Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.
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DOI：
10.1016/j.mimet.2009.09.012
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发表时间：
2009-12
影响因子：
2.2
通讯作者：
Francois, Patrice
中科院分区：
文献类型：
--
作者：
Lazarevic, Vladimir;Whiteson, Katrine;Huse, Susan;Hernandez, David;Farinelli, Laurent;Osteras, Magne;Schrenzel, Jacques;Francois, Patrice
到目前为止，元基因组研究一直依赖于使用454焦磷酸测序获得的读数的利用和分析，以取代传统的Sanger测序。在广泛扫描16S核糖体RNA(RRNA)基因后，我们发现V5高变区是一个短区域，为公共数据库(如人类口腔微生物组数据库)中提供的细菌序列提供了可靠的鉴定。我们使用覆盖V5环~82碱基片段的引物从三名健康人的口腔中扩增样本，并使用Illumina技术进行单方向测序。我们从得到的1,373,824个序列中鉴定出135个属或更高的分类级别。虽然最常见的菌门(Firmicum、变形杆菌、放线杆菌、梭杆菌和TM7)的丰度与以前的研究基本相当，但类杆菌的存在较少。这种差异的潜在来源包括16S rRNA基因这一区域的分类偏差、人类样本变异、样本制备和引物偏差。使用Illumina测序方法，我们实现了比以前的口腔微生物区系研究更深入的覆盖，使我们能够确定在这些类型的样本中尚未发现的几个分类群，并评估至少需要30,000个额外的阅读才能仅确定一个额外的系统型。高通量测序技术的发展及其随后在读取长度上的改进使不同的平台能够用于研究复杂的菌群。对大量数据的获取已经导致以合理的成本更好地表示样本多样性。
To date, metagenomic studies have relied on the utilization and analysis of reads obtained using 454 pyrosequencing to replace conventional Sanger sequencing. After extensively scanning the 16S ribosomal RNA (rRNA) gene, we identified the V5 hypervariable region as a short region providing reliable identification of bacterial sequences available in public databases such as the Human Oral Microbiome Database. We amplified samples from the oral cavity of three healthy individuals using primers covering an ~82-base segment of the V5 loop, and sequenced using the Illumina technology in a single orientation. We identified 135 genera or higher taxonomic ranks from the resulting 1,373,824 sequences. While the abundances of the most common phyla (Firmicutes, Proteobacteria, Actinobacteria, Fusobacteria and TM7) are largely comparable to previous studies, Bacteroidetes were less present. Potential sources for this difference include classification bias in this region of the 16S rRNA gene, human sample variation, sample preparation and primer bias. Using an Illumina sequencing approach, we achieved a much greater depth of coverage than previous oral microbiota studies, allowing us to identify several taxa not yet discovered in these types of samples, and to assess that at least 30,000 additional reads would be required to identify only one additional phylotype. The evolution of high-throughput sequencing technologies, and their subsequent improvements in read length enable the utilization of different platforms for studying communities of complex flora. Access to large amounts of data is already leading to a better representation of sample diversity at a reasonable cost.
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影响因子：
11.8
作者：
Nakamura S;Maeda N;Miron IM;Yoh M;Izutsu K;Kataoka C;Honda T;Yasunaga T;Nakaya T;Kawai J;Hayashizaki Y;Horii T;Iida T
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Iida T
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作者：
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Stoneking, Mark
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2.9
作者：
Nasidze, Ivan;Quinque, Dominique;Stoneking, Mark
通讯作者：
Stoneking, Mark
影响因子：
3.7
作者：
Andersson, Anders F.;Lindberg, Mathilda;Jakobsson, Hedvig;Backhed, Fredrik;Nyren, Pal;Engstrand, Lars
通讯作者：
Engstrand, Lars