Microbial community drivers of PK/NRP gene diversity in selected global soils
Abstract Background The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natural products allowing the exploitation of a larger fraction of the micr...
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ftdatacite:10.6084/m9.figshare.c.4514324 2023-05-15T13:45:08+02:00 Microbial community drivers of PK/NRP gene diversity in selected global soils Borsetto, Chiara Amos, Gregory Rocha, Ulisses Mitchell, Alex Finn, Robert Rabah Laidi Vallin, Carlos Pearce, David Newsham, Kevin Wellington, Elizabeth 2019 https://dx.doi.org/10.6084/m9.figshare.c.4514324 https://springernature.figshare.com/collections/Microbial_community_drivers_of_PK_NRP_gene_diversity_in_selected_global_soils/4514324 unknown Figshare https://dx.doi.org/10.1186/s40168-019-0692-8 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Biochemistry Microbiology FOS Biological sciences Genetics Molecular Biology Biotechnology Ecology 69999 Biological Sciences not elsewhere classified Collection article 2019 ftdatacite https://doi.org/10.6084/m9.figshare.c.4514324 https://doi.org/10.1186/s40168-019-0692-8 2021-11-05T12:55:41Z Abstract Background The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natural products allowing the exploitation of a larger fraction of the microbial community. Polyketide (PK) and non-ribosomal pepetide (NRP) natural products have been reported to be related to compounds with antimicrobial and anticancer activities. We report here a new culture-independent approach to explore bacterial biosynthetic diversity and determine bacterial phyla in the microbial community associated with PK and NRP diversity in selected soils. Results Through amplicon sequencing, we explored the microbial diversity (16S rRNA gene) of 13 soils from Antarctica, Africa, Europe and a Caribbean island and correlated this with the amplicon diversity of the adenylation (A) and ketosynthase (KS) domains within functional genes coding for non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), which are involved in the production of NRP and PK, respectively. Mantel and Procrustes correlation analyses with microbial taxonomic data identified not only the well-studied phyla Actinobacteria and Proteobacteria, but also, interestingly, the less biotechnologically exploited phyla Verrucomicrobia and Bacteroidetes, as potential sources harbouring diverse A and KS domains. Some soils, notably that from Antarctica, provided evidence of endemic diversity, whilst others, such as those from Europe, clustered together. In particular, the majority of the domain reads from Antarctica remained unmatched to known sequences suggesting they could encode enzymes for potentially novel PK and NRP. Conclusions The approach presented here highlights potential sources of metabolic novelty in the environment which will be a useful precursor to metagenomic biosynthetic gene cluster mining for PKs and NRPs which could provide leads for new antimicrobial metabolites. Article in Journal/Newspaper Antarc* Antarctica DataCite Metadata Store (German National Library of Science and Technology) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Biochemistry Microbiology FOS Biological sciences Genetics Molecular Biology Biotechnology Ecology 69999 Biological Sciences not elsewhere classified |
spellingShingle |
Biochemistry Microbiology FOS Biological sciences Genetics Molecular Biology Biotechnology Ecology 69999 Biological Sciences not elsewhere classified Borsetto, Chiara Amos, Gregory Rocha, Ulisses Mitchell, Alex Finn, Robert Rabah Laidi Vallin, Carlos Pearce, David Newsham, Kevin Wellington, Elizabeth Microbial community drivers of PK/NRP gene diversity in selected global soils |
topic_facet |
Biochemistry Microbiology FOS Biological sciences Genetics Molecular Biology Biotechnology Ecology 69999 Biological Sciences not elsewhere classified |
description |
Abstract Background The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natural products allowing the exploitation of a larger fraction of the microbial community. Polyketide (PK) and non-ribosomal pepetide (NRP) natural products have been reported to be related to compounds with antimicrobial and anticancer activities. We report here a new culture-independent approach to explore bacterial biosynthetic diversity and determine bacterial phyla in the microbial community associated with PK and NRP diversity in selected soils. Results Through amplicon sequencing, we explored the microbial diversity (16S rRNA gene) of 13 soils from Antarctica, Africa, Europe and a Caribbean island and correlated this with the amplicon diversity of the adenylation (A) and ketosynthase (KS) domains within functional genes coding for non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), which are involved in the production of NRP and PK, respectively. Mantel and Procrustes correlation analyses with microbial taxonomic data identified not only the well-studied phyla Actinobacteria and Proteobacteria, but also, interestingly, the less biotechnologically exploited phyla Verrucomicrobia and Bacteroidetes, as potential sources harbouring diverse A and KS domains. Some soils, notably that from Antarctica, provided evidence of endemic diversity, whilst others, such as those from Europe, clustered together. In particular, the majority of the domain reads from Antarctica remained unmatched to known sequences suggesting they could encode enzymes for potentially novel PK and NRP. Conclusions The approach presented here highlights potential sources of metabolic novelty in the environment which will be a useful precursor to metagenomic biosynthetic gene cluster mining for PKs and NRPs which could provide leads for new antimicrobial metabolites. |
format |
Article in Journal/Newspaper |
author |
Borsetto, Chiara Amos, Gregory Rocha, Ulisses Mitchell, Alex Finn, Robert Rabah Laidi Vallin, Carlos Pearce, David Newsham, Kevin Wellington, Elizabeth |
author_facet |
Borsetto, Chiara Amos, Gregory Rocha, Ulisses Mitchell, Alex Finn, Robert Rabah Laidi Vallin, Carlos Pearce, David Newsham, Kevin Wellington, Elizabeth |
author_sort |
Borsetto, Chiara |
title |
Microbial community drivers of PK/NRP gene diversity in selected global soils |
title_short |
Microbial community drivers of PK/NRP gene diversity in selected global soils |
title_full |
Microbial community drivers of PK/NRP gene diversity in selected global soils |
title_fullStr |
Microbial community drivers of PK/NRP gene diversity in selected global soils |
title_full_unstemmed |
Microbial community drivers of PK/NRP gene diversity in selected global soils |
title_sort |
microbial community drivers of pk/nrp gene diversity in selected global soils |
publisher |
Figshare |
publishDate |
2019 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.4514324 https://springernature.figshare.com/collections/Microbial_community_drivers_of_PK_NRP_gene_diversity_in_selected_global_soils/4514324 |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_relation |
https://dx.doi.org/10.1186/s40168-019-0692-8 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.4514324 https://doi.org/10.1186/s40168-019-0692-8 |
_version_ |
1766213725932486656 |