Dr. Justin Pachebat, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University
Tuesday 15th March, 1.00 p.m., Cornwallis Octagon Lecture Theatre 2 (COLT2)
Genome sequencing been revolutionized by the advent of next generation sequencing (NGS) platforms. Whereby once it would take years to sequence a single organism, researchers can now sequence multiple genomes within a week. This has lead to a paradigm shift in pathogen research, the study of microbiomes and clinical diagnostics. Genome sequencing can give a wealth of information about infectivity, phylogeny, and host specificity, but there are still significant challenges in the generation of genome sequence data from samples in a diagnostic setting.
This talk will discuss the advantages and disadvantages of using: 1) single molecule genomics and NGS technologies to characterise pathogens of animals, humans and plants; 2) meta-genomic and meta-transcriptomic approaches to study host – pathogen – microbiome interactions. Examples covered will include the development of techniques to sequence Cryptosporidium from clinical isolates; detection of novel human enteric viruses; the use of meta-genomics to characterize the lung microbiome in COPD and lung cancer patients.
Biography:
Started off as a parasitologist, then discovered single molecule genomics and next generation sequencing. After a PhD on malaria vaccine targets at the MRC NIMR, I spent 7 years as a post-doc in the Single Molecule Genomics laboratory at the MRC LMB, before moving to the University of Cambridge where I developed an interest in next generation sequencing. Since 2010 I have been a Senior Lecturer in microbial genomics at IBERS, Aberystwyth University.
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).