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Establishment of a polymerase chain reaction-based method for strain-level management of Enterococcus faecalis EF-2001 using species-specific sequences identified by whole genome sequences

In the development and manufacture of fermented foods, it is crucial to control and manage the bacterial species used in the products. We previously reported a complete genome sequence analysis of the Enterococcus faecalis EF-2001 strain that was used for supplements. By comparing this sequence to t...

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Autores principales: Hamamoto, Hiroshi, Ogasawara, Akihiko Ano, Iwasa, Masahiro, Sekimizu, Kazuhisa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9411961/
https://www.ncbi.nlm.nih.gov/pubmed/36033901
http://dx.doi.org/10.3389/fmicb.2022.959063
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author Hamamoto, Hiroshi
Ogasawara, Akihiko Ano
Iwasa, Masahiro
Sekimizu, Kazuhisa
author_facet Hamamoto, Hiroshi
Ogasawara, Akihiko Ano
Iwasa, Masahiro
Sekimizu, Kazuhisa
author_sort Hamamoto, Hiroshi
collection PubMed
description In the development and manufacture of fermented foods, it is crucial to control and manage the bacterial species used in the products. We previously reported a complete genome sequence analysis of the Enterococcus faecalis EF-2001 strain that was used for supplements. By comparing this sequence to the publicly available complete genome sequence of E. faecalis strains, we were able to identify specific sequences of the EF-2001 strain. We designed primer sets to amplify these specific regions and performed a polymerase chain reaction (PCR). We confirmed that the DNA fragments were specifically amplified in the genome of the EF-2001 strain, but not those of other lactic acid bacteria (LABs) or strains of the same genus. Furthermore, these primers amplified DNA fragments even in genomic DNA extracted from heat-treated bacteria at 121°C and foods containing the EF-2001 strain. These results suggest that this method allows for simple and highly accurate identification of specific fermentation strains, such as LABs at the strain level, which will be useful for controlling the quality of fermented foods.
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spelling pubmed-94119612022-08-27 Establishment of a polymerase chain reaction-based method for strain-level management of Enterococcus faecalis EF-2001 using species-specific sequences identified by whole genome sequences Hamamoto, Hiroshi Ogasawara, Akihiko Ano Iwasa, Masahiro Sekimizu, Kazuhisa Front Microbiol Microbiology In the development and manufacture of fermented foods, it is crucial to control and manage the bacterial species used in the products. We previously reported a complete genome sequence analysis of the Enterococcus faecalis EF-2001 strain that was used for supplements. By comparing this sequence to the publicly available complete genome sequence of E. faecalis strains, we were able to identify specific sequences of the EF-2001 strain. We designed primer sets to amplify these specific regions and performed a polymerase chain reaction (PCR). We confirmed that the DNA fragments were specifically amplified in the genome of the EF-2001 strain, but not those of other lactic acid bacteria (LABs) or strains of the same genus. Furthermore, these primers amplified DNA fragments even in genomic DNA extracted from heat-treated bacteria at 121°C and foods containing the EF-2001 strain. These results suggest that this method allows for simple and highly accurate identification of specific fermentation strains, such as LABs at the strain level, which will be useful for controlling the quality of fermented foods. Frontiers Media S.A. 2022-08-12 /pmc/articles/PMC9411961/ /pubmed/36033901 http://dx.doi.org/10.3389/fmicb.2022.959063 Text en Copyright © 2022 Hamamoto, Ogasawara, Iwasa and Sekimizu. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Hamamoto, Hiroshi
Ogasawara, Akihiko Ano
Iwasa, Masahiro
Sekimizu, Kazuhisa
Establishment of a polymerase chain reaction-based method for strain-level management of Enterococcus faecalis EF-2001 using species-specific sequences identified by whole genome sequences
title Establishment of a polymerase chain reaction-based method for strain-level management of Enterococcus faecalis EF-2001 using species-specific sequences identified by whole genome sequences
title_full Establishment of a polymerase chain reaction-based method for strain-level management of Enterococcus faecalis EF-2001 using species-specific sequences identified by whole genome sequences
title_fullStr Establishment of a polymerase chain reaction-based method for strain-level management of Enterococcus faecalis EF-2001 using species-specific sequences identified by whole genome sequences
title_full_unstemmed Establishment of a polymerase chain reaction-based method for strain-level management of Enterococcus faecalis EF-2001 using species-specific sequences identified by whole genome sequences
title_short Establishment of a polymerase chain reaction-based method for strain-level management of Enterococcus faecalis EF-2001 using species-specific sequences identified by whole genome sequences
title_sort establishment of a polymerase chain reaction-based method for strain-level management of enterococcus faecalis ef-2001 using species-specific sequences identified by whole genome sequences
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9411961/
https://www.ncbi.nlm.nih.gov/pubmed/36033901
http://dx.doi.org/10.3389/fmicb.2022.959063
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