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Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets
Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5198984/ https://www.ncbi.nlm.nih.gov/pubmed/28033346 http://dx.doi.org/10.1371/journal.pcbi.1005271 |
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author | Blanco-Míguez, Aitor Meier-Kolthoff, Jan P. Gutiérrez-Jácome, Alberto Göker, Markus Fdez-Riverola, Florentino Sánchez, Borja Lourenço, Anália |
author_facet | Blanco-Míguez, Aitor Meier-Kolthoff, Jan P. Gutiérrez-Jácome, Alberto Göker, Markus Fdez-Riverola, Florentino Sánchez, Borja Lourenço, Anália |
author_sort | Blanco-Míguez, Aitor |
collection | PubMed |
description | Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP) method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future. |
format | Online Article Text |
id | pubmed-5198984 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-51989842017-01-19 Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets Blanco-Míguez, Aitor Meier-Kolthoff, Jan P. Gutiérrez-Jácome, Alberto Göker, Markus Fdez-Riverola, Florentino Sánchez, Borja Lourenço, Anália PLoS Comput Biol Research Article Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP) method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future. Public Library of Science 2016-12-29 /pmc/articles/PMC5198984/ /pubmed/28033346 http://dx.doi.org/10.1371/journal.pcbi.1005271 Text en © 2016 Blanco-Míguez et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Blanco-Míguez, Aitor Meier-Kolthoff, Jan P. Gutiérrez-Jácome, Alberto Göker, Markus Fdez-Riverola, Florentino Sánchez, Borja Lourenço, Anália Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets |
title | Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets |
title_full | Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets |
title_fullStr | Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets |
title_full_unstemmed | Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets |
title_short | Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets |
title_sort | improving phylogeny reconstruction at the strain level using peptidome datasets |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5198984/ https://www.ncbi.nlm.nih.gov/pubmed/28033346 http://dx.doi.org/10.1371/journal.pcbi.1005271 |
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