Enterococcus faecium is a lactic acid bacterium with applications in food engineering and nutrigenomics, including as starter cultures in fermented foods. To differentiate the E. faecium probiotic from pathogenic bacteria, physiological analyses are often used but they do not guarantee that a bacterial strain is not pathogenic. We report here new findings and an approach based on comparison of the genetic mobility of (1) probiotic, (2) pathogenic, and (3) nonpathogenic and non-probiotic strains, so as to differentiate probiotics, and inform their safe use. The region of the 16S ribosomal DNA (rDNA) genes of different E. faecium strains native to Pernambuco-Brazil was used with the GenBank query sequence. Complete genomes were selected and divided into three groups as noted above to identify the mobile genetic elements (MGEs) (transposase, integrase, conjugative transposon protein and phage) and antibiotic resistance genes (ARGs), and to undertake pan-genome analysis and multiple genome alignment. Differences in the number of MGEs were found in ARGs, in the presence and absence of the genes that differentiate E. faecium probiotics and pathogenic bacteria genetically. Our data suggest that genetic mobility appears to be informative in differentiating between probiotic and pathogenic strains. While the present findings are not necessarily applicable to all probiotics, they offer novel molecular insights to guide future research in nutrigenomics, clinical medicine, and food engineering on new ways to differentiate pathogenic from probiotic bacteria.

中文翻译：

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益生菌与病原菌的区别是什么？屎肠球菌的遗传迁移性提供了新的分子见解。

屎肠球菌是一种乳酸菌，可用于食品工程和营养基因组学，包括作为发酵食品中的发酵剂。为了区分粪肠球菌益生菌和致病菌，经常使用生理学分析，但它们并不能保证细菌菌株不会致病。我们在此报告了基于 (1) 益生菌、(2) 致病性和 (3) 非致病性和非益生菌菌株的遗传流动性比较的新发现和方法，以区分益生菌并告知其安全使用。不同屎肠球菌的 16S 核糖体 DNA (rDNA) 基因区域Pernambuco-Brazil 原生菌株与 GenBank 查询序列一起使用。选择完整的基因组并将其分为如上所述的三组以识别移动遗传元件（MGEs）（转座酶、整合酶、接合转座子蛋白和噬菌体）和抗生素抗性基因（ARGs），并进行泛基因组分析和多基因组分析结盟。在区分屎肠球菌的基因存在和不存在的情况下，在 ARG 中发现 MGE 数量的差异益生菌和致病菌遗传。我们的数据表明，遗传流动性似乎有助于区分益生菌和致病菌株。虽然目前的发现不一定适用于所有益生菌，但它们提供了新的分子见解，以指导营养基因组学、临床医学和食品工程的未来研究，以寻找区分致病菌和益生菌的新方法。