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

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 geno


A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancerCameron, S., Lewis, K. E., Huws, S., Hegarty, M., Lewis, P. D., Pachebat, J. A. & Mur, L. 2017 In : PLoS One. 0177062
Terminator Operon Reporter: Combining a transcription termination switch with reporter technology for improved gene synthesis and synthetic biology applicationsZampini, M., Mur, L., Rees Stevens, P., Pachebat, J. A., Newbold, C., Hayes, F. & Kingston-Smith, A. 2016 In : Scientific Reports.6, 26572
Seasonal immunoregulation in a naturally-occurring vertebrateBrown, M., Hablutzel, P., Friberg, I. M., Thomason, A. G., Stewart, A., Pachebat, J. A. & Jackson, J. 2016 In : BMC Genomics. 369
Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease SeverityCameron, S., E. Lewis, K., Huws, S., Lin, W., Hegarty, M., D. Lewis, P., Mur, L. & Pachebat, J. A. 2016 In : PLoS One.11, 2, 0149095
Draft Genome Sequence of Probiotic Enterococcus faecium Strain L-3Karaseva, A., Tsapieva, A., Pachebat, J. A. & Suvorov, A. 2016 In : Genome Announcements.4, 1, e01599-15
Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrassHuws, S., Edwards, J. E., Creevey, C., Rees Stevens, P., Lin, W., Girdwood, S., Pachebat, J. & Kingston-Smith, A. 2016 In : FEMS Microbiology Ecology.92, 1, fiv 137
Transcriptomics of C4 photosynthesis in rice paddyCovshoff, S., Szecowka, M., Hughes, T., Smith-Unna, R., Kelly, S., Bailey, K., Sage, T., Pachebat, J., Leegood, R. & Hibberd, J. 2016 In : Plant Physiology.170, 1, p. 57-73
Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samplesHadfield, S. J., Pachebat, J. A., Swain, M. T., Robinson, G., Cameron, S. J. S., Alexander, J., Hegarty, M. J., Elwin, K. & Chalmers, R. M. 2015 In : BMC Genomics.16, 650
Draft Genomes, Phylogenetic Reconstruction, and Comparative Genomics of Two Novel Cohabiting Bacterial Symbionts Isolated from Frankliniella occidentalisFacey, P. D., Méric, G., Hitchings, M. D., Pachebat, J. A., Hegarty, M. J., Chen, X., Morgan, L. V. A., Hoeppner, J. E., Whitten, M. M. A., Kirk, W. D. J., Dyson, P. J., Sheppard, S. K. & Del Sol, R. 2015 In : Genome Biology and Evolution.7, 8, p. 2188-220215 p.
RapGene: a fast and accurate strategy for synthetic gene assembly in Escherichia coliZampini, M., Rees Stevens, P., Pachebat, J., Kingston-Smith, A., Mur, L. & Hayes, F. 2015 In : Scientific Reports.5, 11302
Neurofibromin controls macropinocytosis and phagocytosis in DictyosteliumBloomfield, G., Traynor, D., Sander, S. P., Veltman, D. M., Pachebat, J. A. & Kay, R. R. 2015 In : eLife.4, e04940
The intergenic transcribed spacer region 1 as a molecular marker for identification and discrimination of Enterobacteriaceae associated with acute oak declineDoonan, J., Denman, S., Gertler, C., Pachebat, J. A., Golyshin, P. N. & McDonald, J. 2015 In : Journal of Applied Microbiology.118, 1, p. 193-20110 p.
Coupled cryoconite ecosystem structure–function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciersEdwards, A., Mur, L., Girdwood, S., Anesio, A. M., Stibal, M., Edwards Rassner, S., Hell, K., Pachebat, J., Post, B., Bussell, J. S., Cameron, S., Griffith, G., Hodson, A. J. & Sattler, B. 2014 In : FEMS Microbiology Ecology.89, 2, p. 222-23715 p.
Draft genome sequence of Rhodococcus rhodnii Strain LMG5362, a symbiont of Rhodnius prolixus (Hemiptera, Reduviidae, Triatominae), the principle vector of Trypanosoma cruzi.Pachebat, J. A., van Keulen, G., Whitten, M., Girdwood, S. E., Del Sol, R., Dyson, P. & Facey, P. 2013 In : Genome Announcements.1, 3, e00329-13
Balancing selection and the maintenance of MHC supertype variation in a selfing vertebrateConsuegra, S., Ellison, A., Allainguillaume, J., Pachebat, J., Peat, K. M. & Wright, P. 2013 In : Proceedings of the Royal Society B: Biological Sciences.280, 1754, 20122854
The dynamic bacterial communities of a melting High Arctic glacier snowpackHell, K., Edwards, A., Zarsky, J., Podmirseg, S. M., Girdwood, S., Pachebat, J. A., Insam, H. & Sattler, B. 2013 In : ISME Journal.7, p. 1814-1826
A metagenomic snapshot of taxonomic and functional diversity in an Alpine glacier cryoconite ecosystem: Alpine cryoconite metagenomeEdwards, A., Pachebat, J. A., Swain, M. T., Hegarty, M. J., Hodson, A. J., Irvine-Fynn, T. D., Edwards Rassner, S. M. & Sattler, B. 2013 In : Environmental Research Letters.8, 3, 035003
A comparison of the microbiome and the metabolome of different regions of the equine hindgutDougal, K., Harris, P. A., Edwards, A., Pachebat, J. A., Blackmore, T. M., Worgan, H. J. & Newbold, C. J. 2012 In : FEMS Microbiology Ecology.82, 3, p. 642-65211 p.
