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Special Issue "Metagenomics in Biodiscovery from Oceans"

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A special issue of Marine Drugs (ISSN 1660-3397).

Deadline for manuscript submissions: closed (31 May 2012)

Special Issue Editor

Guest Editor
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
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Special Issue Information

Dear Colleagues,

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
Guest Editor

Keywords

  • metagenomics
  • metatranscriptomics
  • microbial communities
  • metabolic interactions
  • functional networks
  • interactome
  • systems biology
  • omics

Published Papers (4 papers)

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Research

Open AccessArticle 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 / Revised: 8 October 2012 / Accepted: 10 October 2012 / Published: 18 October 2012
Cited by 11 | PDF Full-text (745 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Marine bioprospecting is the search for new marine bioactive compounds and large-scale screening in extracts represents the traditional approach. Here, we report an alternative complementary protocol, called digital marine bioprospecting, based on deep sequencing of transcriptomes. We sequenced the transcriptomes from the adult
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Marine bioprospecting is the search for new marine bioactive compounds and large-scale screening in extracts represents the traditional approach. Here, we report an alternative complementary protocol, called digital marine bioprospecting, based on deep sequencing of transcriptomes. We sequenced the transcriptomes from the adult polyp stage of two cold-water sea anemones, Bolocera tuediae and Hormathia digitata. We generated approximately 1.1 million quality-filtered sequencing reads by 454 pyrosequencing, which were assembled into approximately 120,000 contigs and 220,000 single reads. Based on annotation and gene ontology analysis we profiled the expressed mRNA transcripts according to known biological processes. As a proof-of-concept we identified polypeptide toxins with a potential blocking activity on sodium and potassium voltage-gated channels from digital transcriptome libraries. Full article
(This article belongs to the Special Issue Metagenomics in Biodiscovery from Oceans)
Open AccessArticle 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 / Revised: 26 July 2012 / Accepted: 31 July 2012 / Published: 20 August 2012
Cited by 12 | PDF Full-text (784 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Deep-sea environments are largely unexplored habitats where a surprising number of species may be found in large communities, thriving regardless of the darkness, extreme cold, and high pressure. Their unique geochemical features result in reducing environments rich in methane and sulfides, sustaining complex
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Deep-sea environments are largely unexplored habitats where a surprising number of species may be found in large communities, thriving regardless of the darkness, extreme cold, and high pressure. Their unique geochemical features result in reducing environments rich in methane and sulfides, sustaining complex chemosynthetic ecosystems that represent one of the most surprising findings in oceans in the last 40 years. The deep-sea Lucky Strike hydrothermal vent field, located in the Mid Atlantic Ridge, is home to large vent mussel communities where Bathymodiolus azoricus represents the dominant faunal biomass, owing its survival to symbiotic associations with methylotrophic or methanotrophic and thiotrophic bacteria. The recent transcriptome sequencing and analysis of gill tissues from B. azoricus revealed a number of genes of bacterial origin, hereby analyzed to provide a functional insight into the gill microbial community. The transcripts supported a metabolically active microbiome and a variety of mechanisms and pathways, evidencing also the sulfur and methane metabolisms. Taxonomic affiliation of transcripts and 16S rRNA community profiling revealed a microbial community dominated by thiotrophic and methanotrophic endosymbionts of B. azoricus and the presence of a Sulfurovum-like epsilonbacterium. Full article
(This article belongs to the Special Issue Metagenomics in Biodiscovery from Oceans)
Open AccessArticle 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 / Revised: 18 May 2012 / Accepted: 21 May 2012 / Published: 25 May 2012
Cited by 9 | PDF Full-text (682 KB) | HTML Full-text | XML Full-text
Abstract
Genomic mining revealed one major nonribosomal peptide synthetase (NRPS) phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. Phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. Additionally, a phylogenetically distinct NRPS
[...] Read more.
Genomic mining revealed one major nonribosomal peptide synthetase (NRPS) phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. Phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. Additionally, a phylogenetically distinct NRPS gene cluster was discovered in the microbial metagenome of the sponge Aplysina aerophoba, which shows highest similarities to NRPS genes that were previously assigned, by ways of single cell genomics, to a Chloroflexi sponge symbiont. Genomic mining studies such as the one presented here for NRPS genes, contribute to on-going efforts to characterize the genomic potential of sponge-associated microbiota for secondary metabolite biosynthesis. Full article
(This article belongs to the Special Issue Metagenomics in Biodiscovery from Oceans)
Open AccessArticle Characterization of a Novel Serine Protease Inhibitor Gene from a Marine Metagenome
Mar. Drugs 2011, 9(9), 1487-1501; doi:10.3390/md9091487
Received: 2 August 2011 / Revised: 22 August 2011 / Accepted: 25 August 2011 / Published: 5 September 2011
Cited by 6 | PDF Full-text (2901 KB) | HTML Full-text | XML Full-text
Abstract
A novel serine protease inhibitor (serpin) gene designated as Spi1C was cloned via the sequenced-based screening of a metagenomic library from uncultured marine microorganisms. The gene had an open reading frame of 642 base pairs, and encoded a 214-amino acid polypeptide with a
[...] Read more.
A novel serine protease inhibitor (serpin) gene designated as Spi1C was cloned via the sequenced-based screening of a metagenomic library from uncultured marine microorganisms. The gene had an open reading frame of 642 base pairs, and encoded a 214-amino acid polypeptide with a predicted molecular mass of about 28.7 kDa. The deduced amino acid sequence comparison and phylogenetic analysis indicated that Spi1C and some partial proteinase inhibitor I4 serpins were closely related. Functional characterization demonstrated that the recombinant Spi1C protein could inhibit a series of serine proteases. The Spi1C protein exhibited inhibitory activity against α-chymotrypsin and trypsin with Ki values of around 1.79 × 10−8 and 1.52 × 10−8 M, respectively. No inhibition activity was exhibited against elastase. Using H-D-Phe-Pip-Arg-pNA as the chromogenic substrate, the optimum pH and temperature of the inhibition activity against trypsin were 7.0–8.0 and 25 °C, respectively. The identification of a novel serpin gene underscores the potential of marine metagenome screening for novel biomolecules. Full article
(This article belongs to the Special Issue Metagenomics in Biodiscovery from Oceans)

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