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Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications

Natural products derived from microbes are crucial innovations that would help in reaching sustainability development goals worldwide while achieving bioeconomic growth. Trichoderma species are well-studied model fungal organisms used for their biocontrol properties with great potential to alleviate...

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Autores principales: Rush, Tomás A., Shrestha, Him K., Gopalakrishnan Meena, Muralikrishnan, Spangler, Margaret K., Ellis, J. Christopher, Labbé, Jesse L., Abraham, Paul E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512312/
https://www.ncbi.nlm.nih.gov/pubmed/37744103
http://dx.doi.org/10.3389/ffunb.2021.716511
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author Rush, Tomás A.
Shrestha, Him K.
Gopalakrishnan Meena, Muralikrishnan
Spangler, Margaret K.
Ellis, J. Christopher
Labbé, Jesse L.
Abraham, Paul E.
author_facet Rush, Tomás A.
Shrestha, Him K.
Gopalakrishnan Meena, Muralikrishnan
Spangler, Margaret K.
Ellis, J. Christopher
Labbé, Jesse L.
Abraham, Paul E.
author_sort Rush, Tomás A.
collection PubMed
description Natural products derived from microbes are crucial innovations that would help in reaching sustainability development goals worldwide while achieving bioeconomic growth. Trichoderma species are well-studied model fungal organisms used for their biocontrol properties with great potential to alleviate the use of agrochemicals in agriculture. However, identifying and characterizing effective natural products in novel species or strains as biological control products remains a meticulous process with many known challenges to be navigated. Integration of recent advancements in various “omics” technologies, next generation biodesign, machine learning, and artificial intelligence approaches could greatly advance bioprospecting goals. Herein, we propose a roadmap for assessing the potential impact of already known or newly discovered Trichoderma species for biocontrol applications. By screening publicly available Trichoderma genome sequences, we first highlight the prevalence of putative biosynthetic gene clusters and antimicrobial peptides among genomes as an initial step toward predicting which organisms could increase the diversity of natural products. Next, we discuss high-throughput methods for screening organisms to discover and characterize natural products and how these findings impact both fundamental and applied research fields.
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spelling pubmed-105123122023-09-22 Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications Rush, Tomás A. Shrestha, Him K. Gopalakrishnan Meena, Muralikrishnan Spangler, Margaret K. Ellis, J. Christopher Labbé, Jesse L. Abraham, Paul E. Front Fungal Biol Fungal Biology Natural products derived from microbes are crucial innovations that would help in reaching sustainability development goals worldwide while achieving bioeconomic growth. Trichoderma species are well-studied model fungal organisms used for their biocontrol properties with great potential to alleviate the use of agrochemicals in agriculture. However, identifying and characterizing effective natural products in novel species or strains as biological control products remains a meticulous process with many known challenges to be navigated. Integration of recent advancements in various “omics” technologies, next generation biodesign, machine learning, and artificial intelligence approaches could greatly advance bioprospecting goals. Herein, we propose a roadmap for assessing the potential impact of already known or newly discovered Trichoderma species for biocontrol applications. By screening publicly available Trichoderma genome sequences, we first highlight the prevalence of putative biosynthetic gene clusters and antimicrobial peptides among genomes as an initial step toward predicting which organisms could increase the diversity of natural products. Next, we discuss high-throughput methods for screening organisms to discover and characterize natural products and how these findings impact both fundamental and applied research fields. Frontiers Media S.A. 2021-09-16 /pmc/articles/PMC10512312/ /pubmed/37744103 http://dx.doi.org/10.3389/ffunb.2021.716511 Text en Copyright © 2021 Rush, Shrestha, Gopalakrishnan Meena, Spangler, Ellis, Labbé and Abraham. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Fungal Biology
Rush, Tomás A.
Shrestha, Him K.
Gopalakrishnan Meena, Muralikrishnan
Spangler, Margaret K.
Ellis, J. Christopher
Labbé, Jesse L.
Abraham, Paul E.
Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications
title Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications
title_full Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications
title_fullStr Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications
title_full_unstemmed Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications
title_short Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol Applications
title_sort bioprospecting trichoderma: a systematic roadmap to screen genomes and natural products for biocontrol applications
topic Fungal Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512312/
https://www.ncbi.nlm.nih.gov/pubmed/37744103
http://dx.doi.org/10.3389/ffunb.2021.716511
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