I lead the foodborne enteric pathogen group at the LSHTM where we study the physiology and pathogenesis of Campylobacter (most common bacterial cause of human gastroenteritis in the world) and other related enteric microorganisms (e.g. Listeria spp. and Vibrio spp.). Importantly, we translate basic microbiological knowledge to real life settings (i.e. by implementing intervention strategies). My group uses classical molecular microbiology techniques, and links bioinformatic skills to apply cutting-edge omics based approaches e.g. genomics, transcriptomics and metagenomics to answer relevant research questions.

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

- Mechanisms of response to environmental and host stress

- Prevalence and characterising the function of Type VI Secretion Systems (T6SS)

- Survival and persistence mechanisms in relation to host cells; the unfolded protein response

- Mechanisms of adhesion and invasion

- Role of outer membrane vesicles

Current translational research relating to intervention and control strategies include: -

- Understanding the host microbiome and why pathogens such as Campylobacter appear and persist within avians

- The food chain and points of control e.g. analysis of Listeria outbreaks

- Effective management practices

- The role and impact of natural antimicrobials

Current Postdoctoral supervision (1):-

- Banaz Star-Shirko (LSHTM) - 2022 - Present. Supervisor Dr Ozan Gundogdu. Project - Investigating the impact of Campylobacter on the chicken gut microbiome

Current PhD students (3):-

- Pranaya Kansakar (LSHTM) - MRC LID studentship - 2023 - 2027. Primary supervisor Dr Ozan Gundogdu and Professor Brendan Wren. Project - Investigating Campylobacter jejuni interactions with endoplasmic reticulum in intestinal epithelial cells resulting in induction of the unfolded protein response.

- Gladys Maria Pangga (LSHTM) - BBSRC LIDo iCASE studentship - 2022 - 2026. Primary supervisor Dr Ozan Gundogdu and Dr Dong Xia, Dr Androniki Psifidi and Dr Anne Richmond. Project - Breeders to broilers: optimising chicken health and performance to reduce susceptibility to zoonotic bacteria, viruses and parasite.

- Zahra Omole (LSHTM) - 2020 - 2024. Primary supervisor 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.

Past PhD students (3):-

- Janie Liaw (LSHTM) - 2016 - 2020. 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.

- Elizabeth Attree (RVC) - 2018 - 2023. 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.

- Geunhye Hong (LSHTM) - 2018 - 2023. 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.

Past Postdoctoral supervision (2):-

- Fauzy Nasher (LSHTM) - 2019 - 2021. Co-supervisors Dr Ozan Gundogdu and Professor Brendan Wren. Project - Microbes in the Food Chain, as part of the Quadram Institute BBSRC Strategic Programme.

- Janie Liaw (LSHTM) - 2020 - 2023. Supervisor Dr Ozan Gundogdu. Project - Investigation of functions of the Campylobacter jejuni Type VI Secretion System.

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 at the LSHTM (15):-

- 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.

- 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.

- Zahra Omole - 2018-19. Project - Investigating the link between the RrpA and RrpB transcriptional regulators and the Campylobacter jejuni Type VI secretion system.

- Luca Robinson - 2019-20. Project - Bioinformatic analysis of the Campylobacter jejuni Type VI secretion system.

- Emily Simpson - 2019-20. Project - Bioinformatic tools for effector identification.

- Aishwarya Arunagirinathan - 2020-21. Project - Functional characterisation of the Campylobacter jejuni Type VI secretion system.

- Amelie Delaitre - 2021-22. Project - Functional characterisation of the Campylobacter jejuni Type VI secretion system.

- Hongxi Chen - 2022-23. Project - Bioinformatic pipelines to interrogate T6SS effectors.

- Phuong Nguyen - 2022-23. Project - Characterisation of the Campylobacter jejuni Type VI secretion system effectors.

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].

- Maria Garza Valles (RVC visiting student) June-Sep 2014. 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).

