Special Issue "Metagenomics in Biodiscovery from Oceans"

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
E-Mail: gilbertjack@gmail.com

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

Submission

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

Type of paper: Review
Title: Marine Microbes: Trends and Prospects
Authors: Peijun Zuo ^1,2,3,4 and Se-Kwon Kim ^1,2
Affiliations: ¹ Department of Chemistry, Pukyong National University, Busan 608-737, Korea; E-Mails: peijunzuo@lycos.com (P.Z.); sknkim@pknu.ac.kr (S.-K.K.)
² Marine Bioprocess Research Center, Pukyong National University, Busan 608-737, Korea
³ KAUST-HKUST Micro/Nanofluidics Joint Laboratory and Department of Physics, The HongKong University of Science and Technology, Kowloon, Hong Kong, China
⁴ King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
Abstract: Oceans, the biggest habitats of microbes, contain the huge microbial communities, and can be subdivided into countless micro-ecological systems. In the micro-ecological system, microbes share resources and exchange products. Rare of the microbes can be grown in culture and are therefore very difficult to study. Sequencing seems to be the right method for studying the microbes from the oceans. In the 2000s, shotgun sequencing techniques for whole genome sequencing were used to sequencing entire communities of microbes, which was called metagenomics. Up today, sequencing is no longer the problem for the biodiscovery from oceans; however, the bottleneck of metagenomics is the computational analysis. The recent trend in metagenomics analysis is cloud computing. Database sharing and interoperability between tools are also important, because computation for metagenomic datasets is more and more used in the near future.

Type of Paper: Article
Title: Digital Marine Bioprospecting – Mining New Drug Candidates from the Transcriptomes of Cold-Water Sea Anemones
Authors: Bård Ove Karlsen ¹, Ilona Urbarova ¹, Åse Emblem ¹, Siri Okkenhaug ¹, Ole Morten Seternes ² and Steinar D. Johansen ^1,3
Affiliations: ¹ Faculty of Health Sciences, Department of Medical Biology – RNA and Transcriptomics Research Group, University of Tromsø, N9037 Tromsø, Norway;  E-Mail: Steinar.Johansen@uit.no (S.D.J.)
² Faculty of Health Sciences, Department of Pharmacy – Molecular Pharmacology Group, University of Tromsø, N9037 Tromsø, Norway
³ Faculty of Biosciences and Aquaculture, Marine Genomics Group, University of Nordland, N8049 Bodø, Norway
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, named digital marine bioprospecting, based on deep sequencing of transcriptomes. We sequenced the whole transcriptomes from the adult polyp stage of two cold-water sea anemones, Bolocera tuediae and Hormathia digitata. We generated approximately 547,000 quality-filtered sequencing reads by 454 pyrosequencing (average length of 545 nt) from both species, which were assembled into more than 5000 contigs longer than 1000 nt. Based on annotation and gene ontology analysis we profiled the expressed mRNA transcripts according to known biological processes. As a proof-of-principal we identified polypeptide toxins with a potential blocking activity on sodium- and potassium voltage-gated channels from digital transcriptome libraries.