Exploiting chaperonin universal targets for detecting and monitoring diversity in natural microbial communities

识别微生物的能力对人类、动物和环境健康以及利用生物技术的行业至关重要。快速、经济地确定微生物全基因组序列的方法的发展给微生物学家提出了新的挑战，因为这些信息揭示了传统定义的物种中惊人数量的多样性，并再次引起了人们对微生物世界中物种构成的问题的关注。对于微生物生态学家来说，当他们确定一个复杂的微生物群落如何应对扰动时，还面临着确定哪些类型的信息是有价值或有信息的挑战。饮食的改变会对生活在肠道中的细菌群落产生影响，但对物种多样性的改变(谁在那里？)值得一看，或者我们应该转而关注社区活动的变化(他们在做什么？)就像大多数重要的生物学问题一样，没有一个简单的解决方案，必须采用各种方法和途径。我们的研究小组正在开发检测和鉴定微生物和微生物种群多样性的工具。我们使用普遍保守的伴侣蛋白基因序列作为条形码，用于区分物种和识别功能相关的亚种组，称为生态型。伴侣序列给了我们比目前可用的通用靶标更高的分辨率，并允许我们使用单个基因序列来区分传统定义物种中表型不同的细菌群体。我们正在努力应用这些基于伴侣的方法来促进微生物的鉴定，并弥合微生物群落中结构和功能之间的差距。作为我们工作的一部分，我们开发了一个称为cpnDB的伴侣蛋白序列参考数据库，目前世界各地的临床医生、分类学家和微生物生态学家正在使用该数据库来检测、鉴定、量化和表征微生物。

The ability to identify microorganisms is critical to human, animal and environmental health, as well as industries that exploit biotechnology. The development of rapid and economical methods for determining the whole genome sequence of microbes has presented new challenges to microbiologists since this information has revealed surprising amounts of diversity within traditionally defined species, and once again drawn attention to questions about what constitutes a species in the microbial world. For microbial ecologists, there is also the challenge of determining what sorts of information are valuable or informative when they are determining how a complex community of microorganisms responds to perturbation. A change in diet can have effects on the bacterial communities that live in the intestine, but are the changes to species diversity (Who is there?) worth looking at, or should we instead focus on community activity changes (What are they doing?). As with most important biological questions, there is not one simple solution and a variety of methods and approaches must be applied. Our research group is developing tools for the detection and identification of diversity among microbes and microbial populations. We are using the sequences of universally conserved chaperonin genes as "barcodes" for discriminating species and identifying functionally related subspecies groups called ecotypes. Chaperonin sequences give us a more resolving power than currently available universal targets and allow us to use a single gene sequence to discriminate phenotypically distinct groups of bacteria within traditionally defined species. We are working to apply these chaperonin-based methods to facilitate identification of microbes and to bridge the gap between structure and function in microbial communities. As part of our work, we have developed a reference database of chaperonin sequences called cpnDB, that is currently being used by clinicians, taxonomists and microbial ecologists around the world as they detect, identify, quantify and characterize microorganisms.