- 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 (Visiting Post-Doctoral researcher, Agri-Food and Biosciences Institute, Belfast, U.K) - March 2018. Project - Whole genome sequencing and bioinformatics analysis of Salmonella, Listeria and Escherichia species. Outcomes: [PMID: 30277811][DOI:10.1099/acmi.ac2019.po0264].

- Cadi Davies (LSHTM) - 2017 - Present. On her PhD thesis (2017-Present) titled - Campylobacter jejuni mechanisms of outer membrane vesicles (OMV) production. Outcomes: [PMID: 31192166].

- Xiaofei Li (Yangzhou University, China) - June 2019 - November 2019. Project - Investigating the new role of FlhF identifies novel interactions with genes involved in flagellar synthesis in Campylobacter jejuni. Outcomes: [PMID: 32265885].

- Po-Yu Liu (Visiting Post-Doctoral Researcher, RVC) - August 2021 - November 2021. Project - Multi-omics analysis of host-parasite microbiome interactions.

- Pedro Miguela Villoldo (Universidad Complutense Madrid, Madrid, Spain) - September 2021 - January 2022. On his PhD thesis (2019-22) titled - Detection and characterization of Escherichia coli from porcine in relation to antimicrobial resistance over time.

- Dr Blaz Jug and Dr Manca Volk, University of Ljubljana, Slovenia - July 2023. Project - Campylobacter survival and biofilm formation.

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

- Agri-Food and Biosciences Institute (AFBI), Belfast, U.K (Professor Nicolae Corcionivoschi)

- Moy Park, Belfast, U.K (Dr Ursula Lavery and Dr Anne Richmond)

- Quadram Institute, Norwich, U.K (Dr Andrew Page, Professor Mark Pallen, Professor John Wain)

- Royal Veterinary College (RVC), London, U.K (Dr Dong Xia, Dr Androniki Psifidi, Professor Damer Blake and Professor Fiona Tomley)

- The MRC Unit The Gambia LSHTM (Professor Martin Antonio)

- University of Aberdeen, Aberdeen, U.K (Dr Alan Walker)

- Universidad Complutense Madrid, Madrid, Spain (Dr Maria Ugarte-Ruiz and Professor Lucas Domínguez Rodríguez)

- University of Glasgow, Glasgow, U.K (Dr Umer Zeeshan Ijaz and Dr Paul Everest)

- University of Melbourne, Melbourne, Australia (Dr Abderrahman Hachani)

- University of Surrey, Guildford, U.K (Dr Arnoud van Vliet)

- University of Urbino, Urbino, Italy (Dr Barbara Canonico)

- UCL GOS Institute of Child Health, London, U.K (Dr Mona Bajaj-Elliott)

- Comsats University Islamabad, Islamabad, Pakistan (Professor Habib Bokhari)

- Mahidol University, Nakhon Pathom, Thailand (Professor Sunee Korbsrisate)

- Universidad Peruana Cayetano Heredia, Lima, Peru (Dr Pablo Tsukayama)

- University of Yangzhou, China (Professor Jinlin Huang and Dr Yuanyue Tang)

- The Research Institute of the University of Bucharest (Professor Carmen Chifiriuc and Dr Gratiela Pircalabioru)

- Nagasaki University (Dr Daniel Inaoka)

Funding awarded:-

Small Scale

- £10,000 from Agri-Food and Biosciences Institute (AFBI) as Principal Investigator 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 Principal 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].

- £12,000 from Royal Society-Newton Mobility Grant as LSHTM Principal Investigator with Professor Sunee Korbsrisate (Mahidol University, Thailand) to study the impact of bacteriophages on adaptation and virulence on pathogenic Burkholderia pseudomallei and non-pathogenic B. thailandensis (2019).

- £11,500 from Houghton Trust as Co-Investigator with Professor Damer Blake, Dr Dong Xia and Dr Androniki Psifidi (RVC) to dissect Campylobacter-Eimeria co-infections to understand pathogen dynamics and develop a model for future poultry studies (2020).

- £81,500 from National Natural Science Foundation of China as Co-Investigator with Professor Jinlin Huang at the University of Yangzhou, China to investigate the biological phenotype and regulatory network of FlhF in Campylobacter jejuni in relation to oxidative stress (2021).

