Genome-reconstruction for eukaryotes from complex natural microbial communities

Genome Research
Patrick T WestJillian F Banfield

Abstract

Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, se...Continue Reading

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Citations

Oct 8, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Patrick J Keeling
Mar 20, 2020·Genome Research·Lin-Xing ChenJillian F Banfield
Jun 5, 2020·The Journal of Eukaryotic Microbiology·Luciana SantoferraraGeorge B McManus
Jul 1, 2020·Annual Review of Microbiology·Felicia N New, Ilana L Brito
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Nov 6, 2020·MSphere·Irina R Arkhipova
Mar 25, 2021·Briefings in Bioinformatics·Masood Ur Rehman KayaniLei Chen
Mar 19, 2021·Bioinformatics·M MirditaE Levy Karin
Mar 12, 2021·Genome Biology and Evolution·Gulnara TagirdzhanovaToby Spribille
Jun 11, 2021·BMC Bioinformatics·Theo R AllnuttLeonard C Harrison
Jun 23, 2021·Proceedings of the National Academy of Sciences of the United States of America·Francisco LatorreRamiro Logares
Jun 10, 2021·Applied and Environmental Microbiology·O G G Almeida, E C P De Martinis
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Oct 7, 2021·Nucleic Acids Research·Francisco ZorrillaAleksej Zelezniak
Oct 13, 2021·Current Biology : CB·Fabien BurkiMahwash Jamy

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