What is Metagenomics? - an Introduction Josef Korbinian Vogt Information Age Do you remember? DNA Sequencing Reading the order of bases in DNA fragments How? Do you remember? Sequencing timeline Do you remember? ‘53 ‘77 ‘83 ‘86 ‘90 ‘95 ‘96 ‘00 ‘03 ‘04 ‘06 2010 - Human Genome Pyro- Completion of 3rd Generation Sanger sequencing Project starts sequencing Human Genome Sequencing Project Illumina Sequencing Polymerase chain First complete reaction developed genome of free- living organisms 454 Discovery of DNA double Pyrosequencing Helix by Watson & Crick Applied Biosystems “Next Generation” markets first automated Sequencing DNA sequencing 2nd Generation sequencing Do you remember? Reading the order of bases in DNA bases From genomics to metagenomics From genomics to metagenomics Genomics E. coli, Science, 1997 Human, Nature/Science, 2001 Metagenomics Saragasso sea, Science, 2004 Human gut, Nature, 2010 Metagenomics What is Metagenomics? Metagenomics (Environmental Genomics, Ecogenomics or Community Genomics) is the study of genetic material recovered directly from environmental samples. Chen & Pachter, Metagenomics is application of modern genomic techniques to the 2005 study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species 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.