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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

I joined the LSHTM in 2004 as a dual qualified bioinformatician and microbiologist. Before joining the School, I completed a BSc Honours in Molecular Biology followed by an MSc Computer Science (Commendation), both at the University of Hertfordshire. My undergraduate also contained an industrial placement year which was completed at RAFT - Institute of Plastic Surgery, where I was research assistant in the Molecular Biology group.

I completed my PhD in 2011 studying the microbial pathogenesis of Campylobacter jejuni and then completed a two-year Bill & Melinda Gates Foundation funded Post-Doctoral researcher investigating pit latrine characteristics using metagenomics based applications within the Department of Disease Control, LSHTM.

I have since continued to study Campylobacter and related enteric pathogens using classical molecular microbiology techniques along with cutting-edge omics based approaches e.g. genomics, transcriptomics and metagenomics.

Summary statistics

  • 33 peer reviewed manuscripts [Full list: PUBLICATIONS.pdf]
  • >£250,000 research funding awarded.
  • Currently co-supervising 3 PhD students.
  • >30 staff/student supervision/advisory/support since 2011.

Loop Frontiers 

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

Affiliations

Department of Infection Biology
Faculty of Infectious and Tropical Diseases

Teaching

I have successfully completed the Postgraduate Certificate in Learning and Teaching (Full Certificate) at the LSHTM and am a Fellow of the Higher Education Academy (FHEA). I have a wide range of teaching activities at the School:-

  • Lecturing on the "Molecular Biology Research Progress & Applications" (3160) module (since 2009)
  • 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 (12 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 
  • Bioinformatics Trainer for MRC Gambia Genomics Training Camp (2018)

I currently co-supervise three PhD students and co-supervise MSc research projects at the LSHTM (ten students since 2006).

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

Research

My research interests and vision are to study the pathogenesis of Campylobacter (the leading cause of bacterial enteritis worldwide), and other related enteric microorganisms, and importantly to translate our basic microbiological knowledge to real life settings (e.g. by implementing intervention strategies to reduce Campylobacter within the food chain). Over the past 15 years, I have utilized classical molecular microbiology techniques, and linked my bioinformatics skills to provide cutting-edge omics based approaches such as genomics, transcriptomics and metagenomics in his research (33 peer reviewed manuscripts).

Current research themes for studying Campylobacter and other enteric microorganisms include:-

  • Mechanisms of response to environmental and host stress
  • Prevalence and characterising the Type Six Secretion Systems (T6SS)
  • Survival and persistence mechanisms in relation to host cells
  • Investigating the genomic and phenotypic properties of foodborne outbreaks e.g. Listeria monocytogenes
  • Explore the chicken microbiome and investigate Campylobacter survival and persistence to infer control strategies within the food chain.

In relation to Campylobacter, I have completed the full re-annotation of the C. jejuni NCTC11168 genome (in collaboration with the Sanger Institute) and have created and run the Campylobacter Resource Facility (CRF) website. 

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 (10):-

  • 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 - Ecology of Campylobacteriosis in a Tanzanian rural village (Supervisor Professor Richard Kock); as part of the Strengthening food and nutrition security through family poultry and crop integration in Tanzania and Zambia (Principle Investigator Professor Robyn Alders).
  • 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. 

I provide ‘hosting’ sessions (>30 since 2011), either wet or dry research for visiting PhD/Post-docs (one week - six months) allowing collaborations, skills transfer and data analysis for publications. Examples include:-

  • 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. Outcomes: [PMID: 29957495][PMID: 25496466]. 
  • 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. Outcomes: Research selected for plenary presentation in Campylobacter, Helicobacter & Related Organisms - CHRO 2017.
  • Lojika Sivaloganathan (RA, LSHTM) - June 2017 – September 2017. Project - Study the gut microbiome of chickens and onset of Campylobacter. Outcomes: [PMID: 30374341].
  • Aaron McKenna (Moy Park, Belfast, U.K) - October 2017 and February 2019. On his PhD thesis (2015 - Present) titled - Efficient prevention of Campylobacter spp. entrance in broiler houses improves flock performance at slaughter. Outcomes: [PMID: 30197638][ PMID: 30374341
  • 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. Outcomes: [PMID: 30277811][DOI:10.1099/acmi.ac2019.po0264].
  • Cadi Davies (LSHTM) - 2017 - Present. Project - Campylobacter jejuni mechanisms of outer membrane vesicles (OMV) production. Outcomes: [PMID: 31192166].

