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INfrastructure for a PHAge REference Database : identification of large-scale biases in the current collection of cultured phage genomes
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Cook, Ryan, Brown, Nathan, Redgwell, Tamsin, Rihtman, Branko, Barnes, Megan, Clokie, Martha, Stekel, Dov J., Hobman, Jon, Jones, Michael A. and Millard, Andrew (2021) INfrastructure for a PHAge REference Database : identification of large-scale biases in the current collection of cultured phage genomes. PHAGE : Therapy, Applications, and Research, 2 (4). pp. 214-223. doi:10.1089/phage.2021.0007 ISSN 2641-6530.
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Official URL: https://doi.org/10.1089/phage.2021.0007
Abstract
Background: With advances in sequencing technology and decreasing costs, the number of phage genomes that have been sequenced has increased markedly in the past decade.
Materials and Methods: We developed an automated retrieval and analysis system for phage genomes (https://github.com/RyanCook94/inphared) to produce the INfrastructure for a PHAge REference Database (INPHARED) of phage genomes and associated metadata.
Results: As of January 2021, 14,244 complete phage genomes have been sequenced. The INPHARED data set is dominated by phages that infect a small number of bacterial genera, with 75% of phages isolated on only 30 bacterial genera. There is further bias, with significantly more lytic phage genomes (∼70%) than temperate (∼30%) within our database. Collectively, this results in ∼54% of temperate phage genomes originating from just three host genera. With much debate on the carriage of antibiotic resistance genes and their potential safety in phage therapy, we searched for putative antibiotic resistance genes. Frequency of antibiotic resistance gene carriage was found to be higher in temperate phages than in lytic phages and again varied with host.
Conclusions: Given the bias of currently sequenced phage genomes, we suggest to fully understand phage diversity, efforts should be made to isolate and sequence a larger number of phages, in particular temperate phages, from a greater diversity of hosts.
Item Type: | Journal Article | ||||||||
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||
SWORD Depositor: | Library Publications Router | ||||||||
Journal or Publication Title: | PHAGE : Therapy, Applications, and Research | ||||||||
Publisher: | Mary Ann Liebert | ||||||||
ISSN: | 2641-6530 | ||||||||
Official Date: | 16 December 2021 | ||||||||
Dates: |
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Volume: | 2 | ||||||||
Number: | 4 | ||||||||
Page Range: | pp. 214-223 | ||||||||
DOI: | 10.1089/phage.2021.0007 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Re-use Statement: | This is the accepted version of the following article: Ryan Cook, Nathan Brown, Tamsin Redgwell, Branko Rihtman, Megan Barnes, Martha Clokie, Dov J. Stekel, Jon Hobman, Michael A. Jones, and Andrew Millard.PHAGE.Dec 2021.214-223.http://doi.org/10.1089/phage.2021.0007, which has now been formally published in final form at PHAGE : Therapy, Applications, and Research at https://doi.org/10.1089/phage.2021.0007. This original submission version of the article may be used for non-commercial purposes in accordance with the Mary Ann Liebert, Inc., publishers’ self-archiving terms and conditions. | ||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||
Date of first compliant deposit: | 14 July 2022 | ||||||||
Date of first compliant Open Access: | 16 December 2022 |
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