Identifying drivers of phage infectivity in natural microbial communities

确定自然微生物群落中噬菌体感染性的驱动因素

• 批准号: BB/X009793/1
• 负责人: Sean Meaden
• 金额: $ 51.24万
• 依托单位: University of York
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FX009793%2F1
• 关键词: Identifying; drivers; phage; infectivity; natural

Bacteria are among the most abundant organisms on earth, and are crucial for global geochemical cycling. Their viruses, bacteriophages (phages) are estimated to commonly outnumber bacteria by at least 10: 1, with phages killing around 20% of bacteria daily in the marine ecosystem. Therefore, the scale of this interaction has profound implications for global geochemical cycling. Phages also act as vectors that spread genes between different bacteria, which can have adverse implications for human health, such as the spread of antimicrobial resistance. Phages have also acted as a source for biotechnology innovation, including commonly used enzymes for gene editing and molecular biology. Despite their importance very little is known regarding how phages shape bacterial communities in natural ecosystems.This lack of information about these interactions is because much of our knowledge is based on the small subset of bacteria and their phages that we can grow, or 'culture', in the laboratory. Only a tiny proportion of bacteria, potentially as low as 1%, can be grown in the lab. One method that circumvents this problem is to study the DNA sequences of the microbes present, directly extracting DNA from the environment and stitching it back together using computational algorithms. This is known as 'metagenomics' and allows us to reconstruct the profile of the microbial community, without needing to isolate or grow these microbes in the lab. However, this is a static picture of the community, and it is impossible to identify which microbes are directly interacting. A recent advance in DNA sequencing technology, called HiC sequencing, allows researchers to link DNA molecules that are present within the same cell. This allows us to link viruses that have successfully injected their genomes into host cells, therefore capturing infections in situ.While this new technology has exciting potential, it relies on having a complete database of viruses and hosts DNA sequences with which to link the HiC sequences. This is problematic because reconstructing all the genomes of the microrganisms present is a fundamental challenge. An analogy often used to describe this challenge is that of reconstructing an entire library of books, when all the pages have been shredded and there are different numbers of copies of each book. In this case, each book represents a microbial genome, and the number of copies is the abundance of each organism. Another new technology, called adaptive sequencing, allows for the depletion of the common organisms, i.e. searching for rare microbes, or books in this analogy. HiC sequencing does the equivalent of providing page numbers i.e. identifying which DNA sequences are in close proximity. Together these technologies will allow the accurate reconstruction microbial communities, and enable me to identify all viral infections in an entire community of microbes.By combining new data from these technologies with an existing dataset of soil metagenomes, I will address fundamental questions in the ecology of phages and their hosts. Namely, who infects who? Why do some phages infect more hosts than others? Which defence mechanisms do hosts use to defend against phages? And does this interaction change across different environments, such as when bacteria are more abundant?The research will be carried out at the University of Exeter, a leading institution for the study of microbial ecology and evolution. I will be surrounded by a collaborative group of scientists, and have access to state-of-the art sequencing technologies via the Exeter Sequencing Service, as well as high performance computing clusters. The research has implications for soil health, by understanding how phages shape the microbial community- which is crucial for plant health and development. There is also great potential for learning more about the defence systems bacteria use against phages, many of which are of interest to biotechnology.

细菌是地球上最丰富的生物体之一，对全球地球化学循环至关重要。据估计，它们的病毒、噬菌体（噬菌体）的数量通常比细菌至少多出 10:1，噬菌体每天杀死海洋生态系统中约 20% 的细菌。因此，这种相互作用的规模对全球地球化学循环具有深远的影响。噬菌体还充当在不同细菌之间传播基因的载体，这可能对人类健康产生不利影响，例如抗菌素耐药性的传播。噬菌体还充当生物技术创新的来源，包括用于基因编辑和分子生物学的常用酶。尽管噬菌体很重要，但人们对噬菌体如何塑造自然生态系统中的细菌群落知之甚少。缺乏有关这些相互作用的信息是因为我们的大部分知识都是基于我们可以在实验室中生长或“培养”的一小部分细菌及其噬菌体。只有一小部分细菌（可能低至 1%）可以在实验室中培养。解决这个问题的一种方法是研究存在的微生物的 DNA 序列，直接从环境中提取 DNA 并使用计算算法将其重新拼接在一起。这被称为“宏基因组学”，使我们能够重建微生物群落的概况，而无需在实验室中分离或培养这些微生物。然而，这是群落的静态图片，不可能识别哪些微生物在直接相互作用。 DNA 测序技术的最新进展称为 HiC 测序，它使研究人员能够将同一细胞内存在的 DNA 分子连接起来。这使我们能够将已成功将其基因组注入宿主细胞的病毒连接起来，从而原位捕获感染。虽然这项新技术具有令人兴奋的潜力，但它依赖于拥有一个完整的病毒和宿主 DNA 序列数据库，用于连接 HiC 序列。这是有问题的，因为重建现有微生物的所有基因组是一项根本挑战。经常用来描述这一挑战的一个类比是重建整个图书馆的图书，其中所有页面都已被撕碎，并且每本书都有不同数量的副本。在这种情况下，每本书代表一个微生物基因组，副本的数量就是每个生物体的丰度。另一种新技术，称为适应性测序，可以消除常见的生物体，即寻找稀有微生物，或者类似的书籍。 HiC 测序相当于提供页码，即识别哪些 DNA 序列非常接近。这些技术将能够准确重建微生物群落，并使我能够识别整个微生物群落中的所有病毒感染。通过将这些技术的新数据与现有的土壤宏基因组数据集相结合，我将解决噬菌体及其宿主生态学中的基本问题。也就是说，谁感染了谁？为什么有些噬菌体比其他噬菌体感染更多的宿主？宿主使用哪些防御机制来防御噬菌体？这种相互作用会在不同的环境中发生变化吗？例如当细菌更加丰富时？这项研究将在埃克塞特大学进行，该大学是微生物生态学和进化研究的领先机构。我将被一群科学家合作，并可以通过埃克塞特测序服务以及高性能计算集群获得最先进的测序技术。该研究通过了解噬菌体如何塑造微生物群落（这对植物健康和发育至关重要）对土壤健康产生影响。了解更多关于细菌针对噬菌体的防御系统也有很大的潜力，其中许多系统对生物技术感兴趣。

项目成果

CRISPR-Cas in Pseudomonas aeruginosa provides transient population-level immunity against high phage exposures

• DOI: 10.1093/ismejo/wrad039
• 发表时间: 2024-01-08
• 期刊: ISME JOURNAL
• 影响因子: 11
• 作者: Watson，Bridget N. J.;Capria，Loris;Meaden，Sean
• 通讯作者: Meaden，Sean