title: Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets.
abstract: 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.
authors.affiliation: ESEI-Department of Computer Science, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, Ourense, Spain.|Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Asturias, Spain.
authors.forename: Aitor
authors.initials: A
authors.lastname: Blanco-Míguez
authors.affiliation: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, Braunschweig, Germany.
authors.forename: Jan P
authors.identifier: 0000-0001-9105-9814
authors.initials: JP
authors.lastname: Meier-Kolthoff
authors.affiliation: ESEI-Department of Computer Science, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, Ourense, Spain.
authors.forename: Alberto
authors.identifier: 0000-0002-9949-1705
authors.initials: A
authors.lastname: Gutiérrez-Jácome
authors.affiliation: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, Braunschweig, Germany.
authors.forename: Markus
authors.identifier: 0000-0002-5144-6200
authors.initials: M
authors.lastname: Göker
authors.affiliation: ESEI-Department of Computer Science, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, Ourense, Spain.
authors.forename: Florentino
authors.identifier: 0000-0002-3943-8013
authors.initials: F
authors.lastname: Fdez-Riverola
authors.affiliation: Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Asturias, Spain.
authors.forename: Borja
authors.initials: B
authors.lastname: Sánchez
authors.affiliation: ESEI-Department of Computer Science, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, Ourense, Spain.|CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal.
authors.forename: Anália
authors.identifier: 0000-0001-8401-5362
authors.initials: A
authors.lastname: Lourenço
mesh_terms: D001407:Bacillus / Q000145:classification* / Q000235:genetics; D001426:Bacterial Proteins / Q000145:classification* / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D030562:Databases, Protein; D008957:Models, Genetic; D010455:Peptides / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D020543:Proteome / Q000145:classification* / Q000235:genetics; D040901:Proteomics / Q000379:methods*; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D010455:Peptides; D020543:Proteome