments without isolating individual species in the lab. It involves sequencing DNA from environmental samples and analyzing the metagenomes. Some key points are that metagenomics can identify uncultivable microbes, bypassing the need for culture, and it has led to advances in understanding microbial ecology, evolution, and diversity. The rumen, home to a complex microbial community important for ruminant digestion, is a important target of metagenomics study. Next generation sequencing techniques now allow more accessible exploration of microbial systems through metagenomics.

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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