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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?

  • 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


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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


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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


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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


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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


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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