Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
Infect Genet Evol. 2011 Oct;11(7):1798-804. doi: 10.1016/j.meegid.2011.07.020. Epub 2011 Aug 5.
Mycoplasmas are Gram-positive wall-less bacteria with a wide environmental and host distribution, causing disease in man and in (wild and farmed) animals. The aim of this study was to analyze the usefulness of a genomic taxonomic approach in Mycoplasma systematics. Multilocus Sequence Analysis (MLSA), average amino acid identity (AAI), and Karlin genomic signature allowed a clear identification of species. For instance, Mycoplasma pneumoniae and Mycoplasma genitalium had only 71% MLSA similarity, 67% AAI, and 88 for Karlin genomic signature. Codon usage (Nc) of the phylogenetically distantly related species Mycoplasma conjunctivae and Mycoplasma gallisepticum was identical, in spite of clear differences in MLSA, AAI, and Karlin, suggesting that these two species were subjected to convergent adaptation due to similar environmental conditions. We suggest that a Mycoplasma species may be better defined based on genomic features. In our hands, a Mycoplasma species is defined as a group of strains that share ≥ 97% DNA identity in MLSA, ≥ 93.9% AAI and ≤ 8 in Karlin genomic signature. This new definition may be useful to advance the taxonomy of Mycoplasmas.
支原体是革兰氏阳性无细胞壁的细菌，具有广泛的环境和宿主分布，可导致人类和（野生和养殖）动物患病。本研究旨在分析基因组分类方法在支原体系统分类学中的有用性。多位点序列分析（MLSA）、平均氨基酸同一性（AAI）和 Karlin 基因组特征可明确识别物种。例如，肺炎支原体和生殖器支原体的 MLSA 相似度仅为 71%，AAI 为 67%，Karlin 基因组特征为 88。尽管在 MLSA、AAI 和 Karlin 上存在明显差异，但亲缘关系较远的结膜支原体和禽支原体的密码子使用（Nc）相同，这表明这两个物种由于相似的环境条件而受到趋同适应。我们建议可以根据基因组特征更好地定义支原体物种。在我们的研究中，支原体物种的定义是一组在 MLSA 中具有≥97%DNA 同一性、≥93.9%AAI 和≤8 的 Karlin 基因组特征的菌株。这个新定义可能有助于推进支原体的分类学。
