Taxonomy and diversity of Caudoviricetes viruses
| dc.contributor.advisor | Shkoporov, Andrey | |
| dc.contributor.advisor | Hill, Colin | |
| dc.contributor.author | Smith, Linda | |
| dc.contributor.funder | Research Ireland | |
| dc.date.accessioned | 2026-09-23T15:15:55Z | |
| dc.date.available | 2026-09-23T15:15:55Z | |
| dc.date.issued | 2026-04-28 | |
| dc.date.submitted | 2026-04-28 | |
| dc.description.abstract | Viruses of the class Caudoviricetes are the most abundant and diverse biological entities on Earth, infecting bacteria and archaea across all known ecosystems. These tailed double-stranded DNA viruses exhibit extraordinary genetic and morphological diversity, occupy broad host ranges, and play central roles in shaping microbial community structure, nutrient cycling, and ecosystem function in environments ranging from the human gut and oceans to terrestrial soils. Historically, viral diversity has been investigated largely within ecosystem-specific contexts, with independent research efforts focusing on dominant phage groups in particular environments, leaving the evolutionary relatedness between these lineages—and the true extent of global Caudoviricetes diversity—unresolved. Despite their ubiquity and ecological importance, the taxonomy of Caudoviricetes has remained difficult to establish due to extensive genome mosaicism, frequent horizontal gene transfer, and the rapid evolution of nucleotide and amino acid sequences, which together obscure evolutionary relationships and limit the resolution of sequence-based classification approaches. As a result, bacteriophage genomes are best viewed as networks of modular genetic elements whose evolutionary histories cannot be reliably captured by single-gene phylogenies, but instead require large-scale, genome-wide comparative analyses. This thesis addresses these challenges by developing and applying a structure-informed, whole-proteome framework for viral classification. The work begins with an in-depth examination of Crassvirales, a highly prevalent yet taxonomically narrow order within the class of Caudoviricetes, using it as a case study to illustrate the biological complexity and depth that can arise from a single viral order within the class. This review highlights how even a relatively small lineage can motivate extensive computational and experimental investigation, while providing a reference for contextualising dominant viral groups within the broader dsDNA tailed virosphere. Building on these insights, we introduce a scalable taxonomic framework based on a comparative analysis of genome-wide structural protein content. By integrating large-scale protein structure prediction, structural clustering, and supervised machine learning, this approach learns patterns of structural protein content associated with distinct viral clades, enabling robust taxonomic classification as well as the detection of novel viral sequences. Finally, these concepts are leveraged to enable viral discovery in Irish soil metagenomes, providing the first insights into the Irish soil virome. In line with observations from other environmental studies, Caudoviricetes emerged as the dominant viral group in Irish soil. Although many detected viruses were spatially restricted, a subset of viral lineages was consistently recovered across all samples, irrespective of site location or soil type, indicating the presence of widespread and ecologically persistent soil phages. Comparative analyses further positioned these viruses within globally connected viral lineages, demonstrating how large-scale approaches can link local viral diversity to the broader virosphere. To support this, Irish soil viruses were placed within a taxonomic framework and compared against global reference databases, including GSVA and VIRE, revealing homology with viruses recovered from geographically and ecologically diverse environments. Whole-proteome structural analyses of isolated Irish soil viral contigs revealed low levels of shared protein structures, highlighting the extensive diversity of the soil virosphere. In addition, we characterised the ecology of Irish soil viruses, including their predicted hosts, persistence strategies, and auxiliary metabolic gene (AMG) repertoires, and investigated the influence of soil physicochemical variables on their abundance and distribution. Collectively, this thesis advances viral taxonomy by establishing a structure-based, machine-learning–driven framework for classifying Caudoviricetes and provides the first high-resolution characterization of the Irish soil virome. | en |
| dc.description.status | Not peer reviewed | en |
| dc.description.version | Accepted Version | en |
| dc.format.mimetype | application/pdf | en |
| dc.identifier.citation | Smith, L. 2026. Taxonomy and diversity of Caudoviricetes viruses. PhD Thesis, University College Cork. | |
| dc.identifier.endpage | 135 | |
| dc.identifier.uri | https://hdl.handle.net/10468/19323 | |
| dc.language.iso | en | en |
| dc.publisher | University College Cork | en |
| dc.relation.project | info:eu-repo/grantAgreement/SFI/NSF Student Mobility Programme/18/CRT/6214 (S1)/IE/18/CRT/6214 Supplement/ | |
| dc.rights | © 2026, Linda Smith. | |
| dc.rights.uri | https://creativecommons.org/licenses/by-nc-nd/4.0/ | |
| dc.subject | Caudoviricetes | en |
| dc.subject | Viruses | en |
| dc.subject | Metagenomics | en |
| dc.subject | Proteomics | en |
| dc.subject | Microbiome | en |
| dc.title | Taxonomy and diversity of Caudoviricetes viruses | |
| dc.type | Doctoral thesis | en |
| dc.type.qualificationlevel | Doctoral | en |
| dc.type.qualificationname | PhD - Doctor of Philosophy | en |
