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What is Metagenomics?

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

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What is Metagenomics?

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  1. 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 © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

  2. 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. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

  3. 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 © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

  4. 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. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

  5. 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 © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

  6. 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 © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458

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