Dr Justin Pachebat PhD, MSc, BSc
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.
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).
- BR22310 - Infectious Diseases
- BRM6400 - Research Methods in the Biosciences
- BRM6420 - Research Methods in the Biosciences
- BR33620 - Microbes in Industry and Research
- BRM1620 - Infection and Immunity
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).
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 Cadair2016.
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 Cadair2016.
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 Cadair2015.
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 Cadair2015.
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 Cadair2014.
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 Cadair2013.
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 Cadair2013.
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 Cadair2012.
Applying next generation sequencing towards understanding microbial-plant interactions. Plant Molecular Biology, Gordon Conference. Cadair2012.
Investigation of a rumen bacterial 'functional core' utilising a metatranscriptomics approach. Gut Microbiota: Friend or Foe?. Cadair2012.
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 Cadair2011.
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 Cadair2007.
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 Cadair2001.