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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ftpubmed:oai:pubmedcentral.nih.gov:8692599 2023-05-15T13:30:59+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 2021-07-12 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8692599/ http://www.ncbi.nlm.nih.gov/pubmed/34253854 https://doi.org/10.1038/s41396-021-01052-3 en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8692599/ http://www.ncbi.nlm.nih.gov/pubmed/34253854 http://dx.doi.org/10.1038/s41396-021-01052-3 © 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . CC-BY ISME J Article Text 2021 ftpubmed https://doi.org/10.1038/s41396-021-01052-3 2022-01-16T01:26:51Z 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. Text Antarc* Antarctic Antarctica PubMed Central (PMC) Antarctic Mars Oasis ENVELOPE(-68.250,-68.250,-71.879,-71.879) The ISME Journal 16 1 101 111 |
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Article 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 |
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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 |
Text |
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 |
Nature Publishing Group UK |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8692599/ http://www.ncbi.nlm.nih.gov/pubmed/34253854 https://doi.org/10.1038/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 |
ISME J |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8692599/ http://www.ncbi.nlm.nih.gov/pubmed/34253854 http://dx.doi.org/10.1038/s41396-021-01052-3 |
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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
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CC-BY |
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https://doi.org/10.1038/s41396-021-01052-3 |
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The ISME Journal |
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16 |
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