Metagenomics is the study of microbial communities directly from environmental samples without culturing individual species. It sequences all DNA from a sample simultaneously, bypassing the need for culture. Analysis of metagenomic data involves screening and phylogenetic studies of the large amounts of sequence data. Metagenomics can provide insights into microbial community structure and interactions, and discover novel enzymes and genes with industrial or pharmaceutical applications. Challenges include DNA purification issues, contamination, sequencing errors, and difficulties assembling less abundant genomes from immense metagenomic datasets.

1. Presented by G.Vijayalakshmi B.Sc.,M.Sc.,
20PY10
Ayya Nadar Janaki Ammal college
Sivakasi
© 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

2. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
What is Metagenomics?
 Traditional microbial genomics
 Sequence the genome of one organism at a time
 Use cultures to isolate microbe of interest
 Metagenomics
 Extract sequence data from microbial
communities as they exist in nature
 Bypass the need for culture techniques
 Sequence all DNA in sample
 Select DNA based on universal sequences

3. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Techniques in Metagenomics
 Isolate DNA
 Depends on sample
type
 Clone DNA
 Insert into plasmid
 Develop sample library
 Screen or sequence
From Figure 2 in Daniel, R. (2005) "The
Metagenomics of Soil" Nature Reviews Microbiology
3: 470-478.

4. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Analysis of Metagenomics Data
 Metagenomes are big
 Soil has as many as 40,000 individual microbial species
 Soil metagenome orders of magnitude bigger than
human genome
 Analyzing the metagenome
 Screens
 Phylogenetic studies
 Sequencing uncultivated organisms
 Studying metagenome under different conditions

5. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Understanding Microbial Communities
 Some questions
metagenomics may
answer
 Are certain adaptations
observable across
environmental
gradients?
 How do different
species interact?
 Can lateral gene
transfer be detected?
From Figure 2 in Schleper, C., et al. (2005) "Genomics
studies of uncultivated Archaea" Nature Reviews
Microbiology 3: 479-488.
Permission for figure 2 granted by K.Knittel and
T.Loesekann,MPI Bremen, www.mumm-research.de.

6. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Applications
 $2.3 billion in sales of industrial enzymes in
2003
 Discovery of novel enzymes and catalysts with
industrial uses by screening thousands of
microbial species simultaneously
 Look for pharmacologically interesting genes
(e.g. antibiotics) that exist in organisms that
cannot be cultured

7. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458
Caveats
 Problems with DNA purification
 Sample contamination
 Issues with sequencing
 Immensity of metagenome (gigabases)
 Errors in assembly due to inter-species
similarities
 Difficulties in sequencing less well-represented
genomes