Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 562696
Title Genomes from uncultivated prokaryotes : A comparison of metagenome-assembled and single-amplified genomes 06 Biological Sciences 0604 Genetics
Author(s) Alneberg, Johannes; Karlsson, Christofer M.G.; Divne, Anna Maria; Bergin, Claudia; Homa, Felix; Lindh, Markus V.; Hugerth, Luisa W.; Ettema, Thijs J.G.; Bertilsson, Stefan; Andersson, Anders F.; Pinhassi, Jarone
Source Microbiome 6 (2018)1. - ISSN 2049-2618
DOI https://doi.org/10.1186/s40168-018-0550-0
Publication type Refereed Article in a scientific journal
Publication year 2018
Keyword(s) Binning - Metagenome-assembled genomes - Metagenomics - Single-amplified genomes - Single-cell genomics
Abstract

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.

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