What is Metagenomics? - an Introduction

Josef Korbinian Vogt

Information AgeDo you remember?

DNA SequencingReading the order of bases in DNA fragments

How?Do you remember?

Sequencing timeline

‘53 ‘77 ‘83 ‘86 ‘90 ‘95 ‘96 ‘00 ‘03 ‘04 ‘06 2010 -

Discovery of DNA double Helix by Watson & Crick

Sanger sequencing

Polymerase chain reaction developed

Applied Biosystems markets first automated DNA sequencing

Human Genome Project starts

First complete genome of free-living organisms

Pyro-sequencing

3rd Generation Sequencing

Completion of Human Genome Project

454 Pyrosequencing

Illumina Sequencing

“Next Generation” Sequencing

2nd Generation sequencing

Do you remember?

Do you remember?

Reading the order of bases in DNA bases

From genomics to metagenomicsFrom genomics to metagenomics

Genomics

E. coli, Science, 1997 Human, Nature/Science, 2001

Metagenomics

Saragasso sea, Science, 2004 Human gut, Nature, 2010

MetagenomicsWhat is Metagenomics?

Metagenomics (Environmental Genomics, Ecogenomics or Community

Genomics) is the study of genetic material recovered directly from environmental samples.

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

Chen &Pachter,2005

Environments

Metagenomics• Investigate all genomic content

(i.e. bacteria, phages, plasmids…)

• culture/non-culturable (~99% of microbial species cannot be cultivated)

• known/unknown

16S rRNA

How to?

How to?

How to?

Methods

Makes analysis hard…

• Lack of references (for novel metagenomes)

• Assembly: shared/similar regions between genomes work as repeats, assign contigs

• Varying abundance

• High diversity, large datasets

Genomic vs Metagenomics

Genomic vs Metagenomics

Genomic vs Metagenomics

Why bother?• Discovery:

• novel products (e.g. Galathea expedition) • antibiotics • new enzymes and bioactive compounds

• Diversity

• Interactions, interplay between human and microbes (human microbiome biome)

• how do microbial communities work

Possibilities