Caro-Quintero Alejandro, Konstantinidis Konstantinos T
School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.
1] School of Biology, Georgia Institute of Technology, Atlanta, GA, USA [2] School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA [3] Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, USA.
ISME J. 2015 Mar 17;9(4):958-67. doi: 10.1038/ismej.2014.193.
Genome sequencing has revealed that horizontal gene transfer (HGT) is a major evolutionary process in bacteria. Although it is generally assumed that closely related organisms engage in genetic exchange more frequently than distantly related ones, the frequency of HGT among distantly related organisms and the effect of ecological relatedness on the frequency has not been rigorously assessed. Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. Our analysis revealed the existence of networks of genetic exchange between organisms with overlapping ecological niches, with mesophilic anaerobic organisms showing the highest frequency of exchange and engaging in HGT twice as frequently as their aerobic counterparts. Examination of individual cases suggested that inter-phylum HGT is more pronounced than previously thought, affecting up to ∼ 16% of the total genes and ∼ 35% of the metabolic genes in some genomes (conservative estimation). In contrast, ribosomal and other universal protein-coding genes were subjected to HGT at least 150 times less frequently than genes encoding the most promiscuous metabolic functions (for example, various dehydrogenases and ABC transport systems), suggesting that the species tree based on the former genes may be reliable. These results indicated that the metabolic diversity of microbial communities within most habitats has been largely assembled from preexisting genetic diversity through HGT and that HGT accounts for the functional redundancy among phyla.
基因组测序显示，水平基因转移（HGT）是细菌中的一个主要进化过程。虽然一般认为亲缘关系近的生物体比亲缘关系远的生物体更频繁地进行基因交换，但亲缘关系远的生物体之间HGT的频率以及生态相关性对该频率的影响尚未得到严格评估。在这里，我们设计了一种新颖的生物信息学流程，通过以标准化三联体分析基因组，最大限度地减少了可用数据库中特定分类群过度代表性的影响以及基于同源性方法的其他局限性，以量化代表不同门的细菌基因组之间的基因交换。我们的分析揭示了具有重叠生态位的生物体之间存在基因交换网络，嗜温厌氧生物体显示出最高的交换频率，其进行HGT的频率是其需氧对应物的两倍。对个别案例的研究表明，门间HGT比以前认为的更为明显，在某些基因组中影响高达约16%的总基因和约35%的代谢基因（保守估计）。相比之下，核糖体和其他通用蛋白质编码基因接受HGT的频率比编码最易发生交换的代谢功能的基因（例如，各种脱氢酶和ABC转运系统）至少低150倍，这表明基于前一类基因的物种树可能是可靠的。这些结果表明，大多数栖息地内微生物群落的代谢多样性在很大程度上是通过HGT从先前存在的遗传多样性中组装而来的，并且HGT解释了各门类之间的功能冗余。
