Rapid Proteomic Characterization of Bacteriocin-Producing Enterococcus faecium Strains from Foodstuffs

Abstract

Enterococcus belongs to a group of microorganisms known as lactic acid bacteria (LAB), which constitute a broad heterogeneous group of generally food-grade microorganisms historically used in food preservation. Enterococci live as commensals of the gastrointestinal tract of warm-blooded animals, although they also are present in food of animal origin (milk, cheese, fermented sausages), vegetables, and plant materials because of their ability to survive heat treatments and adverse environmental conditions. The biotechnological traits of enterococci can be applied in the food industry; however, the emergence of enterococci as a cause of nosocomial infections makes their food status uncertain. Recent advances in high-throughput sequencing allow the subtyping of bacterial pathogens, but it cannot reflect the temporal dynamics and functional activities of microbiomes or bacterial isolates. Moreover, genetic analysis is based on sequence homologies, inferring functions from databases. Here, we used an end-to-end proteomic workflow to rapidly characterize two bacteriocin-producing Enterococcus faecium (Efm) strains. The proteome analysis was performed with liquid chromatography coupled to a trapped ion mobility spectrometry-time-of-flight mass spectrometry instrument (TimsTOF) for high-throughput and high-resolution characterization of bacterial proteins. Thus, we identified almost half of the proteins predicted in the bacterial genomes (>1100 unique proteins per isolate), including quantifying proteins conferring resistance to antibiotics, heavy metals, virulence factors, and bacteriocins. The obtained proteomes were annotated according to function, resulting in 22 complete KEGG metabolic pathway modules for both strains. The workflow used here successfully characterized these bacterial isolates and showed great promise for determining and optimizing the bioengineering and biotechnology properties of other LAB strains in the food industry.

Assessment of the Safety and Probiotic Properties of Enterococcus faecium B13 Isolated from Fermented Chili

“…Enterococcus was widely present in traditional fermented foods, such as milk [1], meat [2], cheese [3], fermented sausage [4], fermented vegetables [5,6], soy milk [7], and other foods [6,8]. Because of its strong proteolytic and esterolytic properties, strong tolerance, and yielding acid, Enterococcus is even intentionally added to the process of food fermentation [9,10].…”

Isolation and Characterization of Bacteriocin Producing <em>Enterococcus species </em>from Ethiopian Traditional Fermented Food and Beverages

“…;Gaaloul et al (2015);Hosseini et al (2009);Quintela-Baluja et al (2022) andSilva et al (2018) large numbers of bacteriocin producing Enterococcus faecium were isolated from raw milk and fermented food origin and various food stuff and demonstrated potential bacteriocin producing…”

Food Safety—Transcriptomics and Proteomics

“…The manuscript published by Quintela-Baluja et al, "Rapid proteomic characterization of bacteriocin-producing Enterococcus faecium strains from foodstuffs", presents the characterization of two bacteriocin-producing Enterococcus faecium strains using a liquid chromatography instrument coupled to a trapped ion mobility spectrometry-time-of-flight mass spectrometry instrument (TimsTOF) [35]. Enterococcus faecium is a lactic acid bacteria (LAB) belonging to the genus Enterococcus [36].…”