Presented by

Suhail Patharvat

Biotechnology Department
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 01 What is Metagenomics?

02 Why Metagenomics?

03 Metagenomics Approach

04 Human Gut

05 Application
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  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 natural sample.
 99% of microbial species cannot currently be cultivated.
 The term “metagenomics” was first used by Jo Handelsman, Jon Clardy,
Robert M. Goodman, and first appeared in publicashion in 1998.
 This relatively new field of genetic research enables studies of organisms
that are not easily cultured in a laboratory as well as studies of organisms
in their natural environment.

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  Metagenomics is the study of genetic material recovered directly from
environment samples. (Wikipedia)

 Metagenome refers to the idea, that a collection of genes sequenced from the
environment could be analysed in way analogous to the study of a single genome.

 Metagenomics is application of modern genomic techniques to the 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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 Metagenomics

E. coli, Science, 1997 Saragasso sea, Science, 2004

Genomics

Human, Nature/Science, 2001 5

Human gut, Nature, 2010

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  Discovery of:
 Novel natural products
 New antibiotics
 New molecules with new function
 New enzymes and bioactive molecules

 Diversity of life
 Interplay between humans and microbes
 How do microbial community works?
MICROBES
RUN THE
W O R L D

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 Gut
Soil Environmental
Samples
Sea

Extract Genomic DNA Fragments

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 Sequenced-based

Create sequencing library

Functional-based
01

Clone fragments into vector

Sequence DNA fragments 01

02

Transform into heterogenous hosts

02 ( e.g., E.coli )
Map to know resistance genes
and/or 03 02
Identify mutations known to
cause resistance
03 Screen transformants for expression of
resistance genes
Resistance Potential
04
03
04 (Novel) resistance genes
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 16S rDNA sequencing Whole-genome sequencing

Sampling Sampling
DNA Extraction DNA Extraction

PCR + sequencing of 16S rDNA Sequencing

Phylogeny analysis

Assembly

Comparison
Gene finding
and annotation

Comparison
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  In medicine, inflammatory bowel disease (IBD) is a group of inflammatory
conditions of the colon and small intestine. The major types of IBD are Crohn's
disease and ulcerative colitis.

Crohn’s disease Ulcerative colitis

The incidence of Crohn's disease The incidence of ulcerative colitis

has been ascertained from
population studies in Norway and
the United States and is similar at 6
to 7.1:100,000.
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in North America is 10–12 cases
per 100,000 per year, with a peak
incidence of ulcerative colitis
occurring between the ages of 15
and 25.
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 3.3 million non-redundant
microbial genes, derived from
576.7 gigabases of sequence, from
faecal samples of 124 European
individuals

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 Human Microbiota
(Isolated)
Weight ~ 50-100 kg ~ 2 kg
Species 1 1000-5000
Cells ~ 1012 1013 - 1014
Genes 25,000 >40,00,000

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  Global Impact: The role of microbes is critical in maintaining atmospheric
balances, as they are
 The main photosynthetic agents
 Responsible for the generation and consumption of greenhouse gases
 Involved at all levels in ecosystems and trophic chains

 Bioremediation: Cleaning up environmental contamination, such as

 The waste from water treatment facilities
 Gasoline leaks on lands or oil spills in the oceans
 Toxic chemicals

 Human Study: Studying the human microbiome may lead to valuable new tools
and guidelines in
 Better understanding of complex diseases (obesity, cancer, asthma...)
 Drug discovery
 Preventative medicine

 Mapping the human microbiome

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 Q.5 How we can find out unknown gene
Q.1 What is Metagenomics ? functions using functional-based
metagenomics approach.
2M 3M

Q.2 Why there is need of metagenomics ? Q.6 What is Human microbiome ?

3M Metageno 2M

mics
Q.3 Explain Whole Genome Sequencing Q.7 What are the applications of
approach to sequence unknown sample. metagenomics ?
3M 5M

Q.4 Explain how 16S rDNA Sequencing Q.8 Explain the main difference between
technique to sequence any gene pool. genomics and metagenomics.
5M 3M

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