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Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden.
Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, Kalmar, Sweden.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2018 (English)In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 6, article id 173Article in journal (Refereed) Published
Abstract [en]

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 (average 99.51% sequence identity; range 98.77-99.84%) 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.

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.

Place, publisher, year, edition, pages
BMC , 2018. Vol. 6, article id 173
Keywords [en]
Single-amplified genomes, Metagenome-assembled genomes, Metagenomics, Binning, Single-cell genomics
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:uu:diva-368105DOI: 10.1186/s40168-018-0550-0ISI: 000446307400001PubMedID: 30266101OAI: oai:DiVA.org:uu-368105DiVA, id: diva2:1268373
Funder
Swedish Research Council, 2011-4369Swedish Research Council, 2015-04254Swedish Research Council, 2011-5689Swedish Research Council, 2015-04959Swedish Research Council FormasEU, European Research Council, 310039-PUZZLE_CELLSwedish Foundation for Strategic Research Available from: 2018-12-05 Created: 2018-12-05 Last updated: 2018-12-05Bibliographically approved

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Divne, Anna-MariaBergin, ClaudiaHoma, FelixEttema, Thijs J. G.Bertilsson, Stefan

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