BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea

Johannes Alneberg; John Sundh; Christin Bennke; Sara Beier; Daniel Lundin; Luisa W. Hugerth; Jarone Pinhassi; Veljo Kisand; Lasse Riemann; Klaus Jürgens; Matthias Labrenz; Anders F. Andersson

doi:10.1038/sdata.2018.146

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea

Johannes Alneberg, John Sundh, Christin Bennke, Sara Beier, Daniel Lundin, Luisa W. Hugerth, Jarone Pinhassi, Veljo Kisand, Lasse Riemann, Klaus Jürgens, Matthias Labrenz, Anders F. Andersson

Marine Biology

10 Citations (Scopus)

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Abstract

The Baltic Sea is one of the world’s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.

Original language	English
Article number	180146
Journal	Scientific Data
Volume	5
Number of pages	10
ISSN	2052-4463
DOIs	https://doi.org/10.1038/sdata.2018.146
Publication status	Published - 7 Aug 2018

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Alneberg et al. 2018_Scientific DataFinal published version, 863 KBLicence: CC BY

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title = "BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea",

abstract = "The Baltic Sea is one of the world{\textquoteright}s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.",

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AU - Alneberg, Johannes

AU - Sundh, John

AU - Bennke, Christin

AU - Beier, Sara

AU - Lundin, Daniel

AU - Hugerth, Luisa W.

AU - Pinhassi, Jarone

AU - Kisand, Veljo

AU - Riemann, Lasse

AU - Jürgens, Klaus

AU - Labrenz, Matthias

AU - Andersson, Anders F.

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N2 - The Baltic Sea is one of the world’s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.

AB - The Baltic Sea is one of the world’s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.

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DO - 10.1038/sdata.2018.146

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M1 - 180146

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BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea

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