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Genomes from uncult...
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
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- Alneberg, Johannes (författare)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Karlsson, Christofer M.G. (författare)
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Barlastgatan 11, 391 82 Kalmar, Sweden
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- Divne, Anna-Maria (författare)
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
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- Bergin, Claudia (författare)
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
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- Homa, Felix (författare)
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
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- Lindh, Markus V. (författare)
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Barlastgatan 11, 391 82 Kalmar, Sweden
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- Hugerth, Luisa W. (författare)
- Karolinska Institutet, Science for Life Laboratory, Department of Molecular, Tumour and Cell Biology, Centre for Translational Microbiome Research, Solna, Sweden
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- Ettema, Thijs JG (författare)
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
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- Bertilsson, Stefan (författare)
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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- Andersson, Anders F. (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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- Pinhassi, Jarone (författare)
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Barlastgatan 11, 391 82 Kalmar, Sweden
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(creator_code:org_t)
- Engelska.
- Relaterad länk:
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https://kth.diva-por... (primary) (Raw object)
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (>98.7% identity) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs; the metagenome assembly was found to cause incompleteness to a higher degree than the binning procedure.Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
Ämnesord
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
Nyckelord
- Single-amplified genomes
- Metagenome-assembled genomes
- Metagenomics
- Binning
- Single-cell genomics
Publikations- och innehållstyp
- vet (ämneskategori)
- ovr (ämneskategori)
- Av författaren/redakt...
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Alneberg, Johann ...
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Karlsson, Christ ...
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Divne, Anna-Mari ...
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Bergin, Claudia
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Homa, Felix
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Lindh, Markus V.
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visa fler...
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Hugerth, Luisa W ...
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Ettema, Thijs JG
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Bertilsson, Stef ...
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Andersson, Ander ...
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Pinhassi, Jarone
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- Om ämnet
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Bioinformatik oc ...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Mikrobiologi
- Av lärosätet
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Kungliga Tekniska Högskolan