Unravelling Phage-Host Attachment and Recognition Modalities (PHARM) in the dairy bacterium Streptococcus thermophilus
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Date
2026-06-12
Authors
Kampff, Zoe
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University College Cork
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Abstract
Streptococcus thermophilus is one of the most economically important bacterial starter cultures employed in the global dairy industry and is used extensively in the manufacture of yoghurt and cheese. Despite its technological importance, bacteriophage infection remains a major cause of fermentation delays and/or failure, resulting in reduced and inconsistent product quality and significant economic losses. Successful phage infection is dependent upon interactions between phage-encoded receptor-binding proteins and specific bacterial receptors. In S. thermophilus, cell wall polysaccharides including rhamnose-glucose polysaccharides (RGPs) and exopolysaccharides (EPSs) are central to phage recognition and binding processes. The overall aim of this thesis was to investigate the diversity, biosynthesis and biological functions of these polysaccharides and determine how variation in their structures influences phage-host interactions.
Comparative genomic analysis demonstrated that genes associated with RGP biosynthesis are widespread throughout the Streptococcus genus. Hierarchical clustering analyses revealed extensive diversity within rgp loci and facilitated the identification of multiple distinct rgp genotypes among members of the salivarius group of streptococci. Additionally, the elucidation of the chemical structures of previously uncharacterised RGPs established direct links between the rgp genotype and the associated RGP structure, providing new insights into the evolution and diversification of streptococcal cell wall polysaccharides.
Functional genomic analyses of bacteriophage-insensitive mutants (BIMs) possessing mutations within the rgp locus of the S. thermophilus strain UCCSt50 provided important insights into the genetic basis of RGP side chain biosynthesis. Structural characterisation of the RGPs of specific BIMs, together with transcriptional analyses and heterologous complementation studies, enabled the construction of a preliminary model of RGP side chain assembly and provided experimental evidence supporting the functional assignment of several genes involved in RGP side chain biosynthesis. Furthermore, these studies demonstrated that structural variation within the RGP directly influences phage susceptibility. The RGP was identified as the receptor for phage P738 and distinct RGP-attracted phages were shown to possess distinct structural requirements for host binding.
Comparative genomic and structural analyses of the EPS biosynthetic loci further revealed extensive diversity among eps genotypes and enabled the assignment of experimentally resolved EPS structures to established genotype groups. Collectively, these findings establish direct relationships between polysaccharide genotype and biochemical structure for both RGP and EPS in S. thermophilus and provide a foundation for predicting polysaccharide structure from genome sequence information.
Overall, the work presented throughout this thesis demonstrates that cell wall polysaccharide diversity is a major determinant of phage-host interactions in S. thermophilus. More broadly, these findings position S. thermophilus as a valuable model through which fundamental aspects of streptococcal cell wall polysaccharide biology can be explored.
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Keywords
Streptococcus thermophilus , Bacteriophage , Phage-host interactions , Cell wall polysaccharides , Exopolysaccharides , Rhamnose-glucose polysaccharides , Dairy fermentation , Lactic acid bacteria
Citation
Kampff, Z. 2026. Unravelling Phage-Host Attachment and Recognition Modalities (PHARM) in the dairy bacterium Streptococcus thermophilus. PhD Thesis, University College Cork.