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

 Funding awarded:-

  • $4.80 Million BMGF Post-Doctoral researcher investigating metagenomics of pit latrines in Tanzania and Vietnam for optimum latrine decomposition. Department of DDC, LSHTM, June 2011 - June 2013, achieved 50% salary recovery. Outcomes: [PMID: 26875588].
  • £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). Outcomes: [PMID: 30277811].
  • £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). Outcomes: [PMID: 28398869].
  • £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). Outcomes [PMID: 30197638, PMID: 30374341].

Conferences & Honourable Invitations:-

I am active in presenting at national and international conferences relating to Campylobacter research (12 since 2007 e.g. CHRO 2017) and have been invited to a give a number of honourable seminars.

Scientific Committee:-

I am a member of the Scientific Committee member for CHRO 2019 (Belfast).

Refereeing Roles:-

I am also active in refereeing manuscripts from different journals (>20 manuscripts since 2013) and grant applications from different funding bodies (>6 totalling £20 million since 2012).  

Editor Roles:-

Recently I have become Guest Editor for Frontiers in Microbiology – Food microbiology; Research Topic - Developments in CampylobacterHelicobacter & Related Organisms Research – CHRO 2019, with co-Editors Professor Nicolae Corcionivoschi (AFBI) and Professor Stuart Thompson (University of Augusta). 

Membership of Learned Societies:-

I am 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).

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 BW; Dorrell N; Gundogdu O
2018
Research in veterinary science
A Novel Natural Antimicrobial Can Reduce the in vitro and in vivo Pathogenicity of T6SS Positive Campylobacter jejuni and Campylobacter coli Chicken Isolates.
Sima F; Stratakos AC; Ward P; Linton M; Kelly C; Pinkerton L; Stef L; Gundogdu O; Lazar V; Corcionivoschi N
2018
Frontiers in microbiology
Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter.
Ijaz UZ; Sivaloganathan L; McKenna A; Richmond A; Kelly C; Linton M; Stratakos AC; Lavery U; Elmi A; Wren BW
2018
Frontiers in microbiology
The bile salt sodium taurocholate induces Campylobacter jejuni outer membrane vesicle production and increases OMV-associated proteolytic activity.
Elmi A; Dorey A; Watson E; Jagatia H; Inglis NF; Gundogdu O; Bajaj-Elliott M; Wren BW; Smith DGE; Dorrell N
2017
Cellular microbiology
Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines.
Torondel B; Ensink JH; Gundogdu O; Ijaz UZ; Parkhill J; Abdelahi F; Nguyen VA; Sudgen S; Gibson W; Walker AW
2016
Microbial biotechnology
The Campylobacter jejuni Oxidative Stress Regulator RrpB Is Associated with a Genomic Hypervariable Region and Altered Oxidative Stress Resistance.
Gundogdu O; da Silva DT; Mohammad B; Elmi A; Wren BW; van Vliet AH; Dorrell N
2016
Frontiers in microbiology
The Campylobacter jejuni MarR-like transcriptional regulators RrpA and RrpB both influence bacterial responses to oxidative and aerobic stresses.
Gundogdu O; da Silva DT; Mohammad B; Elmi A; Mills DC; Wren BW; Dorrell N
2015
Frontiers in microbiology
Prevalence of Type VI Secretion System in Spanish Campylobacter jejuni Isolates.
Ugarte-Ruiz M; Stabler RA; Domínguez L; Porrero MC; Wren BW; Dorrell N; Gundogdu O
2014
Zoonoses and public health
Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence.
Gundogdu O; Bentley SD; Holden MT; Parkhill J; Dorrell N; Wren BW
2007
BMC genomics
Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source.
Champion OL; Gaunt MW; Gundogdu O; Elmi A; Witney AA; Hinds J; Dorrell N; Wren BW
2005
Proceedings of the National Academy of Sciences of the United States of America
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