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Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities

Pathogens resistant to antimicrobials form a significant threat to public health worldwide. Tackling multidrug-resistant pathogens via screening metagenomic libraries has become a common approach for the discovery of new antibiotics from uncultured microorganisms. This study focuses on capturing non...

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Autores principales: Amin, Dina H., Nageeb, Wedad M., Elkelish, Amr, Makharita, Rabab R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10235377/
https://www.ncbi.nlm.nih.gov/pubmed/36977970
http://dx.doi.org/10.1007/s42770-023-00953-z
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author Amin, Dina H.
Nageeb, Wedad M.
Elkelish, Amr
Makharita, Rabab R.
author_facet Amin, Dina H.
Nageeb, Wedad M.
Elkelish, Amr
Makharita, Rabab R.
author_sort Amin, Dina H.
collection PubMed
description Pathogens resistant to antimicrobials form a significant threat to public health worldwide. Tackling multidrug-resistant pathogens via screening metagenomic libraries has become a common approach for the discovery of new antibiotics from uncultured microorganisms. This study focuses on capturing nonribosomal peptide synthase (NRPS) gene clusters implicated in the synthesis of many natural compounds of industrial relevance. A NRPS PCR assay was used to screen 2976 Escherichia coli clones in a soil metagenomic library to target NRPS genes. DNA extracts from 4 clones were sequenced and subjected to bioinformatic analysis to identify NRPS domains, their phylogeny, and substrate specificity. Successfully, 17 NRPS-positive hits with a biosynthetic potential were identified. DNA sequencing and BLAST analysis confirmed that NRPS protein sequences shared similarities with members of the genus Delftia in the Proteobacteria taxonomic position. Multiple alignment and phylogenetic analysis demonstrated that clones no. 15cd35 and 15cd37 shared low bootstrap values (54%) and were distantly far from close phylogenetic neighbors. Additionally, NRPS domain substrate specificity has no hits with the known ones; hence, they are more likely to use different substrates to produce new diverse antimicrobials. Further analysis confirmed that the NRPS hits resemble several transposon elements from other bacterial taxa, confirming its diversity. We confirmed that the analyses of the soil metagenomic library revealed a diverse set of NRPS related to the genus Delftia. An in-depth understanding of those positive NRPS hits is a crucial step for genetic manipulation of NRPS, shedding light on alternative novel antimicrobial compounds that can be used in drug discovery and hence supports the pharmaceutical sector.
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spelling pubmed-102353772023-06-03 Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities Amin, Dina H. Nageeb, Wedad M. Elkelish, Amr Makharita, Rabab R. Braz J Microbiol Environmental Microbiology - Research Paper Pathogens resistant to antimicrobials form a significant threat to public health worldwide. Tackling multidrug-resistant pathogens via screening metagenomic libraries has become a common approach for the discovery of new antibiotics from uncultured microorganisms. This study focuses on capturing nonribosomal peptide synthase (NRPS) gene clusters implicated in the synthesis of many natural compounds of industrial relevance. A NRPS PCR assay was used to screen 2976 Escherichia coli clones in a soil metagenomic library to target NRPS genes. DNA extracts from 4 clones were sequenced and subjected to bioinformatic analysis to identify NRPS domains, their phylogeny, and substrate specificity. Successfully, 17 NRPS-positive hits with a biosynthetic potential were identified. DNA sequencing and BLAST analysis confirmed that NRPS protein sequences shared similarities with members of the genus Delftia in the Proteobacteria taxonomic position. Multiple alignment and phylogenetic analysis demonstrated that clones no. 15cd35 and 15cd37 shared low bootstrap values (54%) and were distantly far from close phylogenetic neighbors. Additionally, NRPS domain substrate specificity has no hits with the known ones; hence, they are more likely to use different substrates to produce new diverse antimicrobials. Further analysis confirmed that the NRPS hits resemble several transposon elements from other bacterial taxa, confirming its diversity. We confirmed that the analyses of the soil metagenomic library revealed a diverse set of NRPS related to the genus Delftia. An in-depth understanding of those positive NRPS hits is a crucial step for genetic manipulation of NRPS, shedding light on alternative novel antimicrobial compounds that can be used in drug discovery and hence supports the pharmaceutical sector. Springer International Publishing 2023-03-28 /pmc/articles/PMC10235377/ /pubmed/36977970 http://dx.doi.org/10.1007/s42770-023-00953-z Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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/) .
spellingShingle Environmental Microbiology - Research Paper
Amin, Dina H.
Nageeb, Wedad M.
Elkelish, Amr
Makharita, Rabab R.
Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities
title Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities
title_full Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities
title_fullStr Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities
title_full_unstemmed Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities
title_short Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities
title_sort mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities
topic Environmental Microbiology - Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10235377/
https://www.ncbi.nlm.nih.gov/pubmed/36977970
http://dx.doi.org/10.1007/s42770-023-00953-z
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