Dataset Information

Detailed sub-proteome analysis of a cheese-isolated Enterococcus faecalis, provide insights into probiotic value and food safety

ABSTRACT: Enterococci are normal inhabitants of the gastrointestinal tracts of humans and animals and thanks to their capability to tolerate different environmental conditions and their high rates of gene transfer, they are able to colonize various ecological niches, as food matrices. Enterococcus faecalis bacteria are defined as “border line” microorganisms. From one side they are used as food starters, bio-control agents and probiotics to improve human or animal health. From the other side, in the last 2 two decades enterococci have emerged as important nosocomial pathogens, because bearing high-level of resistance to antibiotics and several putative virulence factors. In this study the proteomic (LC-MS/MS) and the phenotypic characterization (enzymatic methods) of three strains of E. faecalis with different origin were performed in order to investigate the differences and/or similarities occurring between pathogenic and health promoting bacteria. The E. faecalis D27 isolated as cheese contaminant, E. faecalis Symbioflor 1 a probiotic strain and E. faecalis UW3114 a clinical isolate involved in urinary tract infection were the objects of the study. The comparison of cytosolic protein expression profiles of the three strains, highlighted statistically significant changes in the abundance of proteins mainly involved in specific metabolic pathways, nutrient transport, stress response and cell wall modulation. Moreover, especially in the food contaminant and the clinical isolate, several proteins with potential pathogenic implications were found. The analysis of the extracellular proteome provided interesting results concerning proteins involved in bacterial communication, such as pheromones and conjugative elements and also proteins able to interact with human components.

INSTRUMENT(S): Synapt MS

ORGANISM(S): Enterococcus Faecalis Str. Symbioflor 1

SUBMITTER: Daniela Zuehlke

LAB HEAD: Kathrin Riedel

PROVIDER: PXD011701 | Pride | 2019-08-30

REPOSITORIES: Pride

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Publications

Detailed Soluble Proteome Analyses of a Dairy-Isolated <i>Enterococcus faecalis</i>: A Possible Approach to Assess Food Safety and Potential Probiotic Value.

Cirrincione Simona S Neumann Bernd B Zühlke Daniela D Riedel Katharina K Pessione Enrica E

Frontiers in nutrition 20190517

Enterococci are common inhabitants of the gastrointestinal tracts of humans and animals and thanks to their capability to tolerate different environmental conditions and their high rates of gene transfer, they are able to colonize various ecological niches, as food matrices. <i>Enterococcus faecalis</i> bacteria are defined as controversial microorganisms. From one side they are used as food starters, bio-control agents and probiotics to improve human or animal health. From the other side, in th ...[more]

PMID: 31157229

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Project description:Enterococci are normal inhabitants of the gastrointestinal tracts of humans and animals and thanks to their capability to tolerate different environmental conditions and their high rates of gene transfer, they are able to colonize various ecological niches, as food matrices. Enterococcus faecalis bacteria are defined as “border line” microorganisms. From one side they are used as food starters, bio-control agents and probiotics to improve human or animal health. From the other side, in the last 2 two decades enterococci have emerged as important nosocomial pathogens, because bearing high-level of resistance to antibiotics and several putative virulence factors. In this study the proteomic (LC-MS/MS) and the phenotypic characterization (enzymatic methods) of three strains of E. faecalis with different origin were performed in order to investigate the differences and/or similarities occurring between pathogenic and health promoting bacteria. The E. faecalis D27 isolated as cheese contaminant, E. faecalis Symbioflor 1 a probiotic strain and E. faecalis UW3114 a clinical isolate involved in urinary tract infection were the objects of the study. The comparison of cytosolic protein expression profiles of the three strains, highlighted statistically significant changes in the abundance of proteins mainly involved in specific metabolic pathways, nutrient transport, stress response and cell wall modulation. Moreover, especially in the food contaminant and the clinical isolate, several proteins with potential pathogenic implications were found. The analysis of the extracellular proteome provided interesting results concerning proteins involved in bacterial communication, such as pheromones and conjugative elements and also proteins able to interact with human components. The phenotypic assays evaluating i) biofilm formation ii) hemolytic activity on blood agar plates iii) protease activity, allowed typing of bacteria in relation to well-known pathogenic traits. The obtained results confirmed the pathogenic profile associated to the clinical isolate as compared to the food contaminant and to the probiotic and allowed to elucidate the risks associated with the poor characterized foodborne E. faecalis D27.

