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Genomic insights into the taxonomic status of the Bacillus cereus group

The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clear...

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Autores principales: Liu, Yang, Lai, Qiliang, Göker, Markus, Meier-Kolthoff, Jan P., Wang, Meng, Sun, Yamin, Wang, Lei, Shao, Zongze
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571650/
https://www.ncbi.nlm.nih.gov/pubmed/26373441
http://dx.doi.org/10.1038/srep14082
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author Liu, Yang
Lai, Qiliang
Göker, Markus
Meier-Kolthoff, Jan P.
Wang, Meng
Sun, Yamin
Wang, Lei
Shao, Zongze
author_facet Liu, Yang
Lai, Qiliang
Göker, Markus
Meier-Kolthoff, Jan P.
Wang, Meng
Sun, Yamin
Wang, Lei
Shao, Zongze
author_sort Liu, Yang
collection PubMed
description The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clearly separated 224 strains into 30 clusters, representing eleven known, partially merged species and accordingly 19–20 putative novel species. Additionally, 16S rRNA gene analysis, a novel variant of multi-locus sequence analysis (nMLSA) and screening of virulence genes were performed. The 16S rRNA gene sequence was not sufficient to differentiate the bacteria within this group due to its high conservation. The nMLSA results were consistent with GBDP. Moreover, a fast typing method was proposed using the pycA gene, and where necessary, the ccpA gene. The pXO plasmids and cry genes were widely distributed, suggesting little correlation with the phylogenetic positions of the host bacteria. This might explain why classifications based on virulence characteristics proved unsatisfactory in the past. In summary, this is the first large-scale and systematic study of the taxonomic status of the bacteria within the B. cereus group using whole-genome sequences, and is likely to contribute to further insights into their pathogenicity, phylogeny and adaptation to diverse environments.
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spelling pubmed-45716502015-09-28 Genomic insights into the taxonomic status of the Bacillus cereus group Liu, Yang Lai, Qiliang Göker, Markus Meier-Kolthoff, Jan P. Wang, Meng Sun, Yamin Wang, Lei Shao, Zongze Sci Rep Article The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clearly separated 224 strains into 30 clusters, representing eleven known, partially merged species and accordingly 19–20 putative novel species. Additionally, 16S rRNA gene analysis, a novel variant of multi-locus sequence analysis (nMLSA) and screening of virulence genes were performed. The 16S rRNA gene sequence was not sufficient to differentiate the bacteria within this group due to its high conservation. The nMLSA results were consistent with GBDP. Moreover, a fast typing method was proposed using the pycA gene, and where necessary, the ccpA gene. The pXO plasmids and cry genes were widely distributed, suggesting little correlation with the phylogenetic positions of the host bacteria. This might explain why classifications based on virulence characteristics proved unsatisfactory in the past. In summary, this is the first large-scale and systematic study of the taxonomic status of the bacteria within the B. cereus group using whole-genome sequences, and is likely to contribute to further insights into their pathogenicity, phylogeny and adaptation to diverse environments. Nature Publishing Group 2015-09-16 /pmc/articles/PMC4571650/ /pubmed/26373441 http://dx.doi.org/10.1038/srep14082 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Liu, Yang
Lai, Qiliang
Göker, Markus
Meier-Kolthoff, Jan P.
Wang, Meng
Sun, Yamin
Wang, Lei
Shao, Zongze
Genomic insights into the taxonomic status of the Bacillus cereus group
title Genomic insights into the taxonomic status of the Bacillus cereus group
title_full Genomic insights into the taxonomic status of the Bacillus cereus group
title_fullStr Genomic insights into the taxonomic status of the Bacillus cereus group
title_full_unstemmed Genomic insights into the taxonomic status of the Bacillus cereus group
title_short Genomic insights into the taxonomic status of the Bacillus cereus group
title_sort genomic insights into the taxonomic status of the bacillus cereus group
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571650/
https://www.ncbi.nlm.nih.gov/pubmed/26373441
http://dx.doi.org/10.1038/srep14082
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