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Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics
Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host’s responses to stressors that cause bleaching, disease, and other deleterious effects can...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9987214/ https://www.ncbi.nlm.nih.gov/pubmed/36891260 http://dx.doi.org/10.3389/fmicb.2022.1007877 |
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author | Silva, Denise P. Epstein, Hannah E. Vega Thurber, Rebecca L. |
author_facet | Silva, Denise P. Epstein, Hannah E. Vega Thurber, Rebecca L. |
author_sort | Silva, Denise P. |
collection | PubMed |
description | Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host’s responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade. |
format | Online Article Text |
id | pubmed-9987214 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-99872142023-03-07 Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics Silva, Denise P. Epstein, Hannah E. Vega Thurber, Rebecca L. Front Microbiol Microbiology Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host’s responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade. Frontiers Media S.A. 2023-02-20 /pmc/articles/PMC9987214/ /pubmed/36891260 http://dx.doi.org/10.3389/fmicb.2022.1007877 Text en Copyright © 2023 Silva, Epstein and Vega Thurber. 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 | Microbiology Silva, Denise P. Epstein, Hannah E. Vega Thurber, Rebecca L. Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics |
title | Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics |
title_full | Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics |
title_fullStr | Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics |
title_full_unstemmed | Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics |
title_short | Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics |
title_sort | best practices for generating and analyzing 16s rrna amplicon data to track coral microbiome dynamics |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9987214/ https://www.ncbi.nlm.nih.gov/pubmed/36891260 http://dx.doi.org/10.3389/fmicb.2022.1007877 |
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