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Dr Ozan Gundogdu

BSc MSc PhD

Principal Scientific Officer
- Bioinformatician/Microbiologist

Room
390

LSHTM
Keppel Street
London
WC1E 7HT
United Kingdom

Tel.
02079588383

Ozan Gundogdu joined the LSHTM in 2004 and is a dual qualified bioinformatician and microbiologist. Before joining the School he completed a BSc Honours in Molecular Biology followed by an MSc Computer Science (Commendation), both at the University of Hertfordshire. His undergraduate also contained an industrial placement year which was completed at RAFT - Institute of Plastic Surgery, where he was research assistant in the Molecular Biology group. Ozan completed his PhD in 2011 studying the microbial pathogenesis of Campylobacter jejuni and has continued to study Campylobacter and related pathogens using classical molecular microbiology techniques along with cutting-edge omics based approaches e.g. genomics, transcriptomics and metagenomics

Summary statistics

  • 27 peer reviewed manuscripts; h-index of 11.
  • >£250,000 research funding awarded from three grants.
  • Currently co-supervising 3 PhD students.
  • >25 staff/student supervision/advisory/support since 2011.
  • Reviewed 15 manuscripts for multiple journals since 2013, and four grant applications for multiple funding bodies totalling £14 million since 2013.

Academic websites

Google Scholar

Researchgate

Academia

Loop Frontiers

ORCID ID orcid.org/0000-0002-3550-0545 

Affiliations

Faculty of Infectious and Tropical Diseases
Department of Pathogen Molecular Biology

Teaching

Ozan has successfully completed the Postgraduate Certificate in Learning and Teaching (Full Certificate) at the LSHTM and has become a Fellow of the Higher Education Academy (FHEA). He has a wide range of teaching activities which include:-

  • Lecturing on the "Molecular Biology Research Progress & Applications" (3160) module (since 2010)
  • Lecturing on the "Molecular Biology" (3333) module (since 2011)
  • Both above lectures are part of the Molecular Biology of Infectious Diseases (MBID) and Medical Microbiology (MM) MSc courses at the LSHTM
  • Laboratory and faculty demonstrations as part of MBID and MM courses (since 2006)
  • MSc exam marking and invigilation (since 2006)
  • Tutoring MSc students throughout the academic year (11 students since 2006)
  • Advisory panel for PhD students (two students since 2011)
  • PhD upgrade (two students 2014, 2016) and viva (one student 2017) examiner
  • Teaching internal and external researchers about a number of faculty equipment and also data analysis techniques (since 2004)
  • Setting up modules as part of a distance learning course (IDM602)
  • Member of Senate Council 

Ozan currently co-supervises three PhD students and also co-supervises MSc research projects at the LSHTM (nine students since 2006).

Along with teaching, Ozan is the Head of Sequencing at the LSHTM which includes an Illumina MiSeq and an ABI3730 sequencer. He is actively involved in enhancing the School's sequencing / bioinformatics set-up and is responsible for running and maintaining the Genome Resource Facility within the Pathogen Molecular Biology department and has created and runs the Genome Resource Facility (GRF) website. 

Research

Ozan's research interests and vision are to study the pathogenesis of Campylobacter, the leading human foodborne pathogen, and related microorganisms with the aim of increasing our understanding of virulence mechanisms, survival properties and the physiology of such pathogens, thus allowing us to implement intervention and control strategies. Over the past 15 years, he has utilized classical molecular microbiology techniques, and linked his bioinformatics skills to provide cutting-edge omics based approaches such as genomics, transcriptomics and metagenomics in his research (27 peer reviewed manuscripts; h-index of 11).

