Dr Justin Pachebat

PhD, MSc, BSc

Dr Justin Pachebat

Senior Lecturer in Microbial Genomics

Department of Life Sciences

Contact Details

As a Senior Lecturer in Microbial Genomics at the Department of Life Science (DLS) and School of Veterinary Science, and an Admissions Tutor for DLS Biology schemes, I have a combined research and teaching role. My research focuses on the application of single molecule genomics (SMG), next generation sequencing (NGS) techniques to study microbial populations and characterise pathogens, in particular protozoan parasites. 

I am a parasitologist / microbiologist experienced in SMG and NGS techniques. After degrees in Microbiology (BSC Hons) at Bristol University and Medical Microbiology (MSc & Diploma) at the London School of Hygiene and Tropical Medicine, I did a PhD at the Medical Research Centre 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 with the Sanger, TIGR, and Universities of Glasgow and Oxford. 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). 

As a DLS Admissions Tutor I am responsible for entry into Biochemistry, Biology, Biology and Climate Change, Ecology, Genetics, Genetics and Biochemistry, Microbiology and Plant Sciences undergraduate schemes.  Scheme leader for the MRes in Parasite Control postgraduate scheme. Module Coordinator for MSc Dissertation (BRM3560), Cell and Cancer Biology (BR25920) and Hot Topics in Parasite Control (BRM0920). 

Elected to the British Society for Parasitology (BSP) Council (2015-); Honorary Treasurer (2018-2022), currently providing maternity cover for Dr Poppy Lamberton who took over as Honorary Treasurer in 2022. Member of the UK Standards for Microbiology Investigations Steering Committee (2015-). Previously an elected member of the Society of General Microbiology (now Microbiology Society) Eukaryotic Microbiology Committee (Infectious Disease theme, 2010-2014). Member of the Aberystwyth Learning and Teaching Conference committee. Member of the AberInnovation Academic Advisory Goup.

Organised the 2018 BSP Spring meeting at Aberystwyth University in collaboration with the British Association for Veterinary Parasitology and the British Ecological Society. I have organised several other meetings including the 2009 and 2010  Cambridge NGS Bioinformatics meetings and was one of the organisers of the 2021 on-line BSP Spring meeting. 

Member of the BAVP, BSP, Microbiology Society, Royal Society of Tropical Medicine and Hygiene.

Key words: Anopheles, Campylobacter, Cryptosporidium, Diagnostics, Dictyostelium, Enteric Pathogens, Eimeria, Enterococcus, Honey bee diseases, Host-Pathogen interactions, Illumina, Insect microbiomes, Malaria, Meta-genomics, Meta-transcriptomes, Next Generation Sequencing, Parasites, Phage, Plasmodium, Rhodococcus, Sequencing, Single molecule genomics, Toxoplasma, Triatomines, Viruses, Whole genome amplification.

My research at DLS focuses on: 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 / vaccines; 2) using meta-genomic and meta-transcriptomic approaches to study host - pathogen - microbiome interactions.

Current examples of my research include:

  • Anopheles microbiome (with London School of Hygiene and Tropical Medicine).
  • Development of multiplex PCR and amplicon sequencing techniques to characterise Anopheles and Plasmodium species, genotypes and drug resistance loci (with London School of Hygiene and Tropical Medicine).
  • Drug resistance detection in Echinococcus vermicularis (with Hosptial for Tropical Diseases).
  • 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).
  • Isolation and genomic characterisation of Eimeria species causing coccidiosis in ruminants (Animal Plant Health Agency and Wales Veterinary Sciences Centre).
  • Genomics of commensal gut bacteria isolated from blood sucking Rhodnius prolixus insects (Swansea University).
  • Development of SMG and NGS approaches to characterise genomes of clinical and veterinary isolates of Cryptosporidium spp. (KESS funded, with Animal Plant Health Agency, Kevin Tyler - University of East Anglia, Martin Swain, UK Cryptosporidium Reference Lab, Wales Veterinary Sciences Centre).
  • 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).

  • One Health
  • Epidemiology
  • Parasitology and Helminth Control

Investigating within-host population diversity of Cryptosporidium parvum using BlooMine. / Morris, Arthur V.; Connor, Thomas; Pachebat, Justin et al.
In: BMC Genomics, Vol. 26, No. 1, 1067, 20.11.2025.

Research output: Contribution to journal › Article › peer-review

Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches. / Huws, Sharon A.; Edwards, Joan E.; Lin, Wanchang et al.
In: Microbiome, Vol. 9, No. 1, 143, 01.12.2021.

Research output: Contribution to journal › Article › peer-review

Generating Reliable Genome Assemblies of Intestinal Protozoans from Clinical Samples for the Purpose of Biomarker Discovery. / Morris, Arthur; Pachebat, Justin; Tyson, Graeme et al.
Biomedical Engineering Systems and Technologies - 12th International Joint Conference, BIOSTEC 2019, Revised Selected Papers. ed. / Ana Roque; Hugo Gamboa; Arkadiusz Tomczyk; Elisabetta De Maria; Felix Putze; Roman Moucek; Ana Fred. Springer Nature, 2020. p. 216-241 (Communications in Computer and Information Science; Vol. 1211 CCIS).

Research output: Chapter in Book/Report/Conference proceeding › Conference Proceeding (ISBN)

The Isolation and Genome Sequencing of Five Novel Bacteriophages From the Rumen Active Against Butyrivibrio fibrisolvens. / Friedersdorff, Jessica C.A.; Kingston-Smith, Alison H.; Pachebat, Justin A. et al.
In: Frontiers in Microbiology, Vol. 11, 1588, 14.07.2020.

Research output: Contribution to journal › Article › peer-review

Domestication of Campylobacter jejuni NCTC 11168. / Pascoe, Ben; Williams, Lisa K.; Calland, Jessica K. et al.
In: Microbial genomics, Vol. 5, No. 7, 000279, 16.07.2019.

Research output: Contribution to journal › Article › peer-review

More publications on the Research Portal