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Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter

The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of...

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Autores principales: Schultz, Júnia, Modolon, Flúvio, Rosado, Alexandre S., Voolstra, Christian R., Sweet, Michael, Peixoto, Raquel S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9426423/
https://www.ncbi.nlm.nih.gov/pubmed/35862824
http://dx.doi.org/10.1128/msystems.00367-22
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author Schultz, Júnia
Modolon, Flúvio
Rosado, Alexandre S.
Voolstra, Christian R.
Sweet, Michael
Peixoto, Raquel S.
author_facet Schultz, Júnia
Modolon, Flúvio
Rosado, Alexandre S.
Voolstra, Christian R.
Sweet, Michael
Peixoto, Raquel S.
author_sort Schultz, Júnia
collection PubMed
description The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM “dark matter” (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.
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spelling pubmed-94264232022-08-31 Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter Schultz, Júnia Modolon, Flúvio Rosado, Alexandre S. Voolstra, Christian R. Sweet, Michael Peixoto, Raquel S. mSystems Minireview The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM “dark matter” (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics. American Society for Microbiology 2022-07-05 /pmc/articles/PMC9426423/ /pubmed/35862824 http://dx.doi.org/10.1128/msystems.00367-22 Text en Copyright © 2022 Schultz et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Minireview
Schultz, Júnia
Modolon, Flúvio
Rosado, Alexandre S.
Voolstra, Christian R.
Sweet, Michael
Peixoto, Raquel S.
Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter
title Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter
title_full Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter
title_fullStr Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter
title_full_unstemmed Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter
title_short Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter
title_sort methods and strategies to uncover coral-associated microbial dark matter
topic Minireview
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9426423/
https://www.ncbi.nlm.nih.gov/pubmed/35862824
http://dx.doi.org/10.1128/msystems.00367-22
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