Special Issue "Metagenomics in Biodiscovery from Oceans"
A special issue of Marine Drugs (ISSN 1660-3397).
Deadline for manuscript submissions: closed (31 May 2012)
Dr. Jack A. Gilbert
1 Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
2 Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA
Metagenomics has a lot to live up to. We as a community have made constant promises for the last ten years that metagenomics will open up the black box of the microbial world to enable the bounty of genetic diversity to be accessed. We made this promise because cultivation-independent processes can only access approximately 99% of microbes in a given ecosystem. However, opening the black box has not rapidly translated into identifying the pharmaceutical bonanza we may have promised.
Primarily this is because of the drive towards sequencing platforms with higher throughput but shorter reads than traditional long-insert clone libraries (e.g. BACs, cosmids and fosmids), which yielded such great advances in our understanding of the microbial world (e.g. proteorhodopsin and archaeal ammonia oxidizers). A data-hungry community readily adopted the switch to cheaper, faster, but shorter sequences, which comprised our ability to identify functions, and assembly genetic operons that could be used to generate novel products.
However, metagenomics has recently turned over another leaf. Increases in sequencing depth now yield data from which whole genomes of currently uncultivable organisms can be re-assembled. In addition, novel culturing and microfludics approaches are taking advantage of advances in our understanding of the interactions between members of a microbial community to target specific microbial consortia with pertinent functions. It seems that long-standing promises will be fulfilled and metagenomics will be seen as a useful approach for biotechnological advance.
Dr. Jack A. Gilbert
- microbial communities
- metabolic interactions
- functional networks
- systems biology
Article: Digital Marine Bioprospecting: Mining New Neurotoxin Drug Candidates from the Transcriptomes of Cold-Water Sea Anemones
Mar. Drugs 2012, 10(10), 2265-2279; doi:10.3390/md10102265
Received: 31 August 2012; in revised form: 8 October 2012 / Accepted: 10 October 2012 / Published: 18 October 2012| Download PDF Full-text (745 KB) | View HTML Full-text | Download XML Full-text | Supplementary Files
Article: The Transcriptome of Bathymodiolus azoricus Gill Reveals Expression of Genes from Endosymbionts and Free-Living Deep-Sea Bacteria
Mar. Drugs 2012, 10(8), 1765-1783; doi:10.3390/md10081765
Received: 17 May 2012; in revised form: 26 July 2012 / Accepted: 31 July 2012 / Published: 20 August 2012| Download PDF Full-text (784 KB) | View HTML Full-text | Download XML Full-text | Supplementary Files
Article: Diversity of Nonribosomal Peptide Synthetase Genes in the Microbial Metagenomes of Marine Sponges
Mar. Drugs 2012, 10(6), 1192-1202; doi:10.3390/md10061192
Received: 23 April 2012; in revised form: 18 May 2012 / Accepted: 21 May 2012 / Published: 25 May 2012| Download PDF Full-text (682 KB) | Download XML Full-text
Mar. Drugs 2011, 9(9), 1487-1501; doi:10.3390/md9091487
Received: 2 August 2011; in revised form: 22 August 2011 / Accepted: 25 August 2011 / Published: 5 September 2011| Download PDF Full-text (2901 KB) | View HTML Full-text | Download XML Full-text
Last update: 27 February 2014