Professor Martha Clokie

Professor of Microbiology

Lab: 105, MSB

Office: 106, MSB

Tel: +44 (0)116 252 2959


Personal details

  • PhD Microbiology


Nale, JY, Chutia M, Carr, P, Hickenbotham PT, and Clokie, MRC (2016).  Get in early’; biofilm and wax moth (Galleria mellonella) models reveal new insights into the therapeutic potential of Clostridium difficile bacteriophages. Frontiers in Microbiology 7:1383. doi: 10.3389/fmicb.2016.01383

Rihtman, B, Meaden S., Clokie, MRJ, Koskella, B, Millard, AD (2016).  Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes.  PEERJ 4: e2055. doi: 10.7717/peerj.2055.

Czaplewski, L, Bax, R, Clokie, MRJ et al. (2016).  Alternatives to antibiotics-a pipeline portfolio review. Lancet Infectious Diseases. 16(2): 239-251.  doi: 10.1016/S1473-3099(15)00466-1.

Nale, JY, Spencer, J, Hargreaves KR, Buckley, AM, Trzepiński P, Douce GR, Clokie, MRC (2016). Better together: bacteriophage combinations significantly reduce Clostridium difficile growth in vitro and proliferation in vivo.  Antimicrobial Agents and Chemotherapy. 60(2): 968–981. doi: 10.1128/AAC.01774-15.

Hargreaves KR, Otieno J. R, Blades, M.J., Millard, AD, Browne, HP, Lawley, TD and Clokie, MRC (2015). As clear as mud? Determining the diversity and prevalence of prophages in the draft genomes of estuarine isolates of Clostridium difficile. Genome Biology and Evolution.  27(7):1842-55. doi: 10.1093/gbe/evv094.

Sahota, JS, Smith, CM, Radhakrishan, P, Winstanley C, Goderdzisvili, M, Chanishvili, N, Kadioglu, A, O’Callaghan, C, Clokie, MRC (2015).  Bacteriophage delivery by nebulization and efficacy against phenotypically diverse Pseudomonas aeruginosa from Cystic fibrosis patients.  Journal of Aerosol Medicine and Pulmonary drug delivery.  28:1-8.  DOI: 10.1089/jamp.2014.1172.

Shan, J, Korbsrisate, S, Withatanung, P, Lazar Adler, N, Clokie, MRJ, Galyov E (2014). Temperature dependent bacteriophages of a tropical bacterial pathogen.  Frontiers in Microbiology 5:599.  doi: 10.3389/fmicb.2014.00599.

Baldvinsson, SB, Holst Sørensen MC, Vegge, CS, Clokie, MRJ and Brøndsted L. (2014).  Characterization of the flagellotropic Campylobacter jejuni bacteriophage F341.  Applied and Environmental Microbiology  80(22):7096-106.

Kuppusami S,  Clokie, MRJ, Panayi, T, Ellis AM and Monks, PS (2014).  Metabolite profiling of Clostridium difficileribotypes using small molecular weight volatile organic compounds.  Metabolomics DOI 10.1007/s11306-014-0692-4.

Hargreaves KR, Flores CO, Thanki AM, Lawley TD, Weitz JS, Clokie, MRJ (2014).  The CRISPR system in Clostridium difficile reveals fundamental aspects of phage-host interactions. mBio doi:10.1128/mBio.01045-13.

Hargreaves KR, Kropinski A, Clokie, MRJ. Bacteriophage behavioral ecology (2014): How phages alter their bacterial host’s habits.  Bacteriophage 4, e29866.

Hargreaves KR, Kropinski A, Clokie, MRJ. What does the talking? (2014): Quorum sensing signalling genes discovered in a bacteriophage genome. PLoS ONE; 7:   DOI: 10.1371/journal.pone.0085131

Traving, S., Clokie, MRJ,*  Middelboe, M* (joint last authors) (2014). Increased acidification has a profound effect on the interactions between the cyanobacterium Synechococcus sp. WH7803 and its viruses. FEMS Microbiology Ecology. Increased acidification has a profound effect on the interactions between the cyanobacterium Synechococcus 87:133-141.

