Optimization of DNA extraction for advancing coral microbiota investigations
MetadataShow full item record
We 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.
© 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.
The following license files are associated with this item:
Showing items related by title, author, creator and subject.
Neodymium isotope analyses after combined extraction of actinide and lanthanide elements from seawater and deep-sea coral aragonite Struve, Torben; van de Flierdt, Tina; Robinson, Laura F.; Bradtmiller, Louisa I.; Hines, Sophia K.; Adkins, Jess F.; Lambelet, Myriam; Crocket, Kirsty C.; Kreissig, Katharina; Coles, Barry; Auro, Maureen E. (John Wiley & Sons, 2016-01-09)Isotopes of the actinide elements protactinium (Pa), thorium (Th), and uranium (U), and the lanthanide element neodymium (Nd) are often used as complementary tracers of modern and past oceanic processes. The extraction of ...
Solow, Andrew R.; Huppert, Amit (American Geophysical Union, 2004-10-08)Past sea surface temperatures have been reconstructed using coral measurements of single geochemical proxies. There is some interest in improving reconstruction by combining results from different proxies. The construction ...
Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics Lee, Sonny T. M.; Kahn, Stacy A.; Delmont, Tom O.; Shaiber, Alon; Esen, Ozcan C.; Hubert, Nathaniel A.; Morrison, Hilary G.; Antonopoulos, Dionysios A.; Rubin, David T.; Eren, A. Murat (BioMed Central, 2017-05-04)Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack ...