Dr Justin Pachebat

PhD, MSc, BSc

Dr Justin Pachebat

Senior Lecturer in Microbial Genomics


Contact Details


I am a parasitologist and specialist in single molecule genomics and next generation sequencing (NGS). After degrees in Microbiology at Bristol and Medical Microbiology at the London School of Hygiene and Tropical Medicine, I did a PhD at the MRC National Institute for Medical Research on the characterisation and biosynthesis of a malaria vaccine target: Merozoite Surface Protein 7 in Plasmodium falciparum merozoites.

After my PhD I did several post-docs at the MRC Laboratory of Molecular Biology (2000-2007) and the University of Cambridge (2007-2009). At the MRC-LMB, I ran the HAPPY genome mapping project as part of the international Dictyostelium discoideum genome consortium (see Nature papers), I also ran several R&D projects. At the University of Cambridge, I was based in Jim Haseloff's laboratory at Plant Sciences, and developed an interest in synthetic biology; whilst David Baulcombe developed my interest in NGS which lead to collaborations with: Jim Ajioka (Pathology) and Carolina Marcano (Illumina) to characterise Campylobacter bacteriophage genomes; Gareth Bloomfield and Rob Kay (MRC-LMB) on D. discoideum phenotypic mutants (see E Life paper), Sarah Covshoff and Julian Hibberd on Echinochloa and Rice transcriptomics (see Plant Physiology paper). In 2009 and 2010 I organised the annual Cambridge NGS Bioinformatics meetings.

Additional Information

Responsibilities As Senior Lecturer in Microbial Genomics, I have a combined research and teaching role. My research focuses on the application of NGS technologies to the study of microbial populations and in characterising pathogens. My teaching focuses on molecular biology, genomics and infectious diseases. Module coordinator for the Research Project, Molecular Genetics of Microbes, and Infectious Diseases modules, and contribute to several other modules. I am also an Elected Member of the Society of General Microbiology Eukaryotic Microbiology Committee (Infectious Disease theme).


Module Coordinator
Course Viewer

Tutor: Biology, Microbiology, Microbiology & Zoology degree scheme undergraduate students.

Lead supervisor: Jenna Alexander (KESS MPhil studentship with Cryptosporidium Reference Unit, Public Health Wales), Julia Tello Velamazan (KESS MPhil studentship with Natural Feeds and Fertilizers Ltd), Adrian Horton (TSB PhD studentship with 2SFG Ltd as lead partner). Previous students: Szymon Callus.

Co-supervisor: Laura Lyons (EU BEACON PhD studentship); Simon Cameron (Aberystwyth University PhD Studentship); James Doonan (with Bangor University, Forest Research PhD studentship).


Key words: Campylobacter, Cryptosporidium, Diagnostics, Dictyostelium, Enteric Pathogens, Eimeria, Enterococcus, Host-Pathogen interactions, Illumina, Meta-genomics, Meta-transcriptomes, Next Generation Sequencing, Parasites, Phage, Rhodococcus, Sequencing, Single molecule genomics, Toxoplasma, Viruses, Whole genome amplification.

My research has two main focuses: 1) using single molecule genomics and NGS technologies to characterise pathogens of animals, humans and plants with the aim of developing novel diagnostics / methods of control; 2) using meta-genomic and meta-transcriptomic approaches to study host - pathogen - microbiome interactions.

Current examples of my research include:

  • The detection and characterisation of unknown human viruses (with Public Health England, Liverpool and Cambridge Universities).
  • Meta-genomics to identify microbiota associated with chronic lung disease (MEDLUNG project led by Luis Mur in collaboration with the NHS and Swansea University).
  • Campylobacter jejuni bacteriophage genomics (in collaboration with Jim Ajioka, Cambridge University and Illumina UK Ltd).
  • Control of Campylobacter jejuni in chickens using novel antimicrobial agents (KESS and TSB funded with several commercial partners).
  • Control of Eimeria species in chickens (collaboration with Damer Blake, Royal Veterinary College and Natural Feeds and Fertilizers Ltd).
  • Genomics of commensal gut bacteria isolated from blood sucking Rhodnius prolixus insects (Swansea University).
  • Genomic characterisation of clinical isolates of Cryptosporidium spp. (KESS funded, with Martin Swain & UK Cryptosporidium Reference Lab).
  • Genomics of pathogenic and probiotic Enterococcal spp. (Institute of Experimental Medicine, St. Petersberg, Russia).
  • Slime mould mutant genomics (collaboration with Rob Kay and Gareth Bloomfield, MRC LMB).

Research Groups

  • Parasitology and Helminth Control
  • One Health
  • Epidemiology


Huws, SA, Edwards, JE, Lin, W, Rubino, F, Alston, M, Swarbreck, D, Caim, S, Stevens, PR, Pachebat, J, Won, MY, Oyama, LB, Creevey, CJ & Kingston-Smith, AH 2021, 'Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches', Microbiome, vol. 9, no. 1, 143. https://doi.org/10.1186/s40168-021-01087-w
Friedersdorff, JCA, Kingston-Smith, AH, Pachebat, JA, Cookson, AR, Rooke, D & Creevey, CJ 2020, 'The Isolation and Genome Sequencing of Five Novel Bacteriophages From the Rumen Active Against Butyrivibrio fibrisolvens', Frontiers in Microbiology, vol. 11, 1588. https://doi.org/10.3389/fmicb.2020.01588
Pascoe, B, Williams, LK, Calland, JK, Meric, G, Hitchings, MD, Dyer, M, Ryder, J, Shaw, S, Lopes, BS, Chintoan-Uta, C, Allan, E, Vidal, A, Fearnley, C, Everest, P, Pachebat, JA, Cogan, TA, Stevens, MP, Humphrey, TJ, Wilkinson, TS, Cody, AJ, Colles, FM, Jolley, KA, Maiden, MCJ, Strachan, N, Pearson, BM, Linton, D, Wren, BW, Parkhill, J, Kelly, DJ, van Vliet, AHM, Forbes, KJ & Sheppard, SK 2019, 'Domestication of Campylobacter jejuni NCTC 11168', Microbial Genomics. https://doi.org/10.1099/mgen.0.000279
Doonan, J, Denman, S, Pachebat, JA & McDonald, J 2019, 'Genomic analysis of bacteria in the Acute Oak Decline pathobiome', Microbial Genomics, vol. 5, no. 1, 0240. https://doi.org/10.1099/mgen.0.000240
Morris, A, Pachebat, J, Robinson, G, Chalmers, RM & Swain, M 2019, Identifying and Resolving Genome Misassembly Issues Important for Biomarker Discovery in the Protozoan Parasite, Cryptosporidium. in Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies : Volume 3: BIOINFORMATICS. vol. 3, Biomedical Engineering Systems and Technologies, SciTePress, Prague, pp. 90-100, BIOSTEC 2019: 12th International Joint Conference on Biomedical Engineering Systems and Technologies, Czech Republic, 22 Feb 2019. https://doi.org/10.5220/0007397200900100
More publications on the Research Portal