KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computational Bioscience Research Center (CBRC)
Online Publication Date2015-11-02
Print Publication Date2016-02
Permanent link to this recordhttp://hdl.handle.net/10754/581767
MetadataShow full item record
AbstractThe metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database.
CitationDatabases of the marine metagenomics 2015 Gene
- Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan.
- Authors: Yoshitake K, Kimura G, Sakami T, Watanabe T, Taniuchi Y, Kakehi S, Kuwata A, Yamaguchi H, Kataoka T, Kawachi M, Ikeo K, Tan E, Igarashi Y, Ohtsubo M, Watabe S, Suzuki Y, Asakawa S, Ishino S, Tashiro K, Ishino Y, Kobayashi T, Mineta K, Gojobori T
- Issue date: 2021 Jun 9
- Metagenomic studies of the Red Sea.
- Authors: Behzad H, Ibarra MA, Mineta K, Gojobori T
- Issue date: 2016 Feb 1
- MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.
- Authors: Kushwaha SK, Manoharan L, Meerupati T, Hedlund K, Ahrén D
- Issue date: 2015 Feb 28
- Metagenomic approach in the investigation of new bioactive compounds in the marine environment.
- Authors: Felczykowska A, Bloch SK, Nejman-Faleńczyk B, Barańska S
- Issue date: 2012
- An Agile Functional Analysis of Metagenomic Data Using SUPER-FOCUS.
- Authors: Silva GGZ, Lopes FAC, Edwards RA
- Issue date: 2017