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PHERI—Phage Host ExploRation Pipeline

Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly lik...

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Autores principales: Baláž, Andrej, Kajsik, Michal, Budiš, Jaroslav, Szemes, Tomáš, Turňa, Ján
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10305434/
https://www.ncbi.nlm.nih.gov/pubmed/37374901
http://dx.doi.org/10.3390/microorganisms11061398
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author Baláž, Andrej
Kajsik, Michal
Budiš, Jaroslav
Szemes, Tomáš
Turňa, Ján
author_facet Baláž, Andrej
Kajsik, Michal
Budiš, Jaroslav
Szemes, Tomáš
Turňa, Ján
author_sort Baláž, Andrej
collection PubMed
description Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages’ host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm-based tool called PHERI. PHERI predicts the suitable bacterial host genus for the purification of individual viruses from different samples. In addition, it can identify and highlight protein sequences that are important for host selection.
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spelling pubmed-103054342023-06-29 PHERI—Phage Host ExploRation Pipeline Baláž, Andrej Kajsik, Michal Budiš, Jaroslav Szemes, Tomáš Turňa, Ján Microorganisms Article Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages’ host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm-based tool called PHERI. PHERI predicts the suitable bacterial host genus for the purification of individual viruses from different samples. In addition, it can identify and highlight protein sequences that are important for host selection. MDPI 2023-05-26 /pmc/articles/PMC10305434/ /pubmed/37374901 http://dx.doi.org/10.3390/microorganisms11061398 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Baláž, Andrej
Kajsik, Michal
Budiš, Jaroslav
Szemes, Tomáš
Turňa, Ján
PHERI—Phage Host ExploRation Pipeline
title PHERI—Phage Host ExploRation Pipeline
title_full PHERI—Phage Host ExploRation Pipeline
title_fullStr PHERI—Phage Host ExploRation Pipeline
title_full_unstemmed PHERI—Phage Host ExploRation Pipeline
title_short PHERI—Phage Host ExploRation Pipeline
title_sort pheri—phage host exploration pipeline
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10305434/
https://www.ncbi.nlm.nih.gov/pubmed/37374901
http://dx.doi.org/10.3390/microorganisms11061398
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