Hargreaves KR, Colivn HV, Patel KV, Clokie JJ, Clokie MRJ (2013). The estuarine environment has genetically diverse Clostridium difficile which harbour abundant prophages, Appl. Environ. Microbiol. 79: 6236-6243.

Malik, DJ, Patel KV, Clokie MRJ and Shama G (2013).  On the difficulties of isolating Clostridium difficile from hospital environments.  Journal of Hospital infection 84:181-183.

Adriaenssens E.M., Lehman SM, Vandersteegen K, Vandenheuvel D, Philippe DL, Cornelissen A, Clokie, MRJ, Garcı´AJ, De Proft M, Maes, M, Lavigne R (2012).  CIMs monolithic anion-exchangechromatography as a useful alternative to CsCl gradientpurification of bacteriophage particles. Virology.  DOI:10.1016/j.virol.2012.09.018.

Hargreaves KR, Anderson NJ, Clokie MRJ. Recovery of viable cyanophages from the sediments of a eutrophic lake at decadal timescales. FEMS Microbiology Ecology 2012:DOI:10.1111/1574-6941.1200

Shan J, Patel KV, Hickenbotham PT, Nale JY, Hargreaves KR, Clokie MRJ. Prophage carriage and diversity within clinically relevant strains of Clostridium difficile. Applied and Environmental Microbiology 2012;78:6027-34

Nale JY, Shan J, Hickenbotham PT, Fawley WN, Wilcox MH, Clokie MRJ. Diverse temperate bacteriophage carriage in Clostridium difficile 027 strains. PLoS ONE 2012;7:DOI.10.1371/journal.pone.0037263

Ray JL, Dondrup M, Mohda S, Steen IH, Saanda RA, Clokie MRJ. Finding the needle in the metagenomic viral haystack - micro-metagenome analysis captures a snapshot of the evolution of a bacteriophage armoire. PLoS ONE 2012;7:DOI.10.1371/journal.pone.0034238

Gatedee J, Kritsiriwuthinan K, Galyov E,  Shan J, Dubinina E, Intarak N, Clokie MRJ, Korbsrisate S. Isolation and characterization of a novel podovirus which infects Burkholderia pseudomallei. Virology Journal 2011;8:DOI: 10.1186/1743-422X-8-366

Chan Y-W, Mohr R, Millard AD, Holmes AB, Larkum AW, Whitworth AL, Mann NH, Scanlan DJ, Hess WR, Clokie MRJ. Discovery of cyanophage genomes which contain mitochondrial DNA polymerase.  Molecular Biology and Evolution 2011;8:2269-74

Clokie MRJ, Millard AD, Mann NH. T4 genes in the marine ecosystem: Studies of theT4 like cyanophages and their role in marine ecology. Virology Journal 2010;7:291

Jia Y, Shan J, Millard AD, Clokie MRJ, Mann NH. Light-dependent adsorption of photosynthetic cyanophages to Synechococcus sp. WH7803.  FEMS Microbiology Letters 2010;310:120-6

Millard AD, Gierga G, Clokie MRJ, Evans DJ, Hess WR, Scanlan DJ.  An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease. The ISME Journal 2010;1–15



My primary research interest is in understanding the ecology and molecular biology of bacteriophages and their relationships with bacterial hosts; both in bacterial pathogens and environmentally important bacteria.

Much of my work focuses on the exploitation of bacteriophages and phage-derived products as an alternative to treating antibiotic resistant bacterial infections.

The system that I have progressed furthest is Clostridium difficile where my research group have identified a large set of phages that effectively target this pathogen and are currently developing them as therapeutics (AmpliPhi funded, see press release and publications below).

Other projects include:

  • determining the impact of phages on the gut microbiota (Gates Funded, see press release below)
  • isolating and exploiting phages that target Borrelia, the causative agent of Lyme disease (Phelix Funded)
  • the development of phages that target respiratory infections (including Pseudomonas, Burkholderia and Haemophilus) and the developing phages to target Salmonella (Innovate UK/BBSRC funded)


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Contact Details

Department of Genetics
University of Leicester

Adrian Building
University Road
United Kingdom

Tel: +44 (0)116 252 3374
E Mail:

Head of Department
Professor Jacqui Shaw

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