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Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, Kalmar, Sweden..
Uppsala Univ, Dept Cell & Mol Biol, SciLifeLab, Uppsala, Sweden..
Uppsala Univ, Dept Cell & Mol Biol, SciLifeLab, Uppsala, Sweden..
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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
Microbiology
Identifiers
URN: urn:nbn:se:kth:diva-237125DOI: 10.1186/s40168-018-0550-0ISI: 000446307400001PubMedID: 30266101Scopus ID: 2-s2.0-85054254141OAI: oai:DiVA.org:kth-237125DiVA, id: diva2:1259227
Funder
Swedish Research Council, 2011-4369 2015-04254 2011-5689 2015-04959Swedish Research Council FormasEU, European Research Council, 310039-PUZZLE_CELLSwedish Foundation for Strategic Research Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20180729

Available from: 2018-10-29 Created: 2018-10-29 Last updated: 2019-08-20Bibliographically approved

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Alneberg, JohannesHugerth, LuisaAndersson, Anders F.
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