Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing
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) div...
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Springer Nature
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ftnerc:oai:nora.nerc.ac.uk:530735 2023-05-15T13:41:45+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 2022-01 text http://nora.nerc.ac.uk/id/eprint/530735/ https://nora.nerc.ac.uk/id/eprint/530735/1/s41396-021-01052-3.pdf https://www.nature.com/articles/s41396-021-01052-3 en eng Springer Nature https://nora.nerc.ac.uk/id/eprint/530735/1/s41396-021-01052-3.pdf Waschulin, Valentin; Borsetto, Chiara; James, Robert; Newsham, Kevin K. orcid:0000-0002-9108-0936 Donadio, Stefano; Corre, Christophe; Wellington, Elizabeth. 2022 Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing. ISME Journal, 16. 101-111. https://doi.org/10.1038/s41396-021-01052-3 <https://doi.org/10.1038/s41396-021-01052-3> cc_by_4 CC-BY Publication - Article PeerReviewed 2022 ftnerc https://doi.org/10.1038/s41396-021-01052-3 2023-02-04T19:52:20Z 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 Natural Environment Research Council: NERC Open Research Archive Antarctic Mars Oasis ENVELOPE(-68.250,-68.250,-71.879,-71.879) The ISME Journal 16 1 101 111 |
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Open Polar |
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Natural Environment Research Council: NERC Open Research Archive |
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ftnerc |
language |
English |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Waschulin, Valentin Borsetto, Chiara James, Robert Newsham, Kevin K. Donadio, Stefano Corre, Christophe Wellington, Elizabeth |
spellingShingle |
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 |
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 Nature |
publishDate |
2022 |
url |
http://nora.nerc.ac.uk/id/eprint/530735/ https://nora.nerc.ac.uk/id/eprint/530735/1/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_relation |
https://nora.nerc.ac.uk/id/eprint/530735/1/s41396-021-01052-3.pdf Waschulin, Valentin; Borsetto, Chiara; James, Robert; Newsham, Kevin K. orcid:0000-0002-9108-0936 Donadio, Stefano; Corre, Christophe; Wellington, Elizabeth. 2022 Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing. ISME Journal, 16. 101-111. https://doi.org/10.1038/s41396-021-01052-3 <https://doi.org/10.1038/s41396-021-01052-3> |
op_rights |
cc_by_4 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1038/s41396-021-01052-3 |
container_title |
The ISME Journal |
container_volume |
16 |
container_issue |
1 |
container_start_page |
101 |
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111 |
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1766157524003717120 |