Dr Philip Warburton
Profiles

Dr Philip Warburton

Lecturer in Medical Microbiology

School of Biomedical Sciences (Faculty of Health)

Biography

Biography

Lecturer in Medical Microbiology within the School of Biomedical Sciences. 


Graduated in Microbiology from University of Central Lancashire in 2001, followed by a PhD in Molecular Microbiology from King's College London in 2006 investigating antibiotic resistance in periodontal disease. Worked as a Post-Doctoral Researcher at University College London: Eastman Dental Institute across three projects: investigating mobile genetic elements in the oral metagenome, hypervirulence in Clostridioides difficile, and pathogenicity in Staphylococcus aureus. In 2012, he undertook a Lectureship in Microbiology at Anglia Ruskin University before joining the University of Plymouth in 2015.

Research activities focus on the the development and spread of antimicrobial resistance through mobile genetic elements, and the development of novel antimicrobial therapies through the Plantimicrobials project looking at new antimicrobials from plants.

Current PhD students

  • Madeleine Steer (PhD candidate – co-supervisor with Professor Richard Thompson). Quantifying the influence of waste water treatment on the release of microplastics to the environment, 2018-present (Funding: NERC Industrial CASE with UKWIR).
  • Darshana Srivastava (PhD candidate - Director of Studies, with co-supervisors Professor Mathew Upton and Dr Lee Hutt). Plantimicrobials: Botanical epiphytic bacteria as a source of novel bioactive compounds for the treatment of pathogenic infections. 2023-present.
Recently completed PhD students

  • Dr Matthew Koch (co-supervised with Professor Mat Upton). Deep-sea discovery – mining marine environments for novel biologics, 2017-2022. (Funding: Society for Applied Microbiology)
  • Dr Poppy Hesketh-Best (co-supervised with Professor Kerry Howell). Investigating the microbial ecology of deep-sea sponges, 2017-2022. (Funding: Faculty of Science & Technology, University of Plymouth)

Qualifications

2015: Fellow of the Higher Education Academy (FHEA No.PR085534)
2013: PG Cert. Learning & Teaching in Higher Education. Anglia Ruskin University
2006: PhD Microbiology, "Molecular epidemiology of tetracycline resistance in periodontitis." King's College London
2001: BSc (Hons) Microbiology. University of Central Lancashire

Professional membership

Fellow of the Higher Education Academy

Member of the Microbiology Society
Member of the British Society for Antimicrobial Chemotherapy
Member of Applied Microbiology International (formerly SfAM)

Roles on external bodies

Journal Reviewer:

  • Journal of Antimicrobial Chemotherapy
  • FEMS Microbiology Ecology
  • Journal of Medical Microbiology
  • Environmental Microbiology
  • Environmental Pollution
  • Microbiology journal
  • Frontiers in Microbiology

Grant Reviewer:

  • Biotechnology and Biological Sciences Research Council (BBSRC)
  • Health Research Board, Ireland

External Examiner:

  • Edinburgh Napier University - Applied Microbiology programme and Microbiology & Biotechnology programme
  • University College London - PhD examiner

Teaching

Teaching

Teaching interests

Teaching general microbiology, molecular genetics, infectious diseases and antibiotic resistance, plus research methods, understanding and development across all levels (foundation, undergraduate and postgraduate). Also supervise both undergraduate and postgraduate project students, as well as co-supervise PhD students.


Winner of the 'Made a Difference' award, Anglia Ruskin University, 2015
Winner of the 'Most Dedicated Project/Dissertation Supervisor' award for the Faculty of Medicine & Dentistry at the UPSU SSTAR awards, University of Plymouth, 2019

Programme Lead:
  • MSc Biomedical Science (Cancer Biology, Clinical Neuroscience, and Infection & Immunity pathways)

Module Leader:
  • BIOM5005 Research Design and Development
  • BIOM5006 Research Project

Research project supervision:
  • BHCS3001 Personal research Project for BSc (Hons) Biomedical Science & BSc (Hons) Human Biosciences programmes
  • BIOM5006 Research Project for MSc Biomedical Science programme

Other Teaching Involvement:
  • BHCS001 Infection, Immunity and Therapeutics
  • BHCS1006: Infection and Immunity
  • BHCS2002: Evidence-Based Practice in Biomedical Science
  • BHCS2006: Infection, Immunity and Disease
  • BHCS2027: Placements and Employability
  • BHCS3003: Clinical Microbiology
  • BHCS3008: Current Developments in Biomedical Science (infection topic)
  • BHCS3030: Biomedical Science Placement
  • BIOM5001: Molecular Biology: Genomics, Transcriptomics and Proteomics
  • BIOM5008: Infection and Immunity
  • FMD003 Learning Skills for Healthcare

Research

Research

Research interests

Antibiotic Resistance and Novel Antimicrobials

The World Health Organisation has declared antibiotic resistance as one of the major threats facing public health as bacteria are becoming increasingly resistant to antibiotics of last resort which are critical in the treatