Dr Justin Pachebat PhD, MSc, BSc

Dr Justin Pachebat

Senior Lecturer in Microbial Genomics

Contact Details

Profile

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).

Teaching

Module Coordinator
Tutor
Lecturer

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).

Research

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).

Publications

2017

Cameron, S., Lewis, K.E., Huws, S., Hegarty, M., Lewis, P.D., Pachebat, J.A., Mur, L. 2017. A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancer. PLoS One 0177062 10.1371/journal.pone.0177062 Cadair

2016

Zampini, M., Mur, L., Rees Stevens, P., Pachebat, J.A., Newbold, C., Hayes, F., Kingston-Smith, A. 2016. Terminator Operon Reporter: Combining a transcription termination switch with reporter technology for improved gene synthesis and synthetic biology applications. Scientific Reports 6 26572 10.1038/srep26572 Cadair

Brown, M., Hablutzel, P., Friberg, I.M., Thomason, A.G., Stewart, A., Pachebat, J.A., Jackson, J. 2016. Seasonal immunoregulation in a naturally-occurring vertebrate. BMC Genomics 369 10.1186/s12864-016-2701-7 Cadair

Cameron, S., E. Lewis, K., Huws, S., Lin, W., Hegarty, M., D. Lewis, P., Mur, L., Pachebat, J.A. 2016. Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity. PLoS One 11 (2) 0149095 10.1371/journal.pone.0149095 Cadair

Karaseva, A., Tsapieva, A., Pachebat, J.A., Suvorov, A. 2016. Draft Genome Sequence of Probiotic Enterococcus faecium Strain L-3. Genome Announcements 4 (1) e01599-15 10.1128/genomeA.01622-15 Cadair

Huws, S., Edwards, J.E., Creevey, C., Rees Stevens, P., Lin, W., Girdwood, S., Pachebat, J., Kingston-Smith, A. 2016. Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrass. FEMS Microbiology Ecology 92 (1) fiv 137 10.1093/femsec/fiv137 Cadair

Covshoff, S., Szecowka, M., Hughes, T., Smith-Unna, R., Kelly, S., Bailey, K., Sage, T., Pachebat, J., Leegood, R., Hibberd, J. 2016. Transcriptomics of C4 photosynthesis in rice paddy. Plant Physiology 170 (1) pp. 57-73. 10.1104/pp.15.00889 Cadair

2015

Hadfield, 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. Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples. BMC Genomics 16 650 10.1186/s12864-015-1805-9 Cadair

Facey, 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. Draft Genomes, Phylogenetic Reconstruction, and Comparative Genomics of Two Novel Cohabiting Bacterial Symbionts Isolated from Frankliniella occidentalis. Genome Biology and Evolution 7 (8) pp. 2188-2202. 10.1093/gbe/evv136 Cadair

Zampini, M., Rees Stevens, P., Pachebat, J., Kingston-Smith, A., Mur, L., Hayes, F. 2015. RapGene: a fast and accurate strategy for synthetic gene assembly in Escherichia coli. Scientific Reports 5 11302 10.1038/srep11302 Cadair

Bloomfield, G., Traynor, D., Sander, S.P., Veltman, D.M., Pachebat, J.A., Kay, R.R. 2015. Neurofibromin controls macropinocytosis and phagocytosis in Dictyostelium. eLife 4 e04940 10.7554/eLife.04940 Cadair

Doonan, J., Denman, S., Gertler, C., Pachebat, J.A., Golyshin, P.N., McDonald, J. 2015. The intergenic transcribed spacer region 1 as a molecular marker for identification and discrimination of Enterobacteriaceae associated with acute oak decline. Journal of Applied Microbiology 118 (1) pp. 193-201. 10.1111/jam.12677 Cadair

2014

Edwards, 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. Coupled cryoconite ecosystem structure–function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers. FEMS Microbiology Ecology 89 (2) pp. 222-237. 10.1111/1574-6941.12283 Cadair

2013

Pachebat, J.A., van Keulen, G., Whitten, M., Girdwood, S.E., Del Sol, R., Dyson, P., Facey, P. 2013. Draft genome sequence of Rhodococcus rhodnii Strain LMG5362, a symbiont of Rhodnius prolixus (Hemiptera, Reduviidae, Triatominae), the principle vector of Trypanosoma cruzi. Genome Announcements 1 (3) e00329-13 10.1128/genomeA.00329-13 Cadair