Maintaining functional major histocompatibility complex diversity under inbreeding: the case of a selfing vertebrateEllison, A., Allainguillaume, J., Girdwood, S., Pachebat, J., Peat, K. M., Wright, P. & Consuegra, S. 2012 In : Proceedings of the Royal Society B: Biological Sciences.279, 1749, p. 5004-5013
Applying next generation sequencing towards understanding microbial-plant interactionsPachebat, J. A., Cope-Selby, N., Edwards, J. E., Huws, S., Lyonds, L., Swarbreck, D., Rees Stevens, P., Febrer, M., Bryant, D., Donnison, I., Kingston-Smith, A. & Farrar, K. 2012
Investigation of a rumen bacterial 'functional core' utilising a metatranscriptomics approachEdwards, J. E., Huws, S., Swarbreck, D., Rees Stevens, P., Febrer, M., Alston, M., Pachebat, J. A. & Kingston-Smith, A. 2012
Comparison of bacterial populations from the caecum, right dorsal colon and faeces of horses' using terminal restriction fragment length polymorphism (TRFLP)Dougal, K., Blackmore, T., Pachebat, J., Harris, P. & Newbold, C. J. 2011 In : Journal of Equine Veterinary Science.31, 5-6, p. 261-2622 p.
Extensive proteolytic processing of the malaria parasite merozoite surface protein 7 during biosynthesis and parasite release from erythrocytesPachebat, J. A., Kadekoppala, M., Grainger, M., Dluzewski, A. R., Gunaratne, R. S., Scott-Finnigan, T. J., Ogun, S. A., Ling, I. T., Bannister, L. H., Taylor, H. M., Mitchell, G. H. & Holder, A. A. 2007 In : Molecular and Biochemical Parasitology.151, 1, p. 59-6911 p.
The genome of the social amoeba Dictyostelium discoideumEichinger, L., Pachebat, J. A., Glöckner, G., Rajandream, M-A., Sucgang, R., Berriman, M., Song, J., Olsen, R., Szafranski, K., Xu, Q., Tunggal, B., Kummerfeld, S., Madera, M., Konfortov, B. A., Rivero, F., Bankier, A. T., Lehmann, R., Hamlin, N., Davies, R., Gaudet, P., Fey, P., Pilcher, K., Chen, G., Saunders, D., Sodergren, E., Davis, P., Kerhornou, A., Nie, X., Hall, N., Anjard, C., Hemphill, L., Bason, N., Farbrother, P., Desany, B., Just, E., Morio, T., Rost, R., Churcher, C., Cooper, J., Haydock, S., van Driessche, N., Cronin, A., Goodhead, I., Muzny, D., Mourier, T., Pain, A., Lu, M., Harper, D., Lindsay, R., Hauser, H., James, K., Quiles, M., Madan Babu, M., Saito, T., Buchrieser, C., Wardroper, A., Felder, M., Thangavelu, M., Johnson, D., Knights, A., Loulseged, H., Mungall, K., Oliver, K., Price, C., Quail, M. A., Urushihara, H., Hernandez, J., Rabbinowitsch, E., Steffen, D., Sanders, M., Ma, J., Kohara, Y., Sharp, S., Simmonds, M., Spiegler, S., Tivey, A., Sugano, S., White, B., Walker, D., Woodward, J., Winckler, T., Tanaka, Y., Shaulsky, G., Schleicher, M., Weinstock, G., Rosenthal, A., Cox, E. C., Chisholm, R. L., Gibbs, R., Loomis, W. F., Platzer, M., Kay, R. R., Williams, J., Dear, P. H., Noegel, A. A., Barrell, B. & Kuspa, A. 2005 In : Nature.435, 7038, p. 43-5715 p.
Sequence and analysis of chromosome 2 of Dictyostelium discoideumGlöckner, G., Eichinger, L., Szafranski, K., Pachebat, J. A., Bankier, A. T., Dear, P. H., Lehmann, R., Baumgart, C., Parra, G., Abril, J. F., Guigó, R., Kumpf, K., Tunggal, B., Cox, E., Quail, M. A., Platzer, M., Rosenthal, A., Noegel, A. A., Barrell, B. G., Rajandream, M-A., Williams, J. G., Kay, R. R., Kuspa, A., Gibbs, R., Sucgang, R., Muzny, D. M., Desany, B., Zeng, K., Zhu, B., de Jong, P., Dingermann, T., Gerisch, G., Philippsen, P., Schleicher, M. & Winckler, T. 2002 In : Nature.418, 6893, p. 79-857 p.
The 22 kDa component of the protein complex on the surface of Plasmodium falciparum merozoites is derived from a larger precursor, merozoite surface protein 7Pachebat, J. A., Ling, I. T., Grainger, M., Trucco, C., Howell, S., Fernandez-Reyes, D., Gunaratne, R. & Holder, A. A. 2001 In : Molecular and Biochemical Parasitology.117, 1, p. 83-97 p.
Characterization of N-myristoyltransferase from Plasmodium falciparumGunaratne, R. S., Sajid, M., Ling, I. T., Tripathi, R., Pachebat, J. A. & Holder, A. A. 2000 In : Biochemical Journal.348 , 2, p. 459-635 p.