Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature.
Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature.
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DOI：
10.1371/journal.pone.0205575
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Fontanesi L
中科院分区：
文献类型：
--
作者：
Bovo S;Ribani A;Utzeri VJ;Schiavo G;Bertolini F;Fontanesi L
蜜蜂因其环境探索和觅食活动而被认为是大规模监测工具。这些活动的痕迹可以在蜂蜜中找到，这也可能反映了生产蜂蜜的蜂巢生态微观条件。本研究应用下一代测序平台 (Ion Torrent) 对蜂蜜环境 DNA (eDNA) 进行鸟枪法宏基因组分析。该研究测试了一种解释 DNA 序列信息的方法框架，这些信息有助于描述蜂群超有机体的复杂生态系统、其病圈以及在蜂蜜中留下 DNA 标记的农业生态环境和环境来源的异质性。对两种蜂蜜的分析报告了来自五个主要生物群（界或门）的序列读数：节肢动物（主要包括来自蜜蜂、膜翅目的其他几种成员，以及双翅目、鞘翅目和鳞翅目成员，以及蚜虫和螨虫）、植物（明确证实了两种蜂蜜的植物起源，即橙树花和桉树花）蜂蜜）、真菌和细菌（包括常见的蜂巢和蜜蜂肠道微生物、蜜蜂病原体和植物病原体）和病毒（这两种蜂蜜中的读数最多，主要是意大利蜜蜂丝状病毒）。本研究中使用的鸟枪法宏基因组方法可应用于大规模实验，根据蜂蜜中包含的多界衍生 eDNA，这些实验可能具有多个目标。
Honey bees are considered large-scale monitoring tools due to their environmental exploration and foraging activities. Traces of these activities can be recovered in the honey that also may reflect the hive ecological micro-conditions in which it has been produced. This study applied a next generation sequencing platform (Ion Torrent) for shotgun metagenomic analysis of honey environmental DNA (eDNA). The study tested a methodological framework to interpret DNA sequence information useful to describe the complex ecosystems of the honey bee colony superorganism, its pathosphere and the heterogeneity of the agroecological environments and environmental sources that left DNA marks in the honey. Analysis of two honeys reported sequence reads from five main organism groups (kingdoms or phyla): arthropods (that mainly included reads from Apis mellifera, several other members of the Hymenotpera, in addition to members of the Diptera, Coleoptera and Lepidoptera, as well as aphids and mites), plants (that clearly confirmed the botanical origin of the two honeys, i.e. orange tree blossom and eucalyptus tree blossom honeys), fungi and bacteria (including common hive and honey bee gut microorganisms, honey bee pathogens and plant pathogens), and viruses (which accounted for the largest number of reads in both honeys, mainly assigned to Apis mellifera filamentous virus). The shotgun metagenomic approach that was used in this study can be applied in large scale experiments that might have multiple objectives according to the multi-kingdom derived eDNA that is contained in the honey.
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DOI：
10.3390/v7052654
发表时间：
2015-05-22
期刊：
Viruses
影响因子：
--
作者：
Hartmann U;Forsgren E;Charrière JD;Neumann P;Gauthier L
通讯作者：
Gauthier L
影响因子：
3.7
作者：
Anderson KE;Sheehan TH;Mott BM;Maes P;Snyder L;Schwan MR;Walton A;Jones BM;Corby-Harris V
通讯作者：
Corby-Harris V
影响因子：
4.2
作者：
Israili, Zafar H.
通讯作者：
Israili, Zafar H.
影响因子：
4.4
作者：
Bakonyi, T;Derakhshifar, I;Nowotny, N
通讯作者：
Nowotny, N
影响因子：
3.7
作者：
Bertolini F;Ghionda MC;D'Alessandro E;Geraci C;Chiofalo V;Fontanesi L
通讯作者：
Fontanesi L