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Ecosystem-wide meta...
Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes
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- Alneberg, Johannes (author)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi,KTH Royal instute of technology, Sweden
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- Bennke, Christin (author)
- Leibniz Inst Balt Sea Res, Warnemunde, Germany.
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- Beier, Sara (author)
- Leibniz Inst Balt Sea Res, Warnemunde, Germany.;Sorbonne Univ, CNRS, Lab Oceanog Microbienne, LOMIC, Banyuls Sur Mer, France.
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- Bunse, Carina (author)
- Linnéuniversitetet,Institutionen för biologi och miljö (BOM),Carl von Ossietzky Univ Oldenburg, Germany;Alfred Wegener Institut, Germany,Ctr Ecol & Evolut Microbial Model Syst EEMiS,Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.;Carl von Ossietzky Univ Oldenburg, HIFMB, Oldenburg, Germany.;Helmholtz Zentrum Polar & Meeresforsch, Alfred Wegener Inst, Bremerhaven, Germany.,EcoChange
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- Quince, Christopher (author)
- Univ Warwick, Warwick Med Sch, Coventry, W Midlands, England.
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- Ininbergs, Karolina (author)
- Stockholms universitet,Institutionen för ekologi, miljö och botanik
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- Riemann, Lasse (author)
- Univ Copenhagen, Marine Biol Sect, Dept Biol, Helsingor, Denmark.
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- Ekman, Martin (author)
- Stockholms universitet,Institutionen för ekologi, miljö och botanik
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- Juergens, Klaus (author)
- Leibniz Inst Balt Sea Res, Warnemunde, Germany.
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- Labrenz, Matthias (author)
- Leibniz Inst Balt Sea Res, Warnemunde, Germany.
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- Pinhassi, Jarone (author)
- Linnéuniversitetet,Institutionen för biologi och miljö (BOM),Vatten,Ctr Ecol & Evolut Microbial Model Syst EEMiS,Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.,EcoChange
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- Andersson, Anders F. (author)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi,KTH Royal instute of technology, Sweden
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(creator_code:org_t)
- 2020-03-13
- 2020
- English.
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In: Communications Biology. - : Nature Publishing Group. - 2399-3642. ; 3:1, s. 1-10
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Abstract
Subject headings
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- Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes. The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.
Subject headings
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
Keyword
- Ecology
- Ekologi
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Alneberg, Johann ...
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Bennke, Christin
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Beier, Sara
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Bunse, Carina
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Quince, Christop ...
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Ininbergs, Karol ...
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show more...
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Riemann, Lasse
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Ekman, Martin
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Juergens, Klaus
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Labrenz, Matthia ...
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Pinhassi, Jarone
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Andersson, Ander ...
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Ecology
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Evolutionary Bio ...
- Articles in the publication
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Communications B ...
- By the university
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Linnaeus University
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Royal Institute of Technology
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Umeå University
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Stockholm University
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Karolinska Institutet