What Differentiates Probiotic from Pathogenic Bacteria? The Genetic Mobility of Enterococcus faecium Offers New Molecular Insights

Abstract

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 pangenome 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.

Pathogenic strains of Shewanella putrefaciens contain plasmids that are absent in the probiotic strain Pdp11

“…O23S ( Uhrynowski, Radlinska & Drewniak, 2019 ). The horizontal mobile genetic element (MGE) products encoded by plasmids could be at the root of the differences between probiotic and pathogenic strains, as has been described for the Enterococcus group ( Santos et al, 2020 ). Therefore, the absence of plasmids in S. putrefaciens strain Pdp11 could underlie its probiotic nature.…”

“…Therefore, different strains from the same species can be pathogenic or beneficial, as has been shown for Escherichia coli ( Sonnenborn & Schulze, 2009 ), Bacillus cereus ( Cui et al, 2019 ) or Vibrio proteolyticus ( Bowden, Bricknell & Preziosi, 2018 ; Medina, Moriñigo & Arijo, 2020 ), among others. In order to consider a microorganism as a good candidate for probiotic, each specific strain must be thoroughly analysed ( Santos et al, 2020 ). A good probiotic must meet a series of essential requirements such as the ability to compete, adhere, persist and survive in the conditions of the intestinal tract ( Ghattargi et al, 2018 ).…”

“…, replication, stable inheritance, mobility) ( Conlan et al, 2014 ; Giess et al, 2016 ). Therefore, plasmid characterization could help to discern whether a microorganism is pathogenic or beneficial ( Santos et al, 2020 ).…”

Cadmium stress triggers significant metabolic reprogramming in Enterococcus faecium CX 2–6

“…E. faecium has been intensively studied as some of its strains are vancomycin-resistant and can cause serious infections in the human gastrointestinal tract, urinary tract, and bloodstream [49] , [50] , [51] , [52] . However, other strains of E. faecium are beneficial probiotics and have been used in fermented dairy food production [53] , [54] , [55] , [56] . A recent study has found that this species has an open pan-genome with different strains containing numerous environment-specific genes [57] , due to their adaptions to various ecological environments.…”

Eficácia Das Enterocinas No Desenvolvimento Do Câncer Colorretal: Uma Análise Experimental

“…As cepas 141v e 137v, sob cadastro no Sistema Nacional de Gestão do Patrimônio Genético e do Conhecimento Tradicional Associado (SISGEN) nº AD77AD8, isoladas do queijo de coalho artesanal de Pernambuco, foram classificadas como Enterococcus faecium com base em identificação molecular (Santos et. al.…”