Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing
Abstract The growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster...
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2021
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crspringernat:10.1038/s41396-021-01052-3 2023-05-15T14:10:47+02:00 Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing Waschulin, Valentin Borsetto, Chiara James, Robert Newsham, Kevin K. Donadio, Stefano Corre, Christophe Wellington, Elizabeth EC | Horizon 2020 Framework Programme RCUK | Natural Environment Research Council 2021 http://dx.doi.org/10.1038/s41396-021-01052-3 https://www.nature.com/articles/s41396-021-01052-3.pdf https://www.nature.com/articles/s41396-021-01052-3 en eng Springer Science and Business Media LLC https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 CC-BY The ISME Journal volume 16, issue 1, page 101-111 ISSN 1751-7362 1751-7370 Ecology, Evolution, Behavior and Systematics Microbiology journal-article 2021 crspringernat https://doi.org/10.1038/s41396-021-01052-3 2022-01-04T09:05:07Z Abstract The growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster (BGC) diversity in metagenomes, indicating their potential for producing novel and useful compounds. However, recovering full-length BGC sequences from uncultivated bacteria remains a challenge due to the technological restraints of short-read sequencing, thus making assessment of BGC diversity difficult. Here, long-read sequencing and genome mining were used to recover >1400 mostly full-length BGCs that demonstrate the rich diversity of BGCs from uncultivated lineages present in soil from Mars Oasis, Antarctica. A large number of highly divergent BGCs were not only found in the phyla Acidobacteriota, Verrucomicrobiota and Gemmatimonadota but also in the actinobacterial classes Acidimicrobiia and Thermoleophilia and the gammaproteobacterial order UBA7966. The latter furthermore contained a potential novel family of RiPPs. Our findings underline the biosynthetic potential of underexplored phyla as well as unexplored lineages within seemingly well-studied producer phyla. They also showcase long-read metagenomic sequencing as a promising way to access the untapped genetic reservoir of specialised metabolite gene clusters of the uncultured majority of microbes. Article in Journal/Newspaper Antarc* Antarctic Antarctica Springer Nature (via Crossref) Antarctic Mars Oasis ENVELOPE(-68.250,-68.250,-71.879,-71.879) The ISME Journal |
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Open Polar |
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Springer Nature (via Crossref) |
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language |
English |
topic |
Ecology, Evolution, Behavior and Systematics Microbiology |
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Ecology, Evolution, Behavior and Systematics Microbiology Waschulin, Valentin Borsetto, Chiara James, Robert Newsham, Kevin K. Donadio, Stefano Corre, Christophe Wellington, Elizabeth Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing |
topic_facet |
Ecology, Evolution, Behavior and Systematics Microbiology |
description |
Abstract The growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster (BGC) diversity in metagenomes, indicating their potential for producing novel and useful compounds. However, recovering full-length BGC sequences from uncultivated bacteria remains a challenge due to the technological restraints of short-read sequencing, thus making assessment of BGC diversity difficult. Here, long-read sequencing and genome mining were used to recover >1400 mostly full-length BGCs that demonstrate the rich diversity of BGCs from uncultivated lineages present in soil from Mars Oasis, Antarctica. A large number of highly divergent BGCs were not only found in the phyla Acidobacteriota, Verrucomicrobiota and Gemmatimonadota but also in the actinobacterial classes Acidimicrobiia and Thermoleophilia and the gammaproteobacterial order UBA7966. The latter furthermore contained a potential novel family of RiPPs. Our findings underline the biosynthetic potential of underexplored phyla as well as unexplored lineages within seemingly well-studied producer phyla. They also showcase long-read metagenomic sequencing as a promising way to access the untapped genetic reservoir of specialised metabolite gene clusters of the uncultured majority of microbes. |
author2 |
EC | Horizon 2020 Framework Programme RCUK | Natural Environment Research Council |
format |
Article in Journal/Newspaper |
author |
Waschulin, Valentin Borsetto, Chiara James, Robert Newsham, Kevin K. Donadio, Stefano Corre, Christophe Wellington, Elizabeth |
author_facet |
Waschulin, Valentin Borsetto, Chiara James, Robert Newsham, Kevin K. Donadio, Stefano Corre, Christophe Wellington, Elizabeth |
author_sort |
Waschulin, Valentin |
title |
Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing |
title_short |
Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing |
title_full |
Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing |
title_fullStr |
Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing |
title_full_unstemmed |
Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing |
title_sort |
biosynthetic potential of uncultured antarctic soil bacteria revealed through long-read metagenomic sequencing |
publisher |
Springer Science and Business Media LLC |
publishDate |
2021 |
url |
http://dx.doi.org/10.1038/s41396-021-01052-3 https://www.nature.com/articles/s41396-021-01052-3.pdf https://www.nature.com/articles/s41396-021-01052-3 |
long_lat |
ENVELOPE(-68.250,-68.250,-71.879,-71.879) |
geographic |
Antarctic Mars Oasis |
geographic_facet |
Antarctic Mars Oasis |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_source |
The ISME Journal volume 16, issue 1, page 101-111 ISSN 1751-7362 1751-7370 |
op_rights |
https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1038/s41396-021-01052-3 |
container_title |
The ISME Journal |
_version_ |
1766282872789925888 |