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?
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
Metagenomics• Investigate all genomic content
(i.e. bacteria, phages, plasmids…)
• culture/non-culturable (~99% of microbial species cannot be cultivated)
• known/unknown
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
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