Population genomics of bacteria

细菌群体基因组学

• 批准号: NE/D011485/1
• 负责人: Peter Young
• 金额: $ 46.76万
• 依托单位: University of York
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2006
• 资助国家: 英国
• 起止时间: 2006 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FD011485%2F1
• 关键词: Population; genomics; bacteria

All life on earth depends on bacteria, which drive the global cycles of matter and energy, provide nutrients, decompose waste and clean up pollution. Of course, some of them also make us ill or destroy our crops. Now that we know the complete DNA sequences of hundreds of different bacteria, we can see that nearly all these diverse functions are carried out by 'accessory genes'. Bacteria are like computers: they have a 'basic genome' that keeps the system running and is much the same in all bacteria, rather like the hardware and operating system of a computer. Then there are sets of accessory genes that provide special adaptations, and over time each bacterium acquires a unique collection of these by swapping with other bacteria, just as computers accumulate software packages and data. The goal of our project is to describe and understand how the patterns of occurrence of accessory genes (software packages) relate to the basic genome (operating system) of the bacteria. Are some packages widely popular and others only for specialists? Are some packages limited to particular operating systems? If a system has one package, is there a whole set of other packages that it is likely to have as well? We will sample bacteria from a single spadeful of soil, using certain well-studied properties tosift out just a few related species from all the thousands that are found in soil. First we will check out their hardware and operating system by determining the DNA sequence of their ribosomal RNA genes and some genes that provide 'housekeeping' functions. This is like reading the manufacturer's name (ribosomal RNA is used to identify bacterial species) and checking whether the main hardware components and the operating system are still the versions originally installed. Then we will screen them for hundreds of different software packages (accessory genes). To do this, we make a microarray by printing thousands of tiny spots of DNA on a glass slide. Each DNA spot has the sequence of part of a different gene, so when fluorescently-labelled DNA from a bacterium is washed over the slide, the spots become fluorescent if the matching DNA is present. This happens because a single strand of DNA will bind strongly to a matching strand to make a double helix. The fluorescence of each spot can be measured in a special reader, so in this way we can check hundreds of bacterial strains to see what accessory genes they have installed. We expect that even those bacteria that belong to the same species and have essentially the same basic genome will differ in the accessory genes that they carry. We also expect to see the same accessory genes turn up in different bacterial species. There are already many examples that show that these things happen. The purpose of our project is to assess the situation more systematically, looking at large numbers of genes and bacteria so that we can draw some strong general conclusions and begin to understand what properties of a gene determine whether it will be widespread or restricted in distribution.

地球上的所有生命都取决于驱动全球物质和能量周期的细菌提供营养，分解废物并清理污染。当然，其中一些也会使我们生病或破坏我们的农作物。现在，我们知道了数百种不同细菌的完整DNA序列，我们可以看到几乎所有这些不同的功能都是由“辅助基因”执行的。细菌就像计算机一样：它们具有“基本基因组”，可以使系统运行，并且在所有细菌中都非常相同，而不是计算机的硬件和操作系统。然后是一组提供特殊适应的附件基因，随着时间的流逝，每种细菌通过与其他细菌交换来获取独特的收集，就像计算机积累了软件包和数据一样。我们项目的目的是描述和了解附属基因（软件包）的发生模式与细菌的基本基因组（操作系统）有关。有些软件包是否广受欢迎，而另一些包裹仅适用于专家？某些软件包是否仅限于特定操作系统？如果系统有一个软件包，是否还有一组其他包裹也可能拥有的包装？我们将使用某些经过深入研究的特性从单一的土壤中采样细菌，从土壤中发现的所有成千上万种相关的物种。首先，我们将通过确定其核糖体RNA基因的DNA序列以及一些提供“家政功能”功能的基因来检查其硬件和操作系统。这就像阅读制造商的名称（核糖体RNA用于识别细菌物种），并检查主要的硬件组件和操作系统是否仍然是最初安装的版本。然后，我们将筛选它们的数百个不同的软件包（配件基因）。为此，我们通过在载玻片上打印成千上万的DNA来制作微阵列。每个DNA斑点都有不同基因的一部分的序列，因此，当从载玻片上洗涤荧光标记的DNA时，如果存在匹配的DNA，斑点就会荧光。之所以发生这种情况，是因为单链DNA将与匹配的链强结合以形成双螺旋。每个位置的荧光可以在特殊的读取器中测量，因此，通过这种方式，我们可以检查数百种细菌菌株，以查看它们已安装的配件基因。我们期望即使是属于同一物种并具有相同基本基因组的细菌在它们所携带的辅助基因上也会有所不同。我们还期望看到不同细菌物种中相同的附件基因出现。已经有许多例子表明这些事情发生了。我们项目的目的是更加系统地评估情况，研究大量基因和细菌，以便我们可以得出一些有力的总体结论，并开始了解基因的特性确定它是否会被广泛或分布限制。

项目成果

A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria.

• DOI: 10.1371/journal.pone.0002567
• 发表时间: 2008-07-02
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Crossman LC;Castillo-Ramírez S;McAnnula C;Lozano L;Vernikos GS;Acosta JL;Ghazoui ZF;Hernández-González I;Meakin G;Walker AW;Hynes MF;Young JP;Downie JA;Romero D;Johnston AW;Dávila G;Parkhill J;González V
• 通讯作者: González V

Biological Nitrogen Fixation - Towards Poverty Alleviation Through Sustainable Agriculture: Proceedings of the 15th International Nitrogen Fixation Congress and the 12th International Conference of the African Association for Biological Nitrogen Fixation

生物固氮——通过可持续农业实现扶贫：第十五届国际固氮大会和非洲生物固氮协会第十二届国际会议论文集

• 作者: Dakora, F.D.;Chimphango, S.B.M.;Valentine, Alex J.;Elmerich, Claudine;Newton, William E. (Virginia Polytechnic Institute;State University)
• 通讯作者: State University)

Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum.

• DOI: 10.1098/rsob.140133
• 发表时间: 2015-01
• 期刊: Open biology
• 影响因子: 5.8
• 作者: Kumar N;Lad G;Giuntini E;Kaye ME;Udomwong P;Shamsani NJ;Young JP;Bailly X
• 通讯作者: Bailly X