Thesis
Resolving Streptomyces taxonomy : conflicts between whole-genome, core gene, MLST and 16S classifications
- Creator
- Rights statement
- Awarding institution
- University of Strathclyde
- Date of award
- 2025
- Thesis identifier
- T17389
- Person Identifier (Local)
- 202061059
- Qualification Level
- Qualification Name
- Department, School or Faculty
- Abstract
- Accurate taxonomy is central to comparative genomics, our understanding of microbial evolution, and many aspects of applied microbiology. The current taxonomy of Streptomyces is under active revision, and resolving this could provide a foundational framework for genome-based investigation of this important genus, the source of 60% of clinically-approved antibiotics. Several approaches have been proposed for taxonomic classification, such as single, multi-gene, and whole-genome phylogenies, Multilocus-Sequence Typing (MLST) and Average Nucleotide Identity (ANI). However, these approaches often disagree in detail, in part due to the varying amounts of genomic data they use to define species. Reconstructing phylogeny for 14,239 Streptomyces 16S sequences suggests three major groups but does not place the same species consistently within the tree. Through ANI analysis, I demonstrate that 16S zero-radius Operational Taxonomic Units (zOTUs) are often inconsistent with ANI-based taxonomy. Using six-gene MLST and by updating the canonical pubMLST scheme with 568 new sequence types from all Streptomyces genomes, I find that MLST subdivides Streptomyces into 278 distinct groups. Using ANI, I establish provisional species and genus boundaries within and between MLST subgroups, concluding that the current MLST scheme does not align with genome-based taxonomy, with multiple potential misclassifications. Using a core gene tree constructed from single-copy orthologues across Streptomyces genomes, I obtain a robust phylogeny that recapitulates the three-group structure suggested by 16S and propose that horizontal gene transfer may be common in Streptomyces even for highly conserved genes. By combining this core gene tree with ANI, I propose quantitative thresholds for subdividing Streptomyces into new taxa, identifying distinct groups. Taken together, my analyses support extensive reclassification of Streptomyces, and provide a principled basis for making informed decisions about which methods to prefer for determining Streptomyces taxonomy, and for subdividing these genomes into groups that support comparative genomics analyses for antibiotic discovery.
- Advisor / supervisor
- Hoskisson, Paul
- Pritchard, Leighton
- Resource Type
- DOI
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PDF of thesis T17389 | 2025-06-17 | Public | Download |