Current research interests include investigating the pathogenesis of Campylobacter and other related bacteria with the following themes:-

  • Mechanisms of Campylobacter jejuni response to environmental and host stress
  • Prevalence and characterising C. jejuni Type Six Secretion Systems (T6SS)
  • Survival and persistence mechanisms of C. jejuni in relation to host cells
  • Microbiota studies focusing on C. jejuni and AMR
  • Bacterial omics linked to the above themes e.g. genomics, transcriptomics and metagenomics

Current PhD students (3):-

  • Janie Liaw (LSHTM) - 2016 - Present. Co-supervisors Dr Ozan Gundogdu and Professor Nick Dorrell. Project - Investigation of the role of the Campylobacter jejuni Type VI Secretion System in bacterial secretion of virulence factors and interaction with host cells.
  • Geunhye Hong (LSHTM) - 2018 - Present. Co-supervisors Dr Ozan Gundogdu and Professor Nick Dorrell. Project - Investigating Campylobacter jejuni interactions with endoplasmic reticulum in intestinal epithelial cells resulting in induction of the unfolded protein response.
  • Elizabeth Attree (RVC) - 2018 - Present. Co-supervisors Dr Ozan Gundogdu, Professor Damer Blake, Professor Fiona Tomley and Dr Dong Xia. Project - A multi-omics approach to improve Eimeria functional genome annotation.

Current and past advisory panel for PhD students (2):-

  • Daiani Teixeira (LSHTM) - 2011-16. Project - The role of the MarR transcriptional regulators RrpA and RrpB in the response of Campylobacter jejuni to oxidative and aerobic stress.
  • Mateusz Hasso Agopsowicz (LSHTM) - 2014-18. Project - A Study Of Factors Underlying BCG Immunogenicity Differences Across Countries: The Influence Of DNA Methylation Patterns And Antigen Presenting Cells.

Current and past MSc research project students co-supervised with Professor Nick Dorrell at the LSHTM (9):-

  • Maria Peila - 2004-05. Project - Comparative phylogenomics of the foodborne human pathogen Campylobacter jejuni.
  • Fatma Dalgakiran - 2009-10. Project - Pathogenesis of outer membrane vesicles (OMVs) by using Campylobacter jejuni mutant.
  • Sarah Leir - 2010-11. Project - Characterising the Campylobacter oxidative stress response. 
  • Banaz Mohammad - 2011-12. Project - Investigation of Campylobacter jejuni oxidative and aerobic stress responses.
  • Naomi Henderson - 2012-13. Project - Investigating the oxidative stress response in Campylobacter jejuni
  • Maria Garza Valles (RVC visiting student) - 2013-14. Project - Reducing childhood stunting by improving chicken production and health in Tanzania.
  • Cadi Davies - 2014-15. Project - Investigation of the role of the Campylobacter jejuni Type VI secretion system in bacterial secretion of virulence factors and interactions with host cells.
  • Chloe Wragg-Kerridge - 2015-16. Project - Investigation of the role of Campylobacter jejuni Type VI secretion system in bacterial secretion of virulence factors and interactions with host cells. 
  • Geunhye Hong - 2016-17. Project - Investigation of the role of the Campylobacter jejuni Type VI secretion system (T6SS) and the oxidative stress response.  

Current and past supervision and hosting of visitors with laboratory/bioinformatics based projects (5):-

  • Maria Ugarte-Ruiz (Universidad Complutense Madrid, Madrid, Spain) - June 2014 - March 2015. On her PhD thesis (2012-16) titled - Detection and characterization of Campylobacter from animals, food and sewage. 
  • Gianna Di Sario (University of Urbino, Urbino, Italy) - October 2016 - March 2017. On her PhD thesis (2014-17) titled - Investigation of the effects of Campylobacter jejuni virulence factors in human cells: different pathways involved.  
  • Aaron McKenna (Moy Park, Belfast, U.K) - October 2017. On his PhD thesis (2015 - Present) titled - Efficient prevention of Campylobacter spp. entrance in broiler houses improves flock performance at slaughter.
  • Dr Alexandros Stratakos (Agri-Food and Biosciences Institute, Belfast, U.K) - March 2018. Project - Whole genome sequencing and bioinformatics analysis of SalmonellaListeria and Escherichia species.
  • Cadi Davies (LSHTM) - 2017 - Present. Project - Campylobacter jejuni mechanisms of outer membrane vesicles (OMV) production.

