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Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening

  • Genomics, transcriptomics, proteomics
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Enterococcus spp. are present in the native microbiota of many traditional fermented foods. Their ability to produce antibacterial compounds, mainly against Listeria monocytogenes, has raised interest recently. However, there is scarce information about their proteolytic and lipolytic potential, and their biotechnological application is currently limited because enterococcal strains have been related to nosocomial infections. In this work, next-generation sequencing and optimised bioinformatic pipelines were used to annotate the genomes of two Enterococcus strains—one E. faecium and one E. faecalis—isolated from the Mexican artisanal ripened Cotija cheese. A battery of genes involved in their proteolytic system was annotated. Genes coding for lipases, esterases and other enzymes whose final products contribute to cheese aroma and flavour were identified as well. As for the production of antibacterial compounds, several peptidoglycan hydrolase- and bacteriocin-coding genes were identified in both genomes experimentally and by bioinformatic analyses. E. faecalis showed resistance to aminoglycosides and E. faecium to aminoglycosides and macrolides, as predicted by the genome functional annotation. No pathogenicity islands were found in any of the strains, although traits such as the ability of biofilm formation and cell aggregation were observed. Finally, a comparative genomic analysis was able to discriminate between the food strains isolated and nosocomial strains. In summary, pathogenic strains are resistant to a wide range of antibiotics and contain virulence factors that cause host damage; in contrast, food strains display less antibiotic resistance, include genes that encode class II bacteriocins and express virulence factors associated with host colonisation rather than invasion.

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This work was supported by UNAM-PAPIIT IN222115 and IN222717 grants. We thank Alejandra Escobar-Zepeda, Jérôme Verleyen and Veronica Jiménez-Jacinto for their support in bioinformatic analyses, which were performed in the ‘Unidad de Secuenciación Masiva y Bioinformática’ at the ‘Laboratorio Nacional de Apoyo Tecnológico a las Ciencias Genómicas’, CONACyT #260481, Instituto de Biotecnología/UNAM; to Dr. Edith Ponce Alquicira, from Universidad Autónoma Metropolitana-Iztapalapa (UAM-I) for providing the Enterococcus faecium strain MXVK29 and Enterococcus faecalis NCIMB-700585; and to Dr. Carlos Eslava-Campos, for providing mammal cell lines and for his assistance in performing the adherence experiments. M.O.-G. was granted a doctoral fellowship from Consejo Nacional de Ciencia y Tecnología (CONACyT). We also thank Dr. Romina Rodríguez Sanoja and Dr. Rosa María Gutierrez for their valuable comments and support during the development of this project. María Elena Sánchez-Salazar edited the English manuscript.

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Correspondence to Maricarmen Quirasco Baruch.

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This manuscript is in compliance with ethical standards. This manuscript does not contain any studies with human participants or animals performed by any of the authors.

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The authors declare that they have no conflict of interest.

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Olvera-García, M., Sanchez-Flores, A. & Quirasco Baruch, M. Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening. Appl Microbiol Biotechnol 102, 2251–2267 (2018).

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