Microbial community profiling of human saliva using shotgun metagenomic sequencing.
Microbial community profiling of human saliva using shotgun metagenomic sequencing.
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DOI：
10.1371/journal.pone.0097699
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Colwell RR
中科院分区：
文献类型：
--
作者：
Hasan NA;Young BA;Minard-Smith AT;Saeed K;Li H;Heizer EM;McMillan NJ;Isom R;Abdullah AS;Bornman DM;Faith SA;Choi SY;Dickens ML;Cebula TA;Colwell RR
人类唾液是口腔和一般健康的临床信息。由于下一代鸟枪测序（NGS）现在被广泛用于鉴定和定量细菌，我们研究了两名健康志愿者的唾液微生物组的细菌植物群和来自人类微生物组计划的五个数据集，沿着包含来自代表人类唾液细菌植物群的细菌物种的短NGS读数的对照数据集。GENIUS，一种设计用于使用未组装的短NGS读数鉴定和定量细菌物种的系统，用于鉴定包含唾液样品和数据集的微生物组的细菌物种。在几分钟内获得的结果和大于90%的准确度表明，超过175种细菌组成了人类唾液的细菌植物群，包括已知为人类唾液植物群的细菌，但也包括流感嗜血杆菌、脑膜炎奈瑟菌、肺炎链球菌和γ-变形菌。基本局部比对搜索工具（BLASTn）分析并行，报告ca。比实际包含计算机模拟样品的种类多五倍。对唾液样本的GENIUS和BLAST分析都确定了构成唾液细菌植物群的主要属，但GENIUS提供了对物种组成的更精确描述，在大多数情况下识别菌株，并以至少10，000倍的速度提供结果。因此，GENIUS为宏基因组样品中的细菌物种和/或菌株的鉴定和定量提供了一种简便而准确的系统。
Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUSand BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.
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影响因子：
4.3
作者：
Genco, RJ;Grossi, SG;Murayama, Y
通讯作者：
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7
作者：
Huson, Daniel H.;Auch, Alexander F.;Schuster, Stephan C.
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Schuster, Stephan C.
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4.3
作者：
Colombo AP;Boches SK;Cotton SL;Goodson JM;Kent R;Haffajee AD;Socransky SS;Hasturk H;Van Dyke TE;Dewhirst F;Paster BJ
通讯作者：
Paster BJ