Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.
Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.
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DOI：
10.1371/journal.pone.0160574
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Bhaya D
中科院分区：
文献类型：
--
作者：
Davison M;Treangen TJ;Koren S;Pop M;Bhaya D
黄石国家公园（YNP）蘑菇和章鱼泉中的多微生物生物膜群落具有很好的特征，但对噬菌体种群知之甚少。优势物种聚球藻属JA-2- 3B 'a（2-13）、聚球藻属JA-3-3Ab、绿弯藻属Y-400-fl和玫瑰弯藻属RS-1含有多个CRISPR-Cas阵列，表明与噬菌体捕食者的复杂相互作用。为了分析来自Octopus Spring生物膜的噬菌体群体，我们对病毒富集级分进行测序。为了组装和分析噬菌体宏基因组数据，我们开发了一个自定义模块VIRITAS，在MetAMOS框架内实现。该模块基于四核苷酸频率和CRISPR间隔区-原型间隔区匹配和ORF调用将重叠群分组。使用这个流水线，我们能够将噬菌体序列组装成重叠群，并将它们分成三个簇，这与它们潜在的宿主范围相一致。病毒组包含52，348个预测的ORF;一些明显是噬菌体样的; 9319个ORF具有可识别的Pfam结构域，而其余的是假设的。在具有CRISPR间隔区匹配的识别结构域中，是裂解性噬菌体用于破坏细胞的噬菌体内溶素。对嗜热噬藻体重叠群中存在的内溶素的分析揭示了一个特征性内溶素的子集以及先前与测序的噬藻体不相关的Glyco_hydro_108（PF 05838）结构域。对与所有鉴定的噬菌体内溶素匹配的CRISPR间隔区的搜索表明，大多数内溶素结构域是靶标。这种策略提供了连接宿主和噬菌体的一般方式，因为已知内溶素广泛分布在噬菌体中。内溶素还可以提供关于宿主细胞壁组成的信息，并且具有用作新型治疗剂的靶点的额外潜力。
The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP) are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B'a(2–13), Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838) domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics.
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影响因子：
3.7
作者：
Frank DN;Wilson SS;St Amand AL;Pace NR
通讯作者：
Pace NR
影响因子：
14.9
作者：
Grissa, Ibtissem;Vergnaud, Gilles;Pourcel, Christine
通讯作者：
Pourcel, Christine
DOI：
10.1073/pnas.1402564111
发表时间：
2014-04-01
影响因子：
11.1
作者：
Howe, Adina Chuang;Jansson, Janet K.;Brown, C. Titus
通讯作者：
Brown, C. Titus
影响因子：
3.2
作者：
Deveau, Helene;Barrangou, Rodolphe;Moineau, Sylvain
通讯作者：
Moineau, Sylvain
基于Endolysin的工程“ Artilysins”来对抗耐多药的革兰氏阴性病原体。
影响因子：
6.4
作者：
Briers Y;Walmagh M;Van Puyenbroeck V;Cornelissen A;Cenens W;Aertsen A;Oliveira H;Azeredo J;Verween G;Pirnay JP;Miller S;Volckaert G;Lavigne R
通讯作者：
Lavigne R