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 geno

Publications

Cameron, S, Lewis, KE, Huws, S, Hegarty, M, Lewis, PD, Pachebat, JA & Mur, L 2017, 'A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancer' PLoS One. DOI: 10.1371/journal.pone.0177062
Zampini, M, Mur, L, Rees Stevens, P, Pachebat, JA, 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, vol 6, 26572. DOI: 10.1038/srep26572
Brown, M, Hablutzel, P, Friberg, IM, Thomason, AG, Stewart, A, Pachebat, JA & Jackson, J 2016, 'Seasonal immunoregulation in a naturally-occurring vertebrate' BMC Genomics. DOI: 10.1186/s12864-016-2701-7
Cameron, S, E. Lewis, K, Huws, S, Lin, W, Hegarty, M, D. Lewis, P, Mur, L & Pachebat, JA 2016, 'Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity' PLoS One, vol 11, no. 2, 0149095. DOI: 10.1371/journal.pone.0149095
Karaseva, A, Tsapieva, A, Pachebat, JA & Suvorov, A 2016, 'Draft Genome Sequence of Probiotic Enterococcus faecium Strain L-3' Genome Announcements, vol 4, no. 1, e01599-15. DOI: 10.1128/genomeA.01622-15
Huws, S, Edwards, JE, 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, vol 92, no. 1, fiv 137. DOI: 10.1093/femsec/fiv137
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, vol 170, no. 1, pp. 57-73. DOI: 10.1104/pp.15.00889
Hadfield, SJ, Pachebat, JA, Swain, MT, Robinson, G, Cameron, SJS, Alexander, J, Hegarty, MJ, Elwin, K & Chalmers, RM 2015, 'Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples' BMC Genomics, vol 16, 650. DOI: 10.1186/s12864-015-1805-9
Facey, PD, Méric, G, Hitchings, MD, Pachebat, JA, Hegarty, MJ, Chen, X, Morgan, LVA, Hoeppner, JE, Whitten, MMA, Kirk, WDJ, Dyson, PJ, Sheppard, SK & 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, vol 7, no. 8, pp. 2188-2202. DOI: 10.1093/gbe/evv136
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, vol 5, 11302. DOI: 10.1038/srep11302
Bloomfield, G, Traynor, D, Sander, SP, Veltman, DM, Pachebat, JA & Kay, RR 2015, 'Neurofibromin controls macropinocytosis and phagocytosis in Dictyostelium' eLife, vol 4, e04940. DOI: 10.7554/eLife.04940
Doonan, J, Denman, S, Gertler, C, Pachebat, JA, Golyshin, PN & 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, vol 118, no. 1, pp. 193-201. DOI: 10.1111/jam.12677
Edwards, A, Mur, L, Girdwood, S, Anesio, AM, Stibal, M, Edwards Rassner, S, Hell, K, Pachebat, J, Post, B, Bussell, JS, Cameron, S, Griffith, G, Hodson, AJ & Sattler, B 2014, 'Coupled cryoconite ecosystem structure–function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers' FEMS Microbiology Ecology, vol 89, no. 2, pp. 222-237. DOI: 10.1111/1574-6941.12283
Pachebat, JA, van Keulen, G, Whitten, M, Girdwood, SE, 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, vol 1, no. 3, e00329-13. DOI: 10.1128/genomeA.00329-13
Consuegra, S, Ellison, A, Allainguillaume, J, Pachebat, J, Peat, KM & Wright, P 2013, 'Balancing selection and the maintenance of MHC supertype variation in a selfing vertebrate' Proceedings of the Royal Society B: Biological Sciences, vol 280, no. 1754, 20122854. DOI: 10.1098/rspb.2012.2854
Hell, K, Edwards, A, Zarsky, J, Podmirseg, SM, Girdwood, S, Pachebat, JA, Insam, H & Sattler, B 2013, 'The dynamic bacterial communities of a melting High Arctic glacier snowpack' ISME Journal, vol 7, pp. 1814-1826. DOI: 10.1038/ismej.2013.51
Edwards, A, Pachebat, JA, Swain, MT, Hegarty, MJ, Hodson, AJ, Irvine-Fynn, TD, Edwards Rassner, SM & Sattler, B 2013, 'A metagenomic snapshot of taxonomic and functional diversity in an Alpine glacier cryoconite ecosystem: Alpine cryoconite metagenome' Environmental Research Letters, vol 8, no. 3, 035003. DOI: 10.1088/1748-9326/8/3/035003
Dougal, K, Harris, PA, Edwards, A, Pachebat, JA, Blackmore, TM, Worgan, HJ & Newbold, CJ 2012, 'A comparison of the microbiome and the metabolome of different regions of the equine hindgut' FEMS Microbiology Ecology, vol 82, no. 3, pp. 642-652. DOI: 10.1111/j.1574-6941.2012.01441.x
Ellison, A, Allainguillaume, J, Girdwood, S, Pachebat, J, Peat, KM, 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, vol 279, no. 1749, pp. 5004-5013. DOI: 10.1098/rspb.2012.1929
Pachebat, JA, Cope-Selby, N, Edwards, JE, 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, 2012 - 2012, .
