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A genomic view of food-related and probiotic Enterococcus strains
The study of enterococcal genomes has grown considerably in recent years. While special attention is paid to comparative genomic analysis among clinical relevant isolates, in this study we performed an exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential to be...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381348/ https://www.ncbi.nlm.nih.gov/pubmed/27773878 http://dx.doi.org/10.1093/dnares/dsw043 |
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author | Bonacina, Julieta Suárez, Nadia Hormigo, Ricardo Fadda, Silvina Lechner, Marcus Saavedra, Lucila |
author_facet | Bonacina, Julieta Suárez, Nadia Hormigo, Ricardo Fadda, Silvina Lechner, Marcus Saavedra, Lucila |
author_sort | Bonacina, Julieta |
collection | PubMed |
description | The study of enterococcal genomes has grown considerably in recent years. While special attention is paid to comparative genomic analysis among clinical relevant isolates, in this study we performed an exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential to be used as probiotics. Beyond common genetic features, we especially aimed to identify those that are specific to enterococcal strains isolated from a certain food-related source as well as features present in a species-specific manner. Thus, the genome sequences of 25 Enterococcus strains, from 7 different species, were examined and compared. Their phylogenetic relationship was reconstructed based on orthologous proteins and whole genomes. Likewise, markers associated with a successful colonization (bacteriocin genes and genomic islands) and genome plasticity (phages and clustered regularly interspaced short palindromic repeats) were investigated for lifestyle specific genetic features. At the same time, a search for antibiotic resistance genes was carried out, since they are of big concern in the food industry. Finally, it was possible to locate 1617 FIGfam families as a core proteome universally present among the genera and to determine that most of the accessory genes code for hypothetical proteins, providing reasonable hints to support their functional characterization. |
format | Online Article Text |
id | pubmed-5381348 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-53813482017-04-10 A genomic view of food-related and probiotic Enterococcus strains Bonacina, Julieta Suárez, Nadia Hormigo, Ricardo Fadda, Silvina Lechner, Marcus Saavedra, Lucila DNA Res Full Papers The study of enterococcal genomes has grown considerably in recent years. While special attention is paid to comparative genomic analysis among clinical relevant isolates, in this study we performed an exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential to be used as probiotics. Beyond common genetic features, we especially aimed to identify those that are specific to enterococcal strains isolated from a certain food-related source as well as features present in a species-specific manner. Thus, the genome sequences of 25 Enterococcus strains, from 7 different species, were examined and compared. Their phylogenetic relationship was reconstructed based on orthologous proteins and whole genomes. Likewise, markers associated with a successful colonization (bacteriocin genes and genomic islands) and genome plasticity (phages and clustered regularly interspaced short palindromic repeats) were investigated for lifestyle specific genetic features. At the same time, a search for antibiotic resistance genes was carried out, since they are of big concern in the food industry. Finally, it was possible to locate 1617 FIGfam families as a core proteome universally present among the genera and to determine that most of the accessory genes code for hypothetical proteins, providing reasonable hints to support their functional characterization. Oxford University Press 2017-02 2016-10-23 /pmc/articles/PMC5381348/ /pubmed/27773878 http://dx.doi.org/10.1093/dnares/dsw043 Text en © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Full Papers Bonacina, Julieta Suárez, Nadia Hormigo, Ricardo Fadda, Silvina Lechner, Marcus Saavedra, Lucila A genomic view of food-related and probiotic Enterococcus strains |
title | A genomic view of food-related and probiotic Enterococcus strains |
title_full | A genomic view of food-related and probiotic Enterococcus strains |
title_fullStr | A genomic view of food-related and probiotic Enterococcus strains |
title_full_unstemmed | A genomic view of food-related and probiotic Enterococcus strains |
title_short | A genomic view of food-related and probiotic Enterococcus strains |
title_sort | genomic view of food-related and probiotic enterococcus strains |
topic | Full Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381348/ https://www.ncbi.nlm.nih.gov/pubmed/27773878 http://dx.doi.org/10.1093/dnares/dsw043 |
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