Genomic and taxonomic evaluation of 38 Treponema prophage sequences

Ridgway, Rachel; Lu, Hanshuo; Blower, Tim R.; Evans, Nicholas James; Ainsworth, Stuart

Abstract

Background: Despite Spirochetales being a ubiquitous and medically important order of bacteria infecting both humans and animals, there is extremely limited information regarding their bacteriophages. Of the genus Treponema, there is just a single reported characterised prophage. Results: We applied a bioinformatic approach on 24 previously published Treponema genomes to identify and characterise putative treponemal prophages. Thirteen of the genomes did not contain any detectable prophage regions. The remaining eleven contained 38 prophage sequences, with between one and eight putative prophages in each bacterial genome. The prophage regions ranged from 12.4 to 75.1 kb, with between 27 and 171 protein coding sequences. Phylogenetic analysis revealed that 24 of the prophages formed three distinct sequence clusters, identifying putative myoviral and siphoviral morphology. ViPTree analysis demonstrated that the identified sequences were novel when compared to known double stranded DNA bacteriophage genomes. Conclusions: In this study, we have started to address the knowledge gap on treponeme bacteriophages by characterising 38 prophage sequences in 24 treponeme genomes. Using bioinformatic approaches, we have been able to identify and compare the prophage-like elements with respect to other bacteriophages, their gene content, and their potential to be a functional and inducible bacteriophage, which in turn can help focus our attention on specific prophages to investigate further.

Citation

Ridgway, R., Lu, H., Blower, T. R., Evans, N. J., & Ainsworth, S. (2024). Genomic and taxonomic evaluation of 38 Treponema prophage sequences. BMC Genomics, 25(1), Article 549. https://doi.org/10.1186/s12864-024-10461-5

• Journal Article Type: Article
• Acceptance Date: May 28, 2024
• Online Publication Date: Jun 1, 2024
• Publication Date: Jun 1, 2024
• Deposit Date: Jun 4, 2024
• Publicly Available Date: Jun 4, 2024
• Journal: BMC Genomics
• Electronic ISSN: 1471-2164
• Publisher: BioMed Central
• Peer Reviewed: Peer Reviewed
• Volume: 25
• Issue: 1
• Article Number: 549
• DOI: https://doi.org/10.1186/s12864-024-10461-5
• Keywords: Treponema, Treponema phages, Prophages, Bioinformatics, Genomic analysis, Bacteriophages, Comparative genomics
• Public URL: https://durham-repository.worktribe.com/output/2473062