Edwards, JE, Huws, S, Swarbreck, D, Rees Stevens, P, Febrer, M, Alston, M, Pachebat, JA & Kingston-Smith, A 2012, 'Investigation of a rumen bacterial 'functional core' utilising a metatranscriptomics approach' Gut Microbiota: Friend or Foe?, France, 2012 - 2012, .
Dougal, K, Blackmore, T, Pachebat, J, Harris, P & Newbold, CJ 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, vol 31, no. 5-6, pp. 261-262. DOI: 10.1016/j.jevs.2011.03.069
Pachebat, JA, Kadekoppala, M, Grainger, M, Dluzewski, AR, Gunaratne, RS, Scott-Finnigan, TJ, Ogun, SA, Ling, IT, Bannister, LH, Taylor, HM, Mitchell, GH & Holder, AA 2007, 'Extensive proteolytic processing of the malaria parasite merozoite surface protein 7 during biosynthesis and parasite release from erythrocytes' Molecular and Biochemical Parasitology, vol 151, no. 1, pp. 59-69. DOI: 10.1016/j.molbiopara.2006.10.006
Eichinger, L, Pachebat, JA, Glöckner, G, Rajandream, M-A, Sucgang, R, Berriman, M, Song, J, Olsen, R, Szafranski, K, Xu, Q, Tunggal, B, Kummerfeld, S, Madera, M, Konfortov, BA, Rivero, F, Bankier, AT, 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, MA, 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, EC, Chisholm, RL, Gibbs, R, Loomis, WF, Platzer, M, Kay, RR, Williams, J, Dear, PH, Noegel, AA, Barrell, B & Kuspa, A 2005, 'The genome of the social amoeba Dictyostelium discoideum' Nature, vol 435, no. 7038, pp. 43-57. DOI: 10.1038/nature03481
Glöckner, G, Eichinger, L, Szafranski, K, Pachebat, JA, Bankier, AT, Dear, PH, Lehmann, R, Baumgart, C, Parra, G, Abril, JF, Guigó, R, Kumpf, K, Tunggal, B, Cox, E, Quail, MA, Platzer, M, Rosenthal, A, Noegel, AA, Barrell, BG, Rajandream, M-A, Williams, JG, Kay, RR, Kuspa, A, Gibbs, R, Sucgang, R, Muzny, DM, 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, vol 418, no. 6893, pp. 79-85. DOI: 10.1038/nature00847
Pachebat, JA, Ling, IT, Grainger, M, Trucco, C, Howell, S, Fernandez-Reyes, D, Gunaratne, R & Holder, AA 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, vol 117, no. 1, pp. 83-9. DOI: 10.1016/S0166-6851(01)00336-X
Gunaratne, RS, Sajid, M, Ling, IT, Tripathi, R, Pachebat, JA & Holder, AA 2000, 'Characterization of N-myristoyltransferase from Plasmodium falciparum' Biochemical Journal, vol 348 , no. 2, pp. 459-63. DOI: 10.1042/bj3480459