Consuegra, S., Ellison, A., Allainguillaume, J., Pachebat, J., Peat, K.M., Wright, P. 2013. Balancing selection and the maintenance of MHC supertype variation in a selfing vertebrate. Proceedings of the Royal Society B: Biological Sciences 280 (1754) 20122854 10.1098/rspb.2012.2854 Cadair

Hell, K., Edwards, A., Zarsky, J., Podmirseg, S.M., Girdwood, S., Pachebat, J.A., Insam, H., Sattler, B. 2013. The dynamic bacterial communities of a melting High Arctic glacier snowpack. ISME Journal 7 pp. 1814-1826. 10.1038/ismej.2013.51 Cadair

Edwards, A., Pachebat, J.A., Swain, M.T., Hegarty, M.J., Hodson, A.J., Irvine-Fynn, T.D., Edwards Rassner, S.M., Sattler, B. 2013. A metagenomic snapshot of taxonomic and functional diversity in an Alpine glacier cryoconite ecosystem: Alpine cryoconite metagenome. Environmental Research Letters 8 (3) 035003 10.1088/1748-9326/8/3/035003 Cadair

2012

Dougal, K., Harris, P.A., Edwards, A., Pachebat, J.A., Blackmore, T.M., Worgan, H.J., Newbold, C.J. 2012. A comparison of the microbiome and the metabolome of different regions of the equine hindgut. FEMS Microbiology Ecology 82 (3) pp. 642-652. 10.1111/j.1574-6941.2012.01441.x Cadair

Ellison, A., Allainguillaume, J., Girdwood, S., Pachebat, J., Peat, K.M., Wright, P., Consuegra, S. 2012. Maintaining functional major histocompatibility complex diversity under inbreeding: the case of a selfing vertebrate. Proceedings of the Royal Society B: Biological Sciences 279 (1749) pp. 5004-5013. 10.1098/rspb.2012.1929 Cadair

Pachebat, 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. Applying next generation sequencing towards understanding microbial-plant interactions. Plant Molecular Biology, Gordon Conference. Cadair

Edwards, J.E., Huws, S., Swarbreck, D., Rees Stevens, P., Febrer, M., Alston, M., Pachebat, J.A., Kingston-Smith, A. 2012. Investigation of a rumen bacterial 'functional core' utilising a metatranscriptomics approach. Gut Microbiota: Friend or Foe?. Cadair

2011

Dougal, K., Blackmore, T., Pachebat, J., Harris, P., Newbold, C.J. 2011. Comparison of bacterial populations from the caecum, right dorsal colon and faeces of horses' using terminal restriction fragment length polymorphism (TRFLP). Journal of Equine Veterinary Science 31 (5-6) pp. 261-262. 10.1016/j.jevs.2011.03.069 Cadair

2007

Pachebat, 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. Extensive proteolytic processing of the malaria parasite merozoite surface protein 7 during biosynthesis and parasite release from erythrocytes. Molecular and Biochemical Parasitology 151 (1) pp. 59-69. 10.1016/j.molbiopara.2006.10.006 Cadair

2005

Eichinger, L., Pachebat, J.A., Glöckner, G., Rajandream, M., 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. The genome of the social amoeba Dictyostelium discoideum. Nature 435 (7038) pp. 43-57. 10.1038/nature03481 Cadair

2002

Glöckner, 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., 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. Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature 418 (6893) pp. 79-85. 10.1038/nature00847 Cadair

2001

Pachebat, J.A., Ling, I.T., Grainger, M., Trucco, C., Howell, S., Fernandez-Reyes, D., Gunaratne, R., Holder, A.A. 2001. The 22 kDa component of the protein complex on the surface of Plasmodium falciparum merozoites is derived from a larger precursor, merozoite surface protein 7. Molecular and Biochemical Parasitology 117 (1) pp. 83-9. 10.1016/S0166-6851(01)00336-X Cadair

2000

Gunaratne, R.S., Sajid, M., Ling, I.T., Tripathi, R., Pachebat, J.A., Holder, A.A. 2000. Characterization of N-myristoyltransferase from Plasmodium falciparum. Biochemical Journal 348 (2) pp. 459-63. 10.1042/bj3480459 Cadair