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What's Bioprospecting?


Examples of Genes Identified via Bioprospecting





Reverse Transcriptases


Restriction Endonucleases



GOLD genome projects
GOLD genome projects


Craig Venter and his Yacht

Global Ocean Explorer
Global Ocean Explorer

Examples of Bioprospecting using Metagenomics (Targeted Metagenomics)


----Typical Targeted Metagenomic Pipeline----
  2. Next Gen Sequencing or Mass Spec
  3. Computational analysis for ORFs and homology searches
  4. Heterologous Expression and Testing for function
Cellulosic Biomass degrading genes found in Cow Rumen


Uranium Bioremediation


Current status and the future


List of Parts found by Metagenomics

  1. glycosyl hydrolases (cellulose degradation)
  2. antibiotic resistance (tetracycline/bleomycin)
  3. extradiol dioxygenases (aromatic carbon usage)
  4. sulfate reductases
  5. deaminases
  6. Zn-dependent carboxypeptidases
  7. RNA-binding proteins
  8. many unique ORFans




Often, the search for novel genes amongst divergent microbial species is limited to genes with small identical regions of DNA for cloning. Cloning of genes from a diverse sample can be helped with prior knowledge of the target gene family. Various domains of a given gene family can be targeted with degenerate primers to isolate similar genes in a microbial community sample. On the other hand, even the use of degenerate primers may not capture the entirety of gene families in a diverse sample. Alternatively, phylogenetic analysis of regions with high similarity (low degeneracy) can help for designing primers that better capture the genes.



Rare Genomes and Low Density Environments

Another issue is filtering out the interesting bacteria from the less interesting bacteria in a metagenome. When creating a library, it seems like it would be hard to maintain enough complexity to capture the plausibly rare and beneficial genes you're looking for. One solution to this might be to look into metagenomes where there is a huge selection pressure to have the genes you're looking for. Such an environment would have to be particularly hostile - something with very high concentrations of a given contaminant. While it doesn't allow you to capture the genomes of rare bacteria any better, it would increase the relative population of a bacteria with the physiology of interest. An interesting paper that talks about some of the evolutionary dynamics of such an environment has been recently published [7]. The situation does however create sort of a catch-22. Harsher conditions that lead to over representation of useful genes to cope with the environment also can have significantly lower overall concentrations of cells - on the order of 10,000/g of soil. By traditional library construction methods, this would require you to harvest dozens of kilograms of soil for extraction. A solution is to use φ29 DNA polymerase to amplify low concentrations of environmental DNA for library construction [8]. While this method has a lot of potential to give access to low concentration metagenomes, the innate biases it creates are not well understood.


  1. Chistoserdova L. . pmid:20495950. PubMed HubMed [BiotechLettReview2010]
    Recent progress and new challenges in metagenomics for biotechnology.

    The Sorcerer II Global Ocean Sampling expedition: expanding the universe of

    protein families.

  3. Suenaga H. . pmid:21366818. PubMed HubMed [EnviroMicroReview2011]
    Targeted metagenomics: a high-resolution metagenomics approach for specific gene

    clusters in complex microbial communities.

  4. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, and Rubin EM. . pmid:21273488. PubMed HubMed [Science2011]

  5. Wilkins MJ, Verberkmoes NC, Williams KH, Callister SJ, Mouser PJ, Elifantz H, N'guessan AL, Thomas BC, Nicora CD, Shah MB, Abraham P, Lipton MS, Lovley DR, Hettich RL, Long PE, and Banfield JF. . pmid:19717633. PubMed HubMed [ApplEnviroMicro2009]
    Proteogenomic monitoring of Geobacter physiology during stimulated uranium


  6. Daniel R. . pmid:15193327. PubMed HubMed [Daniel2004]

  7. Hemme CL, Deng Y, Gentry TJ, Fields MW, Wu L, Barua S, Barry K, Tringe SG, Watson DB, He Z, Hazen TC, Tiedje JM, Rubin EM, and Zhou J. . pmid:20182523. PubMed HubMed [Hemme2010]
    Metagenomic insights into evolution of a heavy metal-contaminated groundwater

    microbial community.

  8. Abulencia CB, Wyborski DL, Garcia JA, Podar M, Chen W, Chang SH, Chang HW, Watson D, Brodie EL, Hazen TC, and Keller M. . pmid:16672469. PubMed HubMed [Abulencia2006]
    Environmental whole-genome amplification to access microbial populations in

    contaminated sediments.

All Medline abstracts: PubMed HubMed
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