Species-level classification of the vaginal microbiome.
Species-level classification of the vaginal microbiome.
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DOI：
10.1186/1471-2164-13-s8-s17
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发表时间：
2012
期刊：
影响因子：
4.4
通讯作者：
Buck GA
中科院分区：
文献类型：
--
作者：
Fettweis JM;Serrano MG;Sheth NU;Mayer CM;Glascock AL;Brooks JP;Jefferson KK;Vaginal Microbiome Consortium (additional members);Buck GA
下一代测序在阴道微生物组研究中的应用揭示了人类阴道中微生物群落的谱。细菌分类群的高分辨率鉴定，最低限度到物种水平，对于充分了解阴道微生物组与细菌性阴道病，性传播感染，妊娠并发症，更年期和其他生理和感染状况的关联是必要的。然而，目前大多数基于宏基因组16 S rDNA序列分析的分类学分配策略最多只能提供属级分辨率。虽然16 S rRNA基因序列的调查在微生物组研究中很常见，但很少有精心策划的16 S rRNA基因序列的身体部位特异性参考数据库，并且没有这样的资源可用于阴道微生物组研究。我们构建了阴道16 S rDNA参考数据库，这是一个可能与阴道健康相关的细菌分类群的16 S rDNA参考序列的综合性和非冗余数据库，我们开发了STIRRUPS，这是一种新方法，它采用USESTRUPS算法和策展的参考数据库，用于16 S rDNA部分序列的快速物种级分类。该方法应用于V1-V3 16 S rDNA读数的两个数据集：一个是从含有来自与阴道健康相关的六种细菌菌株的DNA的模拟社区中生成的，第二个是从作为弗吉尼亚联邦大学阴道人类微生物组项目的一部分收集的1,000多个阴道中段样本中生成的。在这两个数据集中，STIRRUPS与阴道16 S rDNA参考数据库结合使用，使用97%的全局身份阈值将超过95%的处理后读数分类到物种级别的分类单元。该数据库和方法提供了宏基因组16 S rDNA序列读数的准确物种水平分类，这将有助于分析和比较来自阴道样品的微生物组谱。如果有合适的16 S rDNA序列参考数据库，STIRRUPS可用于对来自其他生态小生境的16 S rDNA序列读数进行分类。
The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacterial taxa, minimally to the species level, is necessary to fully understand the association of the vaginal microbiome with bacterial vaginosis, sexually transmitted infections, pregnancy complications, menopause, and other physiological and infectious conditions. However, most current taxonomic assignment strategies based on metagenomic 16S rDNA sequence analysis provide at best a genus-level resolution. While surveys of 16S rRNA gene sequences are common in microbiome studies, few well-curated, body-site-specific reference databases of 16S rRNA gene sequences are available, and no such resource is available for vaginal microbiome studies. We constructed the Vaginal 16S rDNA Reference Database, a comprehensive and non-redundant database of 16S rDNA reference sequences for bacterial taxa likely to be associated with vaginal health, and we developed STIRRUPS, a new method that employs the USEARCH algorithm with a curated reference database for rapid species-level classification of 16S rDNA partial sequences. The method was applied to two datasets of V1-V3 16S rDNA reads: one generated from a mock community containing DNA from six bacterial strains associated with vaginal health, and a second generated from over 1,000 mid-vaginal samples collected as part of the Vaginal Human Microbiome Project at Virginia Commonwealth University. In both datasets, STIRRUPS, used in conjunction with the Vaginal 16S rDNA Reference Database, classified more than 95% of processed reads to a species-level taxon using a 97% global identity threshold for assignment. This database and method provide accurate species-level classifications of metagenomic 16S rDNA sequence reads that will be useful for analysis and comparison of microbiome profiles from vaginal samples. STIRRUPS can be used to classify 16S rDNA sequence reads from other ecological niches if an appropriate reference database of 16S rDNA sequences is available.