Yacoub Elhem, Baby Vincent, Sirand-Pugnet Pascal, Arfi Yonathan, Mardassi Helmi, Blanchard Alain, Chibani Salim, Ben Abdelmoumen Mardassi Boutheina
Unit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.
Centre de Diagnostic Vétérinaire de L'Université de Montréal (CDVUM), Faculty of Veterinary Medecine, Université de Montréal, Saint-Hyacinthe, Québec, Canada.
BMC Genomics. 2025 Jan 10;26(1):24. doi: 10.1186/s12864-024-11201-5.
Avian mycoplasmas are small bacteria associated with several pathogenic conditions in many wild and poultry bird species. Extensive genomic data are available for many avian mycoplasmas, yet no comparative studies focusing on this group of mycoplasmas have been undertaken so far.
Here, based on the comparison of forty avian mycoplasma genomes belonging to ten different species, we provide insightful information on the phylogeny, pan/core genome, energetic metabolism, and virulence of these avian pathogens. Analyses disclosed considerable inter- and intra-species genomic variabilities, with genome sizes that can vary by twice as much. Phylogenetic analysis based on concatenated orthologous genes revealed that avian mycoplasmas fell into either Hominis or Pneumoniae groups within the Mollicutes and could split into various clusters. No host co-evolution of avian mycoplasmas can be inferred from the proposed phylogenetic scheme. With 3,237 different gene clusters, the avian mycoplasma group under study proved diverse enough to have an open pan genome. However, a set of 150 gene clusters was found to be shared between all avian mycoplasmas, which is likely encoding essential functions. Comparison of energy metabolism pathways showed that avian mycoplasmas rely on various sources of energy. Superposition between phylogenetic and energy metabolism groups revealed that the glycolytic mycoplasmas belong to two distinct phylogenetic groups (Hominis and Pneumoniae), while all the arginine-utilizing mycoplasmas belong only to Hominis group. This can stand for different evolutionary strategies followed by avian mycoplasmas and further emphasizes the diversity within this group. Virulence determinants survey showed that the involved gene arsenals vary significantly within and between species, and could even be found in species often reported apathogenic. Immunoglobulin-blocking proteins were detected in almost all avian mycoplasmas. Although these systems are not exclusive to this group, they seem to present some particular features making them unique among mycoplasmas.
This comparative genomic study uncovered the significant variable nature of avian mycoplasmas, furthering our knowledge on their biological attributes and evoking new hallmarks.
禽支原体是一类小细菌，与许多野生和家禽物种的多种致病状况相关。目前已有许多禽支原体的广泛基因组数据，但迄今为止尚未开展针对这组支原体的比较研究。
在此，基于对属于十个不同物种的四十个禽支原体基因组的比较，我们提供了关于这些禽病原体的系统发育、泛基因组/核心基因组、能量代谢和毒力的有见地的信息。分析揭示了种间和种内相当大的基因组变异性，基因组大小的变化幅度可达两倍之多。基于串联直系同源基因的系统发育分析表明，禽支原体属于柔膜菌纲中的人型或肺炎型组，并且可分为不同的簇。从所提出的系统发育方案中无法推断出禽支原体与宿主的共同进化。在所研究的禽支原体组中，有3237个不同的基因簇，证明其多样性足以拥有一个开放的泛基因组。然而，发现一组150个基因簇在所有禽支原体中都有共享，这可能编码基本功能。能量代谢途径的比较表明，禽支原体依赖多种能量来源。系统发育组和能量代谢组之间的叠加显示，糖酵解支原体属于两个不同的系统发育组（人型和肺炎型），而所有利用精氨酸的支原体仅属于人型组。这可能代表了禽支原体遵循的不同进化策略，并进一步强调了该组内的多样性。毒力决定因素调查表明，所涉及的基因库在种内和种间有显著差异，甚至在通常报道为无致病性的物种中也能发现。在几乎所有禽支原体中都检测到了免疫球蛋白阻断蛋白。虽然这些系统并非该组所特有，但它们似乎呈现出一些使其在支原体中独一无二的特殊特征。
这项比较基因组研究揭示了禽支原体显著的可变性质，增进了我们对其生物学特性的了解，并引出了新的特征。
