dc.contributor.author | Silva, Denise P. | |
dc.contributor.author | Epstein, Hannah E. | |
dc.contributor.author | Vega Thurber, Rebecca L. | |
dc.date.accessioned | 2023-12-20T18:55:13Z | |
dc.date.available | 2023-12-20T18:55:13Z | |
dc.date.issued | 2023 | |
dc.identifier.citation | Silva DP, Epstein HE and Vega Thurber RL (2023) Best practices for generating
and analyzing 16S rRNA amplicon data to track coral microbiome dynamics.
Frontiers in Microbiology, 13:1007877, 18pp. DOI: | https://doi.org/10.3389/fmicb.2022.1007877 | en_US |
dc.identifier.uri | https://repository.oceanbestpractices.org/handle/11329/2408 | |
dc.description.abstract | 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. | en_US |
dc.language.iso | en | en_US |
dc.rights | Attribution 4.0 International | * |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
dc.subject.other | Coral | en_US |
dc.subject.other | Methods | en_US |
dc.subject.other | High-throughput sequencing (HTS) | en_US |
dc.subject.other | Microbiome | en_US |
dc.subject.other | 16S rRNA amplicon | en_US |
dc.subject.other | Microbiology | en_US |
dc.title | Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics. | en_US |
dc.type | Journal Contribution | en_US |
dc.description.refereed | Refereed | en_US |
dc.format.pagerange | 18pp. | en_US |
dc.identifier.doi | https://doi.org/10.3389/fmicb.2022.1007877 | |
dc.subject.parameterDiscipline | Rock and sediment biota | en_US |
dc.subject.parameterDiscipline | Other biological measurements | en_US |
dc.bibliographicCitation.title | Frontiers in Microbiology | en_US |
dc.bibliographicCitation.volume | 13:. doi: | en_US |
dc.bibliographicCitation.issue | 1007877 | en_US |
dc.description.sdg | 14.a | en_US |
dc.description.maturitylevel | Mature | en_US |
dc.description.adoption | Validated (tested by third parties) | en_US |
dc.description.methodologyType | Method | en_US |
dc.description.methodologyType | Specification of criteria | en_US |
dc.description.methodologyType | Reports with methodological relevance | en_US |
obps.contact.contactname | Denise P. Silva | |
obps.contact.contactemail | dapiedad@oregonstate.edu | |
obps.resourceurl.publisher | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1007877/full | |