MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes
Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native cons...
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ftpubmed:oai:pubmedcentral.nih.gov:8548342 2023-05-15T17:48:03+02:00 MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes Maggiori, Catherine Raymond-Bouchard, Isabelle Brennan, Laura Touchette, David Whyte, Lyle 2021-10-26 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8548342/ https://doi.org/10.1038/s41598-021-00026-x en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8548342/ http://dx.doi.org/10.1038/s41598-021-00026-x © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . CC-BY Sci Rep Article Text 2021 ftpubmed https://doi.org/10.1038/s41598-021-00026-x 2021-10-31T01:00:47Z Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites—HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)—where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus’s only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment. Text Nunavut Sea ice PubMed Central (PMC) Allen Bay ENVELOPE(-36.533,-36.533,-54.183,-54.183) Nunavut Scientific Reports 11 1 |
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Article Maggiori, Catherine Raymond-Bouchard, Isabelle Brennan, Laura Touchette, David Whyte, Lyle MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
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Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites—HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)—where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus’s only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment. |
format |
Text |
author |
Maggiori, Catherine Raymond-Bouchard, Isabelle Brennan, Laura Touchette, David Whyte, Lyle |
author_facet |
Maggiori, Catherine Raymond-Bouchard, Isabelle Brennan, Laura Touchette, David Whyte, Lyle |
author_sort |
Maggiori, Catherine |
title |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_short |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_full |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_fullStr |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_full_unstemmed |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_sort |
minion sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
publisher |
Nature Publishing Group UK |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8548342/ https://doi.org/10.1038/s41598-021-00026-x |
long_lat |
ENVELOPE(-36.533,-36.533,-54.183,-54.183) |
geographic |
Allen Bay Nunavut |
geographic_facet |
Allen Bay Nunavut |
genre |
Nunavut Sea ice |
genre_facet |
Nunavut Sea ice |
op_source |
Sci Rep |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8548342/ http://dx.doi.org/10.1038/s41598-021-00026-x |
op_rights |
© The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
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CC-BY |
op_doi |
https://doi.org/10.1038/s41598-021-00026-x |
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Scientific Reports |
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