FINGERPRINT: Fully Integrated Culturomic Platform for Rapid, High-throughput Microbial Identification and Characterisation

传统的微生物学侧重于在实验室中培养细菌，但近几十年来这种情况发生了变化。DNA测序技术的发展意味着无需培养就可以探索微生物的遗传潜力，这使得对人类消化系统、土壤和海洋中的整个微生物群落的快速研究成为可能。虽然这有好处，但近年来，传统的微生物群落培养（“文化组学”）已经看到了某种程度上的复兴，因为很明显，DNA测序不能取代所有其他技术。例如，虽然DNA测序会告诉你微生物有哪些基因，但它不会告诉你这些基因是否有功能，或者它们何时会被使用。它也不能轻易地告诉你一个新基因的作用，而且许多基因仍未被研究，这对医学或工业应用可能很重要。最后，DNA测序在技术上复杂、缓慢且昂贵，这限制了可以进行的研究数量。然而，培养微生物也不是没有自己的问题。微生物群落可以由数百或数千种组成，在实验室中分离和培养所有这些微生物需要大量的工作。为了保持这些培养物的活力或准备实验，它们需要转移到新鲜的生长培养基上，这对许多分离物来说是乏味而耗时的。这给研究造成了严重的瓶颈，占用了员工宝贵的时间。然而，这个过程很简单：用一个无菌的物体来捡起微生物，然后把它移到新鲜的生长培养基上。这是一个非技术和高度重复的任务，因此是理想的自动化使用机器人系统。菌落拾取器就是为此目的而设计的机器，每小时能够处理数千个微生物，通过计算机视觉系统根据大小、形状或颜色来选择它们。这允许使用最少的工作人员时间来设置大型和复杂格式的许多不同实验。例如，为了找到与某些功能有关的基因，通常需要培养数千个菌株的“文库”，每个菌株都有不同的突变。然后观察这些突变体在行为上的任何变化，这些变化可能揭示它们与所讨论的功能有关。能够用一个菌落选择器自动管理数千个这样的突变体，最大限度地提高了识别驱动该过程的基因的机会，使用了最少的工作时间。虽然菌落拾取器将有助于分离、培养和研究这些微生物，但最终我们需要知道它们的身份。DNA测序是实现这一目标的一个行之有效的过程，但它很昂贵，并且需要大量的手工工作来识别每一种微生物。由于需要专业的机器和专业知识，这通常无法在内部完成，因此珍贵的样品必须邮寄（通常是在国外）给专门从事这项工作的公司。因此，这个过程可能需要几天才能完成，而且成本往往限制了研究人员在一项研究中只能识别几十种微生物。利用MALDI生物分型器开发了一种鉴定微生物的新方法，该方法可以检测与不同物种相关的蛋白质的独特指纹。这使得对大量微生物的鉴定更加快速和廉价，因此将完美地补充由菌落采摘系统培养的大型微生物库。这两个系统将使我们能够极大地扩展我们的研究，研究微生物如何在牛和羊的肠道中产生温室气体，微生物如何在人体中引起疾病，以及自然界中的微生物如何能够生存并控制它们周围的世界。这些问题推动了我们这个时代的重要社会问题，而这个平台将帮助我们回答这些问题。

Traditional microbiology is focused on growing cultures in the lab, but in recent decades this has changed. Developments in DNA sequencing technologies mean that it is possible to explore the genetic potential of a microbe without having to grow it, which has allowed the rapid study of entire communities of microbes in the human digestive system, soil, and oceans. While this has benefits, the traditional culturing of microbial communities ("culturomics") has seen somewhat of a Renaissance in recent years, as it has become clear that DNA sequencing cannot replace all other techniques. For example, while DNA sequencing will tell you which genes a microbe has, it does not tell you if these genes are functional, or when they will be used. It also cannot easily tell you what a new gene does, and many genes remain unstudied which could be important for medical or industrial applications. Finally, DNA sequencing is technically complex, slow, and costly, which restricts the amount of research which can be done. Growing microbes isn't without its own problems, however. Microbial communities can be made of hundreds or thousands of species, and separating and growing all of these in the lab requires enormous amounts of work. To keep these cultures alive or to prepare an experiment they need to be transferred to fresh growth medium, which can be tedious and time-consuming for so many isolates. This creates a serious bottleneck to research and ties up valuable staff time. However, the process is simple: a sterile object is used to pick up the microbe and move it to fresh growth medium. This is a non-skilled and highly repetitive task, and so is ideal for automation using robotic systems. Colony pickers are machines designed with this purpose in mind, and are able to process thousands of microbes per hour, selecting them via computer vision systems based on size, shape, or colour. This allows many different experiments of large and complex formats to be set up using minimal staff time. For example, to find a gene involved in certain functions it is common to culture a "library" of thousands of strains, each with a different mutation. These mutants are then observed for any change in their behaviour which might reveal that they are linked to the function in question. Being able to manage thousands of these mutants automatically with a colony picker maximises the chances of identifying a gene which drives the process, using minimal staff time. While the colony picker will help to separate, culture, and study these microbes, eventually we will need to know their identity. DNA sequencing is a well-established process for achieving this, but it is expensive and requires a lot of manual work for every microbe to be identified. The specialist machines and expertise needed mean it usually cannot be done in-house, and so precious samples must be posted - often abroad - to companies which specialise in this work. As a result, it can take several days for this process to be completed, and the costs often limit researchers to identifying just a few dozen microbes in a study. A new method of identifying microbes has been developed using a MALDI biotyper, which detects the unique fingerprint of proteins associated with different species. This allows much more rapid and inexpensive identification of large numbers of microbes, and so would perfectly complement the large libraries of microbes which would be cultured by the colony picking system. Together, these two systems will enable us to greatly expand our research into how microbes create greenhouse gases in cow and sheep guts, how microbes cause disease in the human body, and how microbes in the natural world are able to survive and control the world around them. These are questions which drive the important societal questions of our time, and this platform will help us to answer them.