Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
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DOI：
10.3791/58239
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发表时间：
2018-08-01
影响因子：
1.2
通讯作者：
Swei, Andrea
中科院分区：
文献类型：
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作者：
Couper, Lisa;Swei, Andrea
近几十年来，病媒传播的疾病再次出现，并以惊人的速度扩大，在世界范围内造成相当大的发病率和死亡率。这些疾病中的大多数缺乏有效和广泛可用的疫苗，因此有必要开发新的疾病缓解战略。为此，一种有希望的疾病控制途径是以媒介微生物群为目标，即居住在媒介上的微生物群落。病媒微生物组在病原体动态中起着关键作用，对微生物组的操纵已经导致了少数病媒传播疾病的病媒丰度或病原体传播的减少。然而，将这些发现转化为疾病控制应用需要对病媒微生物生态学有透彻的了解，这在历史上受到该领域技术不足的限制。下一代测序方法的出现使不同微生物群落的快速、高度并行测序成为可能。以高度保守的16S rRNA基因为靶标，有助于在不同的生态和实验条件下描述载体中存在的微生物的特征。这项技术包括16S rRNA基因的扩增，通过聚合酶链式反应对样本进行条形码编码，将样本加载到流动细胞进行测序，以及将序列数据与系统发育信息进行匹配的生物信息学方法。通过这种方法，通常可以实现对大量重复的物种或属的鉴定，从而绕过了传统培养、显微镜或组织学染色技术的低检测、低分辨率和低输出的挑战。因此，这种方法非常适合在不同条件下表征媒介微生物，但目前不能提供关于微生物功能、在载体中的位置或对抗生素治疗的反应的信息。总体而言，16S下一代测序是一项强大的技术，可以更好地了解病媒微生物在疾病动力学中的身份和作用。
In recent decades, vector-borne diseases have re-emerged and expanded at alarming rates, causing considerable morbidity and mortality worldwide. Effective and widely available vaccines are lacking for a majority of these diseases, necessitating the development of novel disease mitigation strategies. To this end, a promising avenue of disease control involves targeting the vector microbiome, the community of microbes inhabiting the vector. The vector microbiome plays a pivotal role in pathogen dynamics, and manipulations of the microbiome have led to reduced vector abundance or pathogen transmission for a handful of vector-borne diseases. However, translating these findings into disease control applications requires a thorough understanding of vector microbial ecology, historically limited by insufficient technology in this field. The advent of next-generation sequencing approaches has enabled rapid, highly parallel sequencing of diverse microbial communities. Targeting the highly-conserved 16S rRNA gene has facilitated characterizations of microbes present within vectors under varying ecological and experimental conditions. This technique involves amplification of the 16S rRNA gene, sample barcoding via PCR, loading samples onto a flow cell for sequencing, and bioinformatics approaches to match sequence data with phylogenetic information. Species or genus-level identification for a high number of replicates can typically be achieved through this approach, thus circumventing challenges of low detection, resolution, and output from traditional culturing, microscopy, or histological staining techniques. Therefore, this method is well-suited for characterizing vector microbes under diverse conditions but cannot currently provide information on microbial function, location within the vector, or response to antibiotic treatment. Overall, 16S next-generation sequencing is a powerful technique for better understanding the identity and role of vector microbes in disease dynamics.