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Epigenetics in the microbial world

Primary Supervisor: Professor Marco R. Oggioni, Department of Genetics and Genome Biology

Secondary Supervisor: Dr Andrew Morozov, Department of Mathematics

PhD project title: Epigenetics in the microbial world

University of Registration: University of Leicester

Project outline:

New technologies have opened a whole new world relative to non-genetic epigenetic mechanisms for gene regulation both in eukaryotes and prokaryotes. We have recently discovered a phase variable methylation system which allows apparently homogeneous populations of bacteria to generate multiple epigenetically different subpopulations (8). These systems are present in many bacterial species and have a defence role in limiting horizontal gene transfer (3) and bacteriophage infection (5) and often characterise epidemiologically successful clones since they appear to contribute to fitness (2,6). Mathematical modelling of bacterial subpopulations during experimental carriage in human volunteers by the human pathogen Streptococcus pneumoniae show that certain subpopulations of the phase variable methylation system emerge over time (1), indicating a high relevance for interaction between the bacterium and the human host. We now have exciting new data finally demonstrating the epigenetic effect of methylation on gene expression by using synthetic DNA constructs with modified promoter regions which direct reporter gene expression.

Starting from our newest observations we will build this PhD project which will be placed on the interface between cutting edge analysis of bacterial gene regulation and pathogenesis of infection with a contribution of mathematical modelling. The main aim is to nail down the molecular mechanisms driving epigenetic regulation in bacteria. Work will include cloning of synthetic promoter regions with different methylation target sites in both Streptococcus pneumoniae, Lactobacillus casei and Listeria monocytogenes. Quantification of gene expression by reporter luminescence and quantitative PCR will be part of the work. DNA supercoiling and the interactions of histones and transcriptional complexes with synthetic promoter sequences will be tested. Testing the key findings in experimental infection models (4) will aim to translate the pioneering in vitro work to concrete issues characterising treatment and prevention of infection. Findings generated by this project will not only help us to characterise and increase our knowledge of epigenetic-dependent bacterial adaptability mechanisms in environmental and host settings, but also provide new insights into how this recently discovered area of epigenetics can ultimately impact bacterial pathogenesis.

As can be seen from the publication list this work has yielded high-level first-name publications for a number of PhD students (De Ste Croix, Furi, Manso) and this project is aimed to continue in this tradition, by addressing with a unique set of tools a cutting edge question in microbial genomics.


  1. De Ste Croix et al., 2019. Phase variation in pneumococcal populations during carriage in the human nasopharynx. Scientific reports. SREP-19-29807, in press.
  2. De Ste Croix et al., 2017. Phase variable methylation and epigenetic control by Type I Restriction Modification systems. FEMS Microbiology Reviews. 41:S3-15.
  3. De Ste Croix et al., 2019. Recombination of the phase variable spnIII locus is independent of all known pneumococcal site-specific recombinases. Journal of Bacteriology. 201(15). pii: e00233-19.
  4. Ercoli et al., 2018. Intracellular replication of Streptococcus pneumoniae inside splenic macrophages serves as a reservoir for septicaemia. Nature Microbiology. 3(5):600-610.
  5. Furi et al., 2019. Methylation warfare: interaction of pneumococcal bacteriophages with their host. Journal of Bacteriology. 201(19). pii: e00370-19.
  6. Haigh et al., 2017. Draft whole genome sequences of the periodontal pathobionts Porphyromonas gingivalis, Prevotella intermedia and Tannerella forsythia contain phase variable restriction modification systems. Genome Announcements. 5(46). pii: e01229-17.
  7. Kwun et al., 2018. Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition. Nucleic Acids Research, 46(21):11438-11453.
  8. Manso et al., 2014. A random six-phase switch regulates pneumococcal virulence via global epigenetic changes. Nature Commun. 5:5055

BBSRC Strategic Research Priority Sustainable Agriculture and Food, Understanding the Rules of Life, Renewable Resources and Clean Growth, Integrated Understanding of Health: Microbiology


 Techniques that will be undertaken during the project:

  • Molecular microbiology techniques including mutant construction, reporter gene constriction, phenotypic analysis of bacteria including luminescence analysis or antimicrobial drug susceptibility testing.
  • Genome and RNA sequencing, methylome analysis and the relative bioinformatic data analysis using command line interface on high performance computers for which a series of training courses are planned.
  • Experimental infection work including work in cell lines, primary cells and experimental infection to test the phenotypes of bacteria during infection. A Personal Licence will be obtained by the student to perform this work.
  • Mathematical modelling of the empirical data will be based on ordinary and later on partial differential equations.

Contact: Professor Marco R. Oggioni, University of Leicester