Project description:Teixobactin is the first novel antimicrobial to be discovered in decades and represents a new class of antimicrobials. Teixobactin shows great promise with proven efficacy against multi-drug resistant organisms such as methicillin-resistant S. aureus (MRSA), vancomycin-resistant Enterococci (VRE), and Mycobacterium tuberculosis. VRE infections are notoriously difficult to treat with complex and adaptable cell wall stress response systems, which confer intrinsic resistance to a wide variety of antimicrobials. The aim of this study was to isolate the teixobactin-induced transcriptional response by challenging lab strain Enterococcus faecalis JH2-2 with sub-MIC levels of teixobactin using RNA sequencing. Two cultures of E. faecalis were grown to an OD600 of 0.2 and subsequently split into three to form a total of six cultures (two samples, with three technical replicates each), and grown to an OD600 of 0.5. One set of three cultures were treated with 0.5 ug/ml (0.25 x MIC), and all six cultures were grown for a further 1h. Cells were harvested by centrifugation and stored at -80 degrees C. RNA was extracted using TRIzol-chloroform and RNA samples were run through the RNAeasy Minikit (Qiagen). The Agilent RNA 6000 Nano kit and the Agilent 2100 Bioanalyzer (RIN >8), was used to verify RNA quality as per the manufacturer’s instructions, and RNA concentration was determined using a NanoDrop ND-100 spectrophotometer. Ribosomal RNA was removed from total RNA using Ribo-Zero and cDNA libraries were created using the Illumina TruSeq™ stranded total RNA library prep kit. Sequencing was completed using Illumina MiSeq_v3 generating 150 bp single end reads. Adapter sequences were removed from raw fastq files using Flexbar and reads shorter than 50bp were discarded. Sequence reads from each sample were mapped against the E. faecalis JH2-2 genome (NZ_KI518257.1) using Bowtie to produce a table of raw read counts for JH2-2 genes for each of the replicates. Statistical and principal component analysis were performed using the Bioconductor DESeq package.

Project description:In order to successfully survive in and to colonize the gastrointestinal tract, bacteria need to develop strategies to overcome bile acid stress. The most prominent bile acids are the primary bile acids cholic acid (CA) and chenodeoxycholic acid (CDCA) as well as the secondary bile acid deoxycholic acid (DCA). In this study, we investigated the stress response of E. faecalis and E. faecium to sublethal concentrations of these three bile acids on the proteome level using DIA-MS. As both species showed similar IC50 for DCA and CDCA in growth experiments and both were highly resistant towards CA, we assumed similar changes to their protein expression profiles. Moreover, we investigated proteomic differences of E. faecalis grown under aerobic or microaerophilic conditions. Our findings showed similarities, but also species-specific variations in the response to the different bile acids, which reveal potential differences in the adaptation process. DCA and CDCA had a strong effect on down-expression of proteins involved in translation, transcription and replication in E. faecalis, but to a lesser extent in E. faecium. Proteins commonly significantly altered in their expression in all bile acid treated samples were identified for both species and represent a “general bile acid response”. Among these, ABC-transporters, multi-drug transporters and proteins related to cell wall biogenesis were up-expressed in both species and thus seem to play an essential role in bile acid resistance. Specific for all E. faecalis samples was the up-expression of several subunits of a V-type ATPase and the down-expression of proteins involved in pyruvate-, citrate- and folate metabolism. Most of the differentially expressed proteins were also identified when E. faecalis was incubated with low levels of DCA at microaerophilic conditions in comparison to aerobic conditions, indicating that adaptations to bile acids and to a microaerophilic atmosphere can occur simultaneously.

Dataset Information

Detailed sub-proteome analysis of a cheese-isolated Enterococcus faecalis, provide insights into probiotic value and food safety

Publications

Detailed Soluble Proteome Analyses of a Dairy-Isolated <i>Enterococcus faecalis</i>: A Possible Approach to Assess Food Safety and Potential Probiotic Value.

Similar Datasets

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