Table_3_Comparison of Preservation and Extraction Methods on Five Taxonomically Disparate Coral Microbiomes.xlsx
All animals are host to a multitude of microorganisms that are essential to the animal’s health. Host-associated microbes have been shown to defend against potential pathogens, provide essential nutrients, interact with the host’s immune system, and even regulate mood. However, it can be difficult t...
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ftfrontimediafig:oai:figshare.com:article/14980545 2023-05-15T17:08:47+02:00 Table_3_Comparison of Preservation and Extraction Methods on Five Taxonomically Disparate Coral Microbiomes.xlsx Zoe A. Pratte Christina A. Kellogg 2021-07-14T13:15:18Z https://doi.org/10.3389/fmars.2021.684161.s003 https://figshare.com/articles/dataset/Table_3_Comparison_of_Preservation_and_Extraction_Methods_on_Five_Taxonomically_Disparate_Coral_Microbiomes_xlsx/14980545 unknown doi:10.3389/fmars.2021.684161.s003 https://figshare.com/articles/dataset/Table_3_Comparison_of_Preservation_and_Extraction_Methods_on_Five_Taxonomically_Disparate_Coral_Microbiomes_xlsx/14980545 CC BY 4.0 CC-BY Oceanography Marine Biology Marine Geoscience Biological Oceanography Chemical Oceanography Physical Oceanography Marine Engineering preservation extraction coral microbiome bacteria RNAlater liquid nitrogen PowerBiofilm Dataset 2021 ftfrontimediafig https://doi.org/10.3389/fmars.2021.684161.s003 2021-07-14T22:57:06Z All animals are host to a multitude of microorganisms that are essential to the animal’s health. Host-associated microbes have been shown to defend against potential pathogens, provide essential nutrients, interact with the host’s immune system, and even regulate mood. However, it can be difficult to preserve and obtain nucleic acids from some host-associated microbiomes, making studying their microbial communities challenging. Corals are an example of this, in part due to their potentially remote, underwater locations, their thick surface mucopolysaccharide layer, and various inherent molecular inhibitors. This study examined three different preservatives (RNAlater, DNA/RNA Shield, and liquid nitrogen) and two extraction methods (the Qiagen PowerBiofilm kit and the Promega Maxwell RBC kit with modifications) to determine if there was an optimum combination for examining the coral microbiome. These methods were employed across taxonomically diverse coral species, including deep-sea/shallow, stony/soft, and zooxanthellate/azooxanthellate: Lophelia pertusa, Paragorgia johnsoni, Montastraea cavernosa, Porites astreoides, and Stephanocoenia intersepta. Although significant differences were found between preservative types and extraction methods, these differences were subtle, and varied in nature from coral species to coral species. Significant differences between coral species were far more profound than those detected between preservative or extraction method. We suggest that the preservative types presented here and extraction methods using a bead-beating step provide enough consistency to compare coral microbiomes across various studies, as long as subtle differences in microbial communities are attributed to dissimilar methodologies. Additionally, the inclusion of internal controls such as a mock community and extraction blanks can help provide context regarding data quality, improving downstream analyses. Dataset Lophelia pertusa Frontiers: Figshare |
institution |
Open Polar |
collection |
Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Oceanography Marine Biology Marine Geoscience Biological Oceanography Chemical Oceanography Physical Oceanography Marine Engineering preservation extraction coral microbiome bacteria RNAlater liquid nitrogen PowerBiofilm |
spellingShingle |
Oceanography Marine Biology Marine Geoscience Biological Oceanography Chemical Oceanography Physical Oceanography Marine Engineering preservation extraction coral microbiome bacteria RNAlater liquid nitrogen PowerBiofilm Zoe A. Pratte Christina A. Kellogg Table_3_Comparison of Preservation and Extraction Methods on Five Taxonomically Disparate Coral Microbiomes.xlsx |
topic_facet |
Oceanography Marine Biology Marine Geoscience Biological Oceanography Chemical Oceanography Physical Oceanography Marine Engineering preservation extraction coral microbiome bacteria RNAlater liquid nitrogen PowerBiofilm |
description |
All animals are host to a multitude of microorganisms that are essential to the animal’s health. Host-associated microbes have been shown to defend against potential pathogens, provide essential nutrients, interact with the host’s immune system, and even regulate mood. However, it can be difficult to preserve and obtain nucleic acids from some host-associated microbiomes, making studying their microbial communities challenging. Corals are an example of this, in part due to their potentially remote, underwater locations, their thick surface mucopolysaccharide layer, and various inherent molecular inhibitors. This study examined three different preservatives (RNAlater, DNA/RNA Shield, and liquid nitrogen) and two extraction methods (the Qiagen PowerBiofilm kit and the Promega Maxwell RBC kit with modifications) to determine if there was an optimum combination for examining the coral microbiome. These methods were employed across taxonomically diverse coral species, including deep-sea/shallow, stony/soft, and zooxanthellate/azooxanthellate: Lophelia pertusa, Paragorgia johnsoni, Montastraea cavernosa, Porites astreoides, and Stephanocoenia intersepta. Although significant differences were found between preservative types and extraction methods, these differences were subtle, and varied in nature from coral species to coral species. Significant differences between coral species were far more profound than those detected between preservative or extraction method. We suggest that the preservative types presented here and extraction methods using a bead-beating step provide enough consistency to compare coral microbiomes across various studies, as long as subtle differences in microbial communities are attributed to dissimilar methodologies. Additionally, the inclusion of internal controls such as a mock community and extraction blanks can help provide context regarding data quality, improving downstream analyses. |
format |
Dataset |
author |
Zoe A. Pratte Christina A. Kellogg |
author_facet |
Zoe A. Pratte Christina A. Kellogg |
author_sort |
Zoe A. Pratte |
title |
Table_3_Comparison of Preservation and Extraction Methods on Five Taxonomically Disparate Coral Microbiomes.xlsx |
title_short |
Table_3_Comparison of Preservation and Extraction Methods on Five Taxonomically Disparate Coral Microbiomes.xlsx |
title_full |
Table_3_Comparison of Preservation and Extraction Methods on Five Taxonomically Disparate Coral Microbiomes.xlsx |
title_fullStr |
Table_3_Comparison of Preservation and Extraction Methods on Five Taxonomically Disparate Coral Microbiomes.xlsx |
title_full_unstemmed |
Table_3_Comparison of Preservation and Extraction Methods on Five Taxonomically Disparate Coral Microbiomes.xlsx |
title_sort |
table_3_comparison of preservation and extraction methods on five taxonomically disparate coral microbiomes.xlsx |
publishDate |
2021 |
url |
https://doi.org/10.3389/fmars.2021.684161.s003 https://figshare.com/articles/dataset/Table_3_Comparison_of_Preservation_and_Extraction_Methods_on_Five_Taxonomically_Disparate_Coral_Microbiomes_xlsx/14980545 |
genre |
Lophelia pertusa |
genre_facet |
Lophelia pertusa |
op_relation |
doi:10.3389/fmars.2021.684161.s003 https://figshare.com/articles/dataset/Table_3_Comparison_of_Preservation_and_Extraction_Methods_on_Five_Taxonomically_Disparate_Coral_Microbiomes_xlsx/14980545 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fmars.2021.684161.s003 |
_version_ |
1766064637732716544 |