A genomic view of food-related and probiotic Enterococcus strains

J. Bonacina, N. Suárez, R. Hormigo, S. Fadda, Marcus Lechner, L. Saavedra
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引用次数: 41

Abstract

Abstract The study of enterococcal genomes has grown considerably in recent years. While special attention is paid to comparative genomic analysis among clinical relevant isolates, in this study we performed an exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential to be used as probiotics. Beyond common genetic features, we especially aimed to identify those that are specific to enterococcal strains isolated from a certain food-related source as well as features present in a species-specific manner. Thus, the genome sequences of 25 Enterococcus strains, from 7 different species, were examined and compared. Their phylogenetic relationship was reconstructed based on orthologous proteins and whole genomes. Likewise, markers associated with a successful colonization (bacteriocin genes and genomic islands) and genome plasticity (phages and clustered regularly interspaced short palindromic repeats) were investigated for lifestyle specific genetic features. At the same time, a search for antibiotic resistance genes was carried out, since they are of big concern in the food industry. Finally, it was possible to locate 1617 FIGfam families as a core proteome universally present among the genera and to determine that most of the accessory genes code for hypothetical proteins, providing reasonable hints to support their functional characterization.
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食物相关和益生菌肠球菌菌株的基因组观
近年来,肠球菌基因组的研究有了长足的发展。虽然特别关注临床相关分离株的比较基因组分析,但在本研究中,我们对食物来源和/或可能用作益生菌的肠球菌基因组进行了详尽的比较分析。除了常见的遗传特征外,我们特别旨在确定从某种食物相关来源分离的肠球菌菌株所特有的特征,以及以物种特异性方式存在的特征。因此,对来自7个不同物种的25株肠球菌的基因组序列进行了检测和比较。基于同源蛋白和全基因组重建了它们的系统发育关系。同样,与成功定植(细菌素基因和基因组岛)和基因组可塑性(噬菌体和聚集规律间隔的短回文重复序列)相关的标记也被用于研究生活方式特定的遗传特征。与此同时,由于抗生素耐药基因在食品工业中是一个大问题,因此进行了抗生素耐药基因的研究。最后,我们找到了1617个FIGfam家族作为核心蛋白质组,并确定了大多数辅助基因编码假设的蛋白质,为支持其功能表征提供了合理的线索。
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