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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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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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.