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

Lookup NU author(s): Dr Kelly JoblingORCiD, Professor David GrahamORCiD



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


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 warmblooded 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.

Publication metadata

Author(s): Quintela-Baluja M, Jobling K, Graham DW, Tabraiz S, Shamurad B, Alnakip M, Böhme K, Barros-Velázquez J, Carrera M, Calo-Mata P

Publication type: Article

Publication status: Published

Journal: International Journal of Molecular Biosciences

Year: 2022

Volume: 23

Issue: 22

Print publication date: 02/11/2022

Online publication date: 10/11/2022

Acceptance date: 08/11/2022

Date deposited: 13/11/2022

ISSN (electronic): 1422-0067

Publisher: MDPI


DOI: 10.3390/ijms232213830


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Funder referenceFunder name
UK Engineering and Physical Sciences Research Council