- £75,000 from British Council UK-ASEAN Institutional Links as Principal Investigator with Professor Sunee Korbsrisate at the University of Mahidol, Thailand to investigate the genotypic and phenotypic properties of Burkholderia bacteriophage biodiversity (2022).

- £57,000 from Moy Park, Belfast, U.K as Principal Investigator to study environmental parameters impacting gut microbial population structure and pathogenic bacteria (2023).

Medium/Large Scale

- $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 as Co-Investigator 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: [DOI:10.1016/j.foodcont.2017.12.020].

- £612,857 from Department of Agriculture, Environment and Rural Affairs (DAERA) as Co-Investigator with Dr Ramon Muns (AFBI) to study strategies to overcome the removal of zinc oxide from pig diets: maintaining advances in production and reduction of the use of antimicrobials (2020).

- £453,979 from DAERA as Co-Investigator with Dr Ramon Muns (AFBI) to study influencing new born piglets microbiota: an innovative and applied approach (2020).

- £185,000 from BBSRC iCASE Studentship as Principal Supervisor with Moy Park: Breeders to broilers: optimising chicken health and performance to reduce susceptibility to zoonotic bacteria, viruses and parasite colonisation (2021).

- £105,000 from Daphne Jackson to supervise the Fellowship applicant Dr Banaz Star-Shirko: Investigating the impact of Campylobacter on the chicken gut microbiome (2022).

- £115,000 from MRC LID Studentship as Principal Supervisor: Investigating Campylobacter jejuni interactions with endoplasmic reticulum in intestinal epithelial cells resulting in induction of the unfolded protein response (2023).

Honorary Positions:-

Honorary Professor

Banat university of Agricultural Sciences and Veterinary Medicine

King Michael I of Romania, Timisoara

Faculty of Bioengineering of Animal Resources

Associate Member

Kohsar University Murree, Faculty of Biomedical & Life Science

Pakistan

Scientific Committee:-

- Scientific committee member for CHRO 2019 (Belfast)

- Strategic advisory group member for £2 Million MRC CLIMB-BIG-DATA project (2020)

- Co-organiser of CampyUK goes global virtual 2021 conference.

- Nagasaki-LSHTM partnership steering committee (2022)

- Scientific committee member for CHRO 2022 (Yangzhou)

- Theme Leader for LSHTM Centre for Data and Statistical Sciences for Health (DASH)

Editor Roles:-

- Guest Editor for Frontiers in Microbiology – Food microbiology; Research Topic - Developments in Campylobacter, Helicobacter & Related -Organisms Research – CHRO 2019, with co-Editors Professor Nicolae Corcionivoschi (AFBI) and Professor Stuart Thompson (University of Georgia).

- Guest Editor for Microorganisms - Foodborne Pathogen Campylobacter with co-Editor Professor Nicolae Corcionivoschi (AFBI).

- Guest Editor for Frontiers in Microbiology; Research Topic: - Novel Strategies for the Control of Zoonotic Bacteria, with co-Editors Dr Anja Klančnik (University of Ljubljana, Slovenia) and Dr Jerica Sabotič (Institut Jožef Stefan, Slovenia).

- Associate Editor for Frontiers in Microbiology – Microorganisms in Vertebrate Digestive Systems.

- Guest Editor for Frontiers in Microbiology – Infectious Agents and Disease; Research Topic - Recent advances in Campylobacter Research, with co-- Editors Professor Nicolae Corcionivoschi (AFBI) and Professor Stuart Thompson (University of Georgia).

- Guest Editor for The Microbe; Research Topic: Mucosal pathogen physiology and host response: Gut health and disease, with co-Editor Dr Amirul Mallick (IISERK, Pakistan).

Membership of Learned Societies:-

- Full member of the Microbiology Society (Previously known as the Society of General Microbiology).

- Associate Faculty Member of Faculty of 1000 (post-publication peer review).

- Fellow of the Higher Education Academy (FHEA)

Languages:-

English, Turkish and Spanish