Isolation and characterization of <i>Yersinia</i> phage fMtkYen3-01

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Abstract

Yersinia enterocolitica causes yersiniosis, the third most common gastrointestinal infection in humans throughout Europe. The emergence of multidrug resistance and the lack of effective new antibiotics have drawn attention to phage therapy as a treatment option. Here, we report the complete genome sequence of phage fMtkYen3-01, which infects Y. enterocolitica serotype O:3 strains. This phage has a genome 40,415 bp in length with 45.1% GC content and 49 predicted genes. fMtkYen3-01 infected 9.5% of the 42 Y. enterocolitica strains tested and showed stability at 25–40 °C, as well as pH 5.0–10.0. These results suggest the therapeutic potential of this phage.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00705-024-06149-6.

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The RAST Server: Rapid Annotations using Subsystems Technology

Ramy Aziz, Daniela Bartels, Aaron A. Best … (2008)

Background The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. Description We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12–24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. Conclusion By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.

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PHASTER: a better, faster version of the PHAST phage search tool

David L. Arndt, Jason Grant, Ana Marcu … (2016)

PHASTER (PHAge Search Tool – Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. In particular, PHASTER is now 4.3× faster than PHAST when analyzing a typical bacterial genome. More specifically, software optimizations have made the backend of PHASTER 2.7X faster than PHAST, while the addition of 80 CPUs to the PHASTER compute cluster are responsible for the remaining speed-up. PHASTER can now process a typical bacterial genome in 3 min from the raw sequence alone, or in 1.5 min when given a pre-annotated GenBank file. A number of other optimizations have also been implemented, including automated algorithms to reduce the size and redundancy of PHASTER's databases, improvements in handling multiple (metagenomic) queries and higher user traffic, along with the ability to perform automated look-ups against 14 000 previously PHAST/PHASTER annotated bacterial genomes (which can lead to complete phage annotations in seconds as opposed to minutes). PHASTER's web interface has also been entirely rewritten. A new graphical genome browser has been added, gene/genome visualization tools have been improved, and the graphical interface is now more modern, robust and user-friendly. PHASTER is available online at www.phaster.ca.

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NCBI BLAST: a better web interface

Mark Johnson, Irena Zaretskaya, Yan Raytselis … (2008)

Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast, at the NCBI website has recently been reengineered to improve usability and performance. Key new features include simplified search forms, improved navigation, a list of recent BLAST results, saved search strategies and a documentation directory. Here, we describe the BLAST web application's new features, explain design decisions and outline plans for future improvement.

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Author and article information

Contributors

Lotta-Riina Sundberg:

ORCID: http://orcid.org/0000-0003-3510-4398

lotta-riina.sundberg@jyu.fi

Journal

Journal ID (nlm-ta): Arch Virol

Journal ID (iso-abbrev): Arch Virol

Title: Archives of Virology

Publisher: Springer Vienna (Vienna )

ISSN (Print): 0304-8608

ISSN (Electronic): 1432-8798

Publication date (Electronic): 19 October 2024

Publication date PMC-release: 19 October 2024

Publication date (Print): 2024

Volume: 169

Issue: 11

Electronic Location Identifier: 226

Affiliations

[1 ]Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, ( https://ror.org/05n3dz165) Jyväskylä, Finland

[2 ]Human Microbiome Research Program, Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, ( https://ror.org/040af2s02) Helsinki, Finland

[3 ] Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University, ( https://ror.org/05fd1hd85) Tbilisi, Georgia

Author notes

Handling Editor: Handling Editor T. K. Frey.

Author information

Sophia Goladze http://orcid.org/0000-0002-1316-6996

Sheetal Patpatia http://orcid.org/0000-0002-7206-5394

Henni Tuomala http://orcid.org/0000-0001-7404-7723

Matti Ylänne http://orcid.org/0000-0003-0832-6913

Nino Gachechiladze http://orcid.org/0009-0007-3327-6563

Daniel de Oliveira Patricio http://orcid.org/0000-0001-8318-3778

Mikael Skurnik http://orcid.org/0000-0001-8791-9260

Lotta-Riina Sundberg http://orcid.org/0000-0003-3510-4398

Article

Publisher ID: 6149

DOI: 10.1007/s00705-024-06149-6

PMC ID: 11490452

PubMed ID: 39425798

SO-VID: ec37c01e-0f70-4e3d-a24c-e72c3be21f5c

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 15 May 2024

Date accepted : 29 August 2024

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100004801, Shota Rustaveli National Science Foundation;

Award ID: PHDF-21-2176

Award Recipient : Sophia Goladze

Funded by: FundRef http://dx.doi.org/10.13039/501100011842, Opetushallitus;

Funded by: Research Council of Finland

Award ID: #346772

Award Recipient : Lotta-Riina Sundberg

Funded by: University of Jyväskylä (JYU)

Open Access :

Open Access funding provided by University of Jyväskylä (JYU).

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ScienceOpen disciplines: Microbiology & Virology

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ScienceOpen disciplines: Microbiology & Virology

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Isolation and characterization of Yersinia phage fMtkYen3-01

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Abstract

Supplementary Information

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Microbiology Society

Most cited references 25

The RAST Server: Rapid Annotations using Subsystems Technology

PHASTER: a better, faster version of the PHAST phage search tool

NCBI BLAST: a better web interface

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