Biome representational in silico karyotyping
Biome representational in silico karyotyping
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DOI：
10.1101/gr.115758.110
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发表时间：
2011-04-01
期刊：
影响因子：
7
通讯作者：
Van Gelder, Russell N.
中科院分区：
文献类型：
--
作者：
Muthappan, Valliammai;Lee, Aaron Y.;Van Gelder, Russell N.
复杂生物群系的宏基因组表征仍然具有挑战性。在这里，我们描述了一种数字核型的修改-生物群系代表性的硅核型（轻快）-作为分析样品中存在的所有DNA的定义表示的一般技术。BRISK利用IIB型DNA限制性内切酶在样品中创建27 mer DNA的定义表示。这种表示的大规模平行测序允许高分辨率核型的构建和生物群系内多个物种的鉴定。在正常人体组织中的应用显示了染色体标记的线性恢复。我们将这项技术应用于口腔黏膜的生物群落，发现超过25%的恢复DNA是非人类的。从两名受试者的口腔黏膜中鉴定出41种微生物的DNA。在已恢复的非人类序列中，目前有注释的不到30%。我们通过染色体行走表征了7个普遍存在的未知序列，并发现这些序列代表了新的微生物序列，包括两个可能来自新的噬菌体基因组的序列。应用BRISK对一例鼻咽癌档案组织进行检测，鉴定出eb病毒感染。这些结果表明，BRISK是一种分析复杂微生物组和潜在病原体发现的强大技术。
Metagenomic characterization of complex biomes remains challenging. Here we describe a modification of digital karyotyping-biome representational in silico karyotyping (BRISK)-as a general technique for analyzing a defined representation of all DNA present in a sample. BRISK utilizes a Type IIB DNA restriction enzyme to create a defined representation of 27-mer DNAs in a sample. Massively parallel sequencing of this representation allows for construction of high-resolution karyotypes and identification of multiple species within a biome. Application to normal human tissue demonstrated linear recovery of tags by chromosome. We apply this technique to the biome of the oral mucosa and find that greater than 25% of recovered DNA is nonhuman. DNA from 41 microbial species could be identified from oral mucosa of two subjects. Of recovered nonhuman sequences, fewer than 30% are currently annotated. We characterized seven prevalent unknown sequences by chromosome walking and find these represent novel microbial sequences including two likely derived from novel phage genomes. Application of BRISK to archival tissue from a nasopharyngeal carcinoma resulted in identification of Epstein-Barr virus infection. These results suggest that BRISK is a powerful technique for the analysis of complex microbiomes and potentially for pathogen discovery.