DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
Syst Appl Microbiol. 2010 Jun;33(4):175-82. doi: 10.1016/j.syapm.2010.03.003. Epub 2010 Apr 20.
Given the considerable promise whole-genome sequencing offers for phylogeny and classification, it is surprising that microbial systematics and genomics have not yet been reconciled. This might be due to the intrinsic difficulties in inferring reasonable phylogenies from genomic sequences, particularly in the light of the significant amount of lateral gene transfer in prokaryotic genomes. However, recent studies indicate that the species tree and the hierarchical classification based on it are still meaningful concepts, and that state-of-the-art phylogenetic inference methods are able to provide reliable estimates of the species tree to the benefit of taxonomy. Conversely, we suspect that the current lack of completely sequenced genomes for many of the major lineages of prokaryotes and for most type strains is a major obstacle in progress towards a genome-based classification of microorganisms. We conclude that phylogeny-driven microbial genome sequencing projects such as the Genomic Encyclopaedia of Archaea and Bacteria (GEBA) project are likely to rectify this situation.
鉴于全基因组测序在系统发生和分类方面具有巨大的潜力，微生物系统学和基因组学尚未得到统一，这令人感到惊讶。这可能是由于从基因组序列推断合理的系统发育关系存在内在困难，尤其是在原核基因组中存在大量水平基因转移的情况下。然而，最近的研究表明，种系发生树和基于它的层次分类仍然是有意义的概念，并且最先进的系统发育推断方法能够为分类学提供可靠的种系发生树估计。相反，我们怀疑目前许多原核生物的主要谱系以及大多数典型菌株的完全测序基因组的缺乏是朝着基于基因组的微生物分类法取得进展的主要障碍。我们得出结论，以系统发育为驱动的微生物基因组测序项目，例如古菌和细菌基因组百科全书（GEBA）项目，可能会纠正这种情况。
