Fac. de Química, Departamento de Alimentos y Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 3000, C. U, 04510, Ciudad de México, Mexico.
Instituto de Biotecnología, Unidad de Secuenciación Masiva y Bioinformática, Av. Universidad 2001, Chamilpa, 62210, Cuernavaca, Morelos, Mexico.
Appl Microbiol Biotechnol. 2018 Mar;102(5):2251-2267. doi: 10.1007/s00253-018-8765-3. Epub 2018 Jan 25.
Enterococcus spp. are present in the native microbiota of many traditional fermented foods. Their ability to produce antibacterial compounds, mainly against Listeria monocytogenes, has raised interest recently. However, there is scarce information about their proteolytic and lipolytic potential, and their biotechnological application is currently limited because enterococcal strains have been related to nosocomial infections. In this work, next-generation sequencing and optimised bioinformatic pipelines were used to annotate the genomes of two Enterococcus strains-one E. faecium and one E. faecalis-isolated from the Mexican artisanal ripened Cotija cheese. A battery of genes involved in their proteolytic system was annotated. Genes coding for lipases, esterases and other enzymes whose final products contribute to cheese aroma and flavour were identified as well. As for the production of antibacterial compounds, several peptidoglycan hydrolase- and bacteriocin-coding genes were identified in both genomes experimentally and by bioinformatic analyses. E. faecalis showed resistance to aminoglycosides and E. faecium to aminoglycosides and macrolides, as predicted by the genome functional annotation. No pathogenicity islands were found in any of the strains, although traits such as the ability of biofilm formation and cell aggregation were observed. Finally, a comparative genomic analysis was able to discriminate between the food strains isolated and nosocomial strains. In summary, pathogenic strains are resistant to a wide range of antibiotics and contain virulence factors that cause host damage; in contrast, food strains display less antibiotic resistance, include genes that encode class II bacteriocins and express virulence factors associated with host colonisation rather than invasion.
肠球菌属存在于许多传统发酵食品的天然微生物群中。它们产生抗菌化合物的能力，主要是针对单核细胞增生李斯特菌，最近引起了人们的兴趣。然而，关于它们的蛋白水解和脂肪水解潜力的信息很少，而且它们的生物技术应用目前受到限制，因为肠球菌菌株与医院感染有关。在这项工作中，使用下一代测序和优化的生物信息学管道来注释从墨西哥传统成熟的 Cotija 奶酪中分离的两种肠球菌菌株（屎肠球菌和粪肠球菌）的基因组。注释了它们的蛋白水解系统涉及的一系列基因。鉴定了编码脂肪酶、酯酶和其他酶的基因，这些酶的最终产物有助于奶酪的香气和风味。至于抗菌化合物的产生，在两个基因组中，通过实验和生物信息学分析鉴定了几种肽聚糖水解酶和细菌素编码基因。粪肠球菌对氨基糖苷类和屎肠球菌对氨基糖苷类和大环内酯类具有抗性，这是由基因组功能注释预测的。在任何一种菌株中都没有发现致病性岛，尽管观察到了生物膜形成和细胞聚集的能力等特性。最后，比较基因组分析能够区分分离自食物的菌株和医院感染的菌株。总之，致病性菌株对广泛的抗生素具有抗性，并含有导致宿主损伤的毒力因子；相比之下，食物菌株的抗生素耐药性较低，包含编码 II 类细菌素的基因，并表达与宿主定植而不是入侵相关的毒力因子。
