Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.
Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.
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DOI：
10.1371/journal.pone.0022788
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Hayes RB
中科院分区：
文献类型：
--
作者：
Ahn J;Yang L;Paster BJ;Ganly I;Morris L;Pei Z;Hayes RB
人类口腔微生物组可能与多种健康状况相关，高通量技术为高分辨率地检测微生物群落结构提供了可能。我们比较了两种口腔微生物组检测方法：通过16S rRNA基因测序进行广泛的微生物组鉴定以及通过定制DNA微阵列对微生物进行靶向表征。
在纪念斯隆 - 凯特琳癌症中心从20个人收集了口腔漱口水样本。16S rRNA基因检测是通过对V3 - V5区域（450bp）进行454焦磷酸测序来进行的。通过DNA微阵列进行的靶向鉴定是使用人类口腔微生物鉴定微阵列（HOMIM）进行的。在门和属的水平上，对16S rRNA序列读取比例和HOMIM杂交强度之间的相关性和相对丰度进行了比较。
两种方法对主要的门（厚壁菌门、变形菌门、拟杆菌门、放线菌门和梭杆菌门）的鉴定具有高度相关性（r = 0.70 - 0.86）。16S rRNA基因焦磷酸测序鉴定出77个属，HOMIM鉴定出49个属，两种方法都检测到37个属；超过98%的已分类细菌归属于这37个属。对于常见的属（链球菌属、韦荣球菌属、纤毛菌属、普雷沃菌属和嗜血杆菌属；相关性 = 0.70 - 0.84），两种检测方法（存在/不存在）的一致性和相关性都很高。
通过16S rRNA焦磷酸测序和HOMIM评估的微生物组群落图谱在门的水平上高度相关，并且在比较更常见检测到的分类群时，在属的水平上也是如此。这两种方法目前都适用于将已鉴定的以及更常见的口腔微生物分类群与疾病风险相关联的高通量流行病学研究；然而，焦磷酸测序可能提供更广泛的分类群鉴定范围、独特的序列读取记录以及更高的检测灵敏度。
The human oral microbiome is potentially related to diverse health conditions and high-throughput technology provides the possibility of surveying microbial community structure at high resolution. We compared two oral microbiome survey methods: broad-based microbiome identification by 16S rRNA gene sequencing and targeted characterization of microbes by custom DNA microarray. Oral wash samples were collected from 20 individuals at Memorial Sloan-Kettering Cancer Center. 16S rRNA gene survey was performed by 454 pyrosequencing of the V3–V5 region (450 bp). Targeted identification by DNA microarray was carried out with the Human Oral Microbe Identification Microarray (HOMIM). Correlations and relative abundance were compared at phylum and genus level, between 16S rRNA sequence read ratio and HOMIM hybridization intensity. The major phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were identified with high correlation by the two methods (r = 0.70∼0.86). 16S rRNA gene pyrosequencing identified 77 genera and HOMIM identified 49, with 37 genera detected by both methods; more than 98% of classified bacteria were assigned in these 37 genera. Concordance by the two assays (presence/absence) and correlations were high for common genera (Streptococcus, Veillonella, Leptotrichia, Prevotella, and Haemophilus; Correlation = 0.70–0.84). Microbiome community profiles assessed by 16S rRNA pyrosequencing and HOMIM were highly correlated at the phylum level and, when comparing the more commonly detected taxa, also at the genus level. Both methods are currently suitable for high-throughput epidemiologic investigations relating identified and more common oral microbial taxa to disease risk; yet, pyrosequencing may provide a broader spectrum of taxa identification, a distinct sequence-read record, and greater detection sensitivity.
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影响因子：
3.7
作者：
Claesson MJ;O'Sullivan O;Wang Q;Nikkilä J;Marchesi JR;Smidt H;de Vos WM;Ross RP;O'Toole PW
通讯作者：
O'Toole PW
影响因子：
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
DOI：
10.1073/pnas.0306398101
发表时间：
2004-03-23
影响因子：
11.1
作者：
Pei, ZH;Bini, EJ;Blaser, MJ
通讯作者：
Blaser, MJ
影响因子：
4.4
作者：
Wang, Qiong;Garrity, George M.;Cole, James R.
通讯作者：
Cole, James R.
影响因子：
4.3
作者：
Nossa, Carlos W.;Oberdorf, William E.;Pei, Zhiheng
通讯作者：
Pei, Zhiheng