Palmer Marike, Steenkamp Emma T, Coetzee Martin P A, Blom Jochen, Venter Stephanus N
Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
Department of Genetic, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
Front Microbiol. 2018 Feb 6;9:113. doi: 10.3389/fmicb.2018.00113. eCollection 2018.
Bacteriologists have strived toward attaining a natural classification system based on evolutionary relationships for nearly 100 years. In the early twentieth century it was accepted that a phylogeny-based system would be the most appropriate, but in the absence of molecular data, this approach proved exceedingly difficult. Subsequent technical advances and the increasing availability of genome sequencing have allowed for the generation of robust phylogenies at all taxonomic levels. In this study, we explored the possibility of linking biological characters to higher-level taxonomic groups in bacteria by making use of whole genome sequence information. For this purpose, we specifically targeted the genus and its four main lineages. The shared gene sets were determined for , the four lineages within the genus, as well as its sister-genus . This was followed by functional characterization of the gene sets using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In comparison to , various traits involved in nutrient cycling were identified within , providing evidence for increased efficacy in recycling of metabolites within the genus. Additionally, a number of traits associated with pathogenicity were identified within species often associated with opportunistic infections, with some support for adaptation toward overcoming host defenses. Some traits were also only conserved within specific lineages, potentially acquired in an ancestor to the lineage and subsequently maintained. It was also observed that the species isolated from the most diverse sources were generally the most versatile in their carbon metabolism. By investigating evolution, based on the more variable genomic regions, it may be possible to detect biologically relevant differences associated with the course of evolution and speciation.
近100年来，细菌学家一直致力于建立一个基于进化关系的自然分类系统。在20世纪初，人们认为基于系统发育的系统是最合适的，但由于缺乏分子数据，这种方法被证明极其困难。随后的技术进步和基因组测序的日益普及，使得在所有分类水平上都能生成可靠的系统发育树。在本研究中，我们利用全基因组序列信息，探索了将生物学特征与细菌的高级分类群联系起来的可能性。为此，我们专门针对[具体属名]及其四个主要谱系。确定了[具体属名]、该属内的四个谱系以及其姐妹属的共享基因集。随后，使用京都基因与基因组百科全书（KEGG）数据库对基因集进行功能表征。与[姐妹属名]相比，在[具体属名]内发现了参与营养循环的各种特征，这为该属内代谢物循环效率的提高提供了证据。此外，在通常与机会性感染相关的物种中发现了一些与致病性相关的特征，这为适应克服宿主防御提供了一些支持。一些特征也仅在特定谱系中保守，可能是在该谱系的祖先中获得并随后保留下来的。还观察到，从最多样化来源分离的物种在碳代谢方面通常最为多样。通过基于更可变的基因组区域研究进化，有可能检测到与进化过程和物种形成相关的生物学上相关的差异。
