メタデータ

The skin microbiome (based on 16S) of Antarctic Humpback whales (Megaptera novaeangliae)

最新バージョン SCAR - Microbial Antarctic Resource System によって公開 2019/03/19 SCAR - Microbial Antarctic Resource System

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説明

Amplicon sequencing dataset (Illumina MiSeq) of the microbiome (16S) on skin samples of Humpback whales (Megaptera novaeangliae)

バージョン

次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。

引用方法

研究者はこの研究内容を以下のように引用する必要があります。:

Bierlich K, Miller C, DeForce E, Friedlaender A, Johnston D, Apprill A (2019): The skin microbiome (based on 16S) of Antarctic Humpback whales (Megaptera novaeangliae). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=antactice_humpback_whale_skin_microbiome&v=1.1

権利

研究者は権利に関する下記ステートメントを尊重する必要があります。:

パブリッシャーとライセンス保持者権利者は SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF登録

このリソースをはGBIF と登録されており GBIF UUID: 0144ad97-f933-4557-a599-0dd4c736066eが割り当てられています。   Scientific Committee on Antarctic Research によって承認されたデータ パブリッシャーとして GBIF に登録されているSCAR - Microbial Antarctic Resource System が、このリソースをパブリッシュしました。

キーワード

Metadata

連絡先

リソースを作成した人:
-

Kevin Bierlich
Woods Hole Oceanographic Institution
Woods Hole
US
Carolyn Miller
Woods Hole Oceanographic Institution
Woods Hole
US
Emelia DeForce
Woods Hole Oceanographic Institution
Woods Hole
US
Ari Friedlaender
Oregon State University
Newport
US
David Johnston
Duke University Marine Laboratory
Beaufort
US
Amy Apprill
Woods Hole Oceanographic Institution
Woods Hole
US

リソースに関する質問に答えることができる人:

Kevin Bierlich
Woods Hole Oceanographic Institution
Woods Hole
US

メタデータを記載した人:
-

Maxime Sweetlove
Research assistent
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
1000 Brussels
BE

他に、リソースに関連付けられていた人:

データ利用者

地理的範囲

Healthy humpback whales in te Gerlache Strait, Palmer Deep Canyon and Bransfield Strait (Antarctica)

座標(緯度経度) 南 西 [-68.077, -69.898], 北 東 [-64.046, -61.605]

生物分類学的範囲

Bacteria and Archaea were targeted using universal primers for the 16S ssu rRNA gene (V4 region)

Domain Bacteria (Bacteria), Archaea (Archaea)

時間的範囲

生成(収集)期間 2010-2013

プロジェクトデータ

説明がありません

タイトル The skin microbiome (based on 16S) of Antarctic Humpback whales (Megaptera novaeangliae)
ファンデイング Humpback whale skin biopsy samples were collected under NOAA permit 808-735 and ACA permit 2009-14 as part of NSF OPP awards ANT-07-39483 and 1250208. This project was supported by 67 donors to the “Whale Bacterial Buddies” crowd- funded project supported by WHOI, the Edna Bailey Sussman Fund, and the Michael K. Orbach Enrichment Fund awarded.

プロジェクトに携わる要員:

Kevin Bierlich

収集方法

Skin samples were collected from the upper flank near the dorsal fin of humpback whales via standard biopsy techniques. Specifically, a 68-kg pull crossbow and floating Ceta-Dart darts with 40-mm surgical stainless steel tips collected a small skin and blubber sample roughly 5 mm wide and 20 to 30 mm deep, depending on the angle of the sampling dart on impact. Tips were sterilized using 8.25% concentrated bleach, allowed to dry, cleaned, and then doused in 100% ethyl alcohol before each use. The darts were retrieved by hand and the tips immediately placed into a sterile bag (such that the sample was not contaminated) and on ice for no more than 10 h before transfer to a cryovial via sterile tools for freezing at 80°C. The global positioning system (GPS) location and the regional names of the bay, strait, etc. were recorded for each skin sample collected. One skin sample, w132a, was collected from an acoustic tag placed on the animal.

Study Extent Ninety-four skin samples were collected from 89 humpback whales in 12 different locations along the Western Antarctic Peninsula (WAP) during May and June 2010 (fall/late foraging season) and January and February 2013 (early summer/early foraging season). Five individuals were sampled twice during the study; three individuals were resampled on the same day, one a week later, and one was sampled in 2010 and 2013.

Method step description:

  1. DNA was extracted from 1 to 30 mg of the top layer of the epidermis, with an average of 13 mg, from each sample using a DNeasy tissue kit (Qiagen, Valencia, CA, USA) and quantified using the Invitrogen Qubit 2.0 assay fluorometer (Life Technologies, Beverly, MA, USA). The V4 region of the SSU rRNA gene was amplified using barcoded primers (515F-Y, 5=-GTGYCAGCMGCCGCGGTAA-3=; and 806RB, 5=-GGACTACNVGGGTWTCTAAT-3=), broadly targeting bacteria and archaea. Samples and sterile water (negative control) were amplified in triplicate using PCR on a S1000 thermal cycler (Bio-Rad Laboratories, Hercules, CA, USA), as follows: 2 min at 95°C, followed by 30 to 35 cycles of 20 s at 95°C, 15 s at 55°C, and 5 min at 72°C, followed by 10 min at 72°C. Triplicate PCR mixtures contained 1 ul of DNA, 5 ul of GoTaq 5 Flexi buffer, 14.75 l of H2O, 2.5 l of a 25 nM MgCl2 solution, 200 nM each dinucleoside triphosphate (dNTP), and 0.25 l of a 5 units/ l GoTaq DNA polymerase solution per sample, along with 200 nM each primer. After PCR, amplification was assessed by mixing 5u l of each sample with 1 ul of 10,000 Sybr Safe dye run on a 1% agarose–Tris- borate-EDTA (agarose-TBE) gel. The replicate reaction mixtures were purified using Agencourt AMPure XP beads (Beckman Coulter, Inc., Pasadena, CA, USA) and quantified using the Qubit assay. Barcoded amplicons were sequenced using a 2x250-bp MiSeq Illumina format at the University of Illinois W. M. Keck Center for Comparative and Functional Genomics.

書誌情報の引用

  1. Bierlich, K. C., Miller, C., DeForce, E., Friedlaender, A. S., Johnston, D. W., & Apprill, A. (2018). Temporal and regional variability in the skin microbiome of humpback whales along the Western Antarctic Peninsula. Appl. Environ. Microbiol., 84(5), e02574-17. https://doi.org/10 .1128/AEM.02574-17

追加のメタデータ

代替識別子 0144ad97-f933-4557-a599-0dd4c736066e
https://ipt.biodiversity.aq/resource?r=antactice_humpback_whale_skin_microbiome