A number of national and international collaborations have been established to allow future research and funding opportunities:-

 Funding awarded:

  • £187,000 from Safefood in collaboration with Professor Nicolae Corcionivoschi to study risk profiling of Listeria in ready-to-eat foods (RTE) and determination of control strategies and practical interventions (2016).
  • £10,000 from Agri-Food and Biosciences Institute in collaboration with Professor Nicolae Corcionivoschi to study the effects of the natural antimicrobial peptide carvacrol on the delayed onset of Campylobacter (2016).
  • £50,000 from Moy Park, Belfast, U.K as Co-Investigator to study the gut microbiome of chickens over the course of 35 days and to investigate the onset of Campylobacter (2017).

In relation to Campylobacter, he has completed the full re-annotation of the C. jejuni NCTC11168 genome (in collaboration with the Sanger Institute) and has created and runs the Campylobacter Resource Facility (CRF) website. He has also linked to a number of additional internal and external projects which include a next-generation sequencing/bioinformatics theme with the aim of enhancing research output and funding opportunities.

Ozan is active in presenting at national and international conferences relating to Campylobacter research and has presented at a number of meetings (12 since 2007), most recently an oral presentation at the CHRO 2017, Nantes, France. He is a full member of the Microbiology Society (Previously known as the Society of General Microbiology) and an Associate Faculty Member of Faculty of 1000 (post-publication peer review). Recently he has been selected as a Scientific Committee member for CHRO 2019 Belfast. He is also active in refereeing manuscripts from different journals (15 manuscripts since 2013) and grant applications from different funding bodies (four totalling £14 million since 2013).

 

Languages - English, Turkish and Spanish

Research Area
Bacteria
Disease control
Discipline
Genomics
Bacteriology
Microbiology
Molecular biology
Bioinformatics
Disease and Health Conditions
Diarrhoeal diseases
Infectious disease
Zoonotic disease
Region
World

Selected Publications

Exploring the oxidative, antimicrobial and genomic properties of Campylobacter jejuni strains isolated from poultry.
Ugarte-Ruiz, M. ; Domínguez, L. ; Corcionivoschi, N. ; Wren, B.W. ; Dorrell, N. ; Gundogdu, O. ;
2018
Res Vet Sci
Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter
Ijaz, U.Z.; Sivaloganathan, L.; McKenna, A.; Richmond, A.; Kelly, C.; Linton, M.; Stratakos, A.; Lavery, U.; Elmi, A.; Wren, B.W.; Dorrell, N.; Corcionivoschi, N.; Gundogdu, O.
2018
bioRxiv
Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines.
Torondel, B.; Ensink, J.H.; Gundogdu, O.; Ijaz, U.Z.; Parkhill, J.; Abdelahi, F.; Nguyen, V.A.; Sudgen, S.; Gibson, W.; Walker, A.W.; Quince, C.;
2016
Microb Biotechnol
The Campylobacter jejuni Oxidative Stress Regulator RrpB Is Associated with a Genomic Hypervariable Region and Altered Oxidative Stress Resistance.
Gundogdu, O. ; da Silva, D.T. ; Mohammad, B. ; Elmi, A. ; Wren, B.W. ; van Vliet, A.H. ; Dorrell, N. ;
2016
Front Microbiol
Prevalence of Type VI Secretion System in Spanish Campylobacter jejuni Isolates.
Ugarte-Ruiz, M.; Stabler, R.A.; Domínguez, L.; Porrero, M.C.; Wren, B.W.; Dorrell, N.; Gundogdu, O.;
2015
Zoonoses Public Health
The Campylobacter jejuni MarR-like transcriptional regulators RrpA and RrpB both influence bacterial responses to oxidative and aerobic stresses.
Gundogdu, O. ; da Silva, D.T. ; Mohammad, B. ; Elmi, A. ; Mills, D.C. ; Wren, B.W. ; Dorrell, N. ;
2015
Front Microbiol
Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence.
Gundogdu, O.; Bentley, S.D.; Holden, M.T.; Parkhill, J.; Dorrell, N.; Wren, B.W.;
2007
BMC Genomics
Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source.
Champion, O.L.; Gaunt, M.W.; Gundogdu, O.; Elmi, A.; Witney, A.A.; Hinds, J.; Dorrell, N.; Wren, B.W.;
2005
Proc Natl Acad Sci U S A
See all Dr Ozan Gundogdu's Publications