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

TY - JOUR

T1 - BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea

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.

PY - 2018/8/7

Y1 - 2018/8/7

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.

U2 - 10.1038/sdata.2018.146

DO - 10.1038/sdata.2018.146

M3 - Journal article

C2 - 30063227

SN - 2052-4463

VL - 5

JO - Scientific Data

JF - Scientific Data

M1 - 180146

ER -