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4/4/2016
Dr.T.V.Rao MD
Dr.T.V.Rao MD
Dr.T.V.Rao MD
Metagenomics
Metagenomics is the study of genetic material
recovered directly from environmental samples. The
broad field may also be referred to as environmental
genomics, ecogenomics or community genomics.
While traditional microbiology and microbial
genome sequencing and genomics rely upon
cultivated clonal cultures, early environmental gene
sequencing cloned specific genes to produce a profile
of diversity in a natural sample.
4/4/2016
Dr.T.V.Rao MD
Introduction
...functional analysis of the collective genomes of soil
microflora, which we term the metagenome of the soil.
- J. Handelsman et al., 1998
PubMed: metagenom*[Title/Abstract]
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Metagenomics
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Understanding ecosystems
Metabolites
Meta-bolomics
Proteins
Extraction
mRNA
Meta-proteomics
Meta-transcriptomics
DNA
In Situ methods
Community structure
Microbial functions
Meta-genomics
Microbial needs
P-Removal:
N-Removal:
-Removal:
Foaming:
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Ethanol production:
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Extracting genomes
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Introduction
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Introduction
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History of Metagenomics
However, early metagenomic studies revealed
that there are probably large groups of
microorganisms in many environments that
cannot be cultured and thus cannot be
sequenced. These early studies focused on 16S
ribosomal RNA sequences which are relatively
short, often conserved within a species, and
generally different between species
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Metagenomics provides
a new way of examining
the microbial world that
not only will transform
modern microbiology
but has the potential to
revolutionize
understanding of the
entire living world
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Applications of Metagenomics
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Advancement in Medicine
Microbial communities play a key role in preserving human
health, but their composition and the mechanism by which
they do so remains mysterious. Metagenomic sequencing is
being used to characterize the microbial communities from
15-18 body sites from at least 250 individuals. This is part of
the Human Microbiome initiative with primary goals to
determine if there is a core human microbiome, to
understand the changes in the human microbiome that can
be correlated with human health, and to develop new
technological and bioinformatics tools to support these
goals.
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Advancement in Medicine
Another medical study as part of the MetaHit (Metagenomics of
the Human Intestinal Tract) project consisted of 124 individuals
from Denmark and Spain consisting of healthy, overweight, and
irritable bowel disease patients. The study attempted to
categorize the depth and phylogenetic diversity of
gastrointestinal bacteria. Using Illumina GA sequence data and
SOAPdenovo, a de Bruijn graph-based tool specifically designed
for assembly short reads, they were able to generate 6.58
million contigs greater than 500 bp for a total contig length of
10.3 Gb and a N50 length of 2.2 kb
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Experimental approaches to
Metagenomics
Techniques of Metagenomics are generally used to explore
the properties of microorganisms without prior cultivation.
Although still a novel field of research, Metagenomics has
already developed different branches, which contain mainly
the following focuses:
Discovery of new proteins by functional screening
techniques (e.g. screening for an enzyme that is able to
degrade a particular toxic compound),analysis of microbial
diversity in a habitat (e.g. by classical rRNA analysis or
phylum estimation from sequence properties), and gene
discovery by sequence analysis.
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Bioinformatics on Metagenomes
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Metagenomics is employed
Metagenomics is employed as a means of systematically
investigating, classifying, and manipulating the entire genetic
material isolated from environmental samples. This is a multistep process that relies on the efficiency of four main steps .
The procedure consists of
(i) the isolation of genetic material,
(ii) manipulation of the genetic material,
(iii) library construction, and the
(iv) the analysis of genetic material in the metagenomic
library.
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Sampling
he single steps of such a metagenomic study are illustrated below
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Shearing
Shearing: the isolated
genomic DNA is broken into
shorter fragments that can
be cloned into plasmids (a
vector for smaller insert
size). Some DNA isolations
methods already contain a
shearing step by
themselves.
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Cloning
Cloning: the DNA fragments are
cloned into a vector. From here on,
all steps are shown for one
fragment, only. The vector contains
an origin of replication which
enables the host organsim to
multiply the plasmid. It also
contains a marker which assists in
the selection of host organisms that
have incorporated the plasmid
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Transformation
Transformation:
constructs consisting
of a plasmid with an
insert are
transformed into a
host organism
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Multiplication
Multiplication: the
host organism
multiplies (and
obtains) the
transformed
material.
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Sequencing
Sequencing: after another step of
DNA isolation which in this case
isolates the multiplied plasmid
material from the host organism,
the single fragments can be
sequenced by various methods.
Usually, Sanger sequencing with
fluorescence is applied.
Ref pictures: Katharina Hoff. Last
modified November 2007
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Future Direction
New enzymes, antibiotics, and other reagents
identified
More exotic habitats can be intently studied
Can only progress as library technology
progresses, including sequencing technology
Improved bioinformatics will quicken analysis
for library profiling.
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Information Resources
gobics.de [Research: Metagenomics]
METAGENOMICS: THE SCIENCE OF BIOLOGICAL DIVERSITYby
KJSHELSWELL
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