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dc.contributor.authorWeber, Laura  Concept link
dc.contributor.authorDeForce, Emelia A.  Concept link
dc.contributor.authorApprill, Amy  Concept link
dc.date.accessioned2017-02-17T16:23:14Z
dc.date.available2017-02-17T16:23:14Z
dc.date.issued2017-02-08
dc.identifier.citationMicrobiome 5 (2017): 18en_US
dc.identifier.urihttps://hdl.handle.net/1912/8725
dc.description© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 5 (2017): 18, doi:10.1186/s40168-017-0229-y.en_US
dc.description.abstractWe designed a two-phase study in order to propose a comprehensive and efficient method for DNA extraction from microbial cells present in corals and investigate if extraction method influences microbial community composition. During phase I, total DNA was extracted from seven coral species in a replicated experimental design using four different MO BIO Laboratories, Inc., DNA Isolation kits: PowerSoil®, PowerPlant® Pro, PowerBiofilm®, and UltraClean® Tissue & Cells (with three homogenization permutations). Technical performance of the treatments was evaluated using DNA yield and amplification efficiency of small subunit ribosomal RNA (SSU ribosomal RNA (rRNA)) genes. During phase II, potential extraction biases were examined via microbial community analysis of SSU rRNA gene sequences amplified from the most successful DNA extraction treatments. In phase I of the study, the PowerSoil® and PowerPlant® Pro extracts contained low DNA concentrations, amplified poorly, and were not investigated further. Extracts from PowerBiofilm® and UltraClean® Tissue and Cells permutations were further investigated in phase II, and analysis of sequences demonstrated that overall microbial community composition was dictated by coral species and not extraction treatment. Finer pairwise comparisons of sequences obtained from Orbicella faveolata, Orbicella annularis, and Acropora humilis corals revealed subtle differences in community composition between the treatments; PowerBiofilm®-associated sequences generally had higher microbial richness and the highest coverage of dominant microbial groups in comparison to the UltraClean® Tissue and Cells treatments, a result likely arising from using a combination of different beads during homogenization. Both the PowerBiofilm® and UltraClean® Tissue and Cells treatments are appropriate for large-scale analyses of coral microbiota. However, studies interested in detecting cryptic microbial members may benefit from using the PowerBiofilm® DNA treatment because of the likely enhanced lysis efficiency of microbial cells attributed to using a variety of beads during homogenization. Consideration of the methodology involved with microbial DNA extraction is particularly important for studies investigating complex host-associated microbiota.en_US
dc.description.sponsorshipThis project was supported by NSF award OCE-1233612 to AA and NSF GRFP award to LW.en_US
dc.language.isoen_USen_US
dc.publisherBioMed Centralen_US
dc.relation.hasparthttp://www.bco-dmo.org/dataset/662114
dc.relation.urihttps://doi.org/10.1186/s40168-017-0229-y
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectCoral microbiotaen_US
dc.subjectDNA extractionen_US
dc.subjectOptimizationen_US
dc.subjectSSU ribosomal RNA geneen_US
dc.subjectAmplicon sequencingen_US
dc.titleOptimization of DNA extraction for advancing coral microbiota investigationsen_US
dc.typeArticleen_US
dc.identifier.doi10.1186/s40168-017-0229-y


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Attribution 4.0 International
Except where otherwise noted, this item's license is described as Attribution 4.0 International