Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case

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Bacillus pumilus group strains have been studied due their agronomic, biotechnological or pharmaceutical potential. Classifying strains of this taxonomic group at species level is a challenging procedure since it is composed of seven species that share among them over 99.5% of 16S rRNA gene identity...

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Autores principales: Espariz, Martín, Zuljan, Federico A., Esteban, Luis, Magni, Christian
Formato: other Producción en Tecnología publishedVersion
Lenguaje:Inglés
Publicado: 2021
Materias:
Microbiology
Genetics
Evolutionary Biology
Bacterial genomics
Principal component analysis
Phylogenetics
Bacillus pumilus
https://purl.org/becyt/ford/1.6
Ciencias biológicas
Acceso en línea:https://doi.org/10.1371/journal.pone.0163098
http://hdl.handle.net/2133/20073
http://hdl.handle.net/2133/20073
Aporte de:
Repositorio Hipermedial de la Universidad Nacional de Rosario (UNR) de Universidad Nacional de Rosario
id I15-R121-2133-20073
record_format dspace
institution Universidad Nacional de Rosario
institution_str I-15
repository_str R-121
collection Repositorio Hipermedial de la Universidad Nacional de Rosario (UNR)
language Inglés
orig_language_str_mv eng
topic Microbiology
Genetics
Evolutionary Biology
Bacterial genomics
Principal component analysis
Phylogenetics
Bacillus pumilus
https://purl.org/becyt/ford/1.6
Ciencias biológicas
spellingShingle Microbiology
Genetics
Evolutionary Biology
Bacterial genomics
Principal component analysis
Phylogenetics
Bacillus pumilus
https://purl.org/becyt/ford/1.6
Ciencias biológicas
Espariz, Martín
Zuljan, Federico A.
Esteban, Luis
Magni, Christian
Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case
topic_facet Microbiology
Genetics
Evolutionary Biology
Bacterial genomics
Principal component analysis
Phylogenetics
Bacillus pumilus
https://purl.org/becyt/ford/1.6
Ciencias biológicas
description Bacillus pumilus group strains have been studied due their agronomic, biotechnological or pharmaceutical potential. Classifying strains of this taxonomic group at species level is a challenging procedure since it is composed of seven species that share among them over 99.5% of 16S rRNA gene identity. In this study, first, a whole-genome in silico approach was used to accurately demarcate B. pumilus group strains, as a case of highly phylogenetically related taxa, at the species level. In order to achieve that and consequently to validate or correct taxonomic identities of genomes in public databases, an average nucleotide identity correlation, a core-based phylogenomic and a gene function repertory analyses were performed. Eventually, more than 50% such genomes were found to be misclassified. Hierarchical clustering of gene functional repertoires was also used to infer ecotypes among B. pumilus group species. Furthermore, for the first time the machine-learning algorithm Random Forest was used to rank genes in order of their importance for species classification. We found that ybbP, a gene involved in the synthesis of cyclic di-AMP, was the most important gene for accurately predicting species identity among B. pumilus group strains. Finally, principal component analysis was used to classify strains based on the distances between their ybbP genes. The methodologies described could be utilized more broadly to identify other highly phylogenetically related species in metagenomic or epidemiological assessments.
format other
Producción en Tecnología
publishedVersion
author Espariz, Martín
Zuljan, Federico A.
Esteban, Luis
Magni, Christian
author_facet Espariz, Martín
Zuljan, Federico A.
Esteban, Luis
Magni, Christian
author_sort Espariz, Martín
title Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case
title_short Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case
title_full Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case
title_fullStr Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case
title_full_unstemmed Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case
title_sort taxonomic identity resolution of highly phylogenetically related strains and selection of phylogenetic markers by using genome-scale methods: the bacillus pumilus group case
publishDate 2021
url https://doi.org/10.1371/journal.pone.0163098
http://hdl.handle.net/2133/20073
http://hdl.handle.net/2133/20073
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