The Potential of Metatranscriptomics for Identifying Screening Targets for Bacterial Vaginosis
The Potential of Metatranscriptomics for Identifying Screening Targets for Bacterial Vaginosis
复制标题
宏转录组学识别细菌性阴道病筛查靶标的潜力
作者：
J. Twin;C. Bradshaw;S. Garland;C. Fairley;K. Fethers;S. Tabrizi
背景分析从患有细菌性阴道病（BV）的妇女收集的样品的核糖体RNA含量，以确定活性微生物群落，并确定进一步筛选的潜在靶点。方法学/主要发现来自BV患者的样本进行总RNA提取，然后进行人rRNA的物理扣除和全转录组扩增。使用Roche 454钛化学对元转录组进行测序。利用生物信息学管道MG-RAST和桌面DNA分析平台分析结果。普雷沃氏菌属的细菌（主要是P. p.）占16 S rRNA读段的36%，其次是巨球菌属（19%）、Leptotrichia/Sneathia（8%）和梭杆菌属（8%）。几种细菌的丰度与提取的DNA的定量PCR（qPCR）筛选的比较显示出相当的相对丰度。这表明该样品中存在的物质与转录活性之间存在相关性：然而，与通过16 S rRNA基因扩增子测序确定的微生物组相比，观察到了明显的差异。为了评估更大样本池中是否存在P.p.d.，使用qPCR对90名性活跃女性进行了筛查。在90名妇女中发现这种细菌与BV密切相关（P<0.001，OR 23.3（95%CI：2.9-190.7））。结论/意义本研究强调了元转录组学作为表征代谢活性微生物群和识别进一步筛选靶点的工具的潜力。选择普氏普雷沃菌作为示例靶标，普氏普雷沃菌是存在于单个BV患者中的最具代谢活性的菌种，并且发现在31%的BV队列中通过qPCR检测到高浓度，与口腔和阴茎-阴道性行为相关。
Background The ribosomal RNA content of a sample collected from a woman with bacterial vaginosis (BV) was analysed to determine the active microbial community, and to identify potential targets for further screening. Methodology/Principal Findings The sample from the BV patient underwent total RNA extraction, followed by physical subtraction of human rRNA and whole transcriptome amplification. The metatranscriptome was sequenced using Roche 454 titanium chemistry. The bioinformatics pipeline MG-RAST and desktop DNA analysis platforms were utilised to analyse results. Bacteria of the genus Prevotella (predominately P. amnii) constituted 36% of the 16S rRNA reads, followed by Megasphaera (19%), Leptotrichia/Sneathia (8%) and Fusobacterium (8%). Comparison of the abundances of several bacteria to quantitative PCR (qPCR) screening of extracted DNA revealed comparable relative abundances. This suggests a correlation between what was present and transcriptionally active in this sample: however distinct differences were seen when compared to the microbiome determined by 16S rRNA gene amplicon sequencing. To assess the presence of P. amnii in a larger pool of samples, 90 sexually active women were screened using qPCR. This bacterium was found to be strongly associated with BV (P<0.001, OR 23.3 (95%CI:2.9–190.7)) among the 90 women. Conclusions/Significance This study highlighted the potential of metatranscriptomics as a tool for characterising metabolically active microbiota and identifying targets for further screening. Prevotella amnii was chosen as an example target, being the most metabolically active species present in the single patient with BV, and was found to be detected at a high concentration by qPCR in 31% of cohort with BV, with an association with both oral and penile-vaginal sex.
DOI：
10.1111/j.1574-695x.2002.tb00634.x
发表时间：
2002-12-13
影响因子：
--
作者：
Zariffard, MR;Saifuddin, M;Spear, GT
通讯作者：
Spear, GT
影响因子：
6.4
作者：
Gupta, K;Stapleton, AE;Stamm, WE
通讯作者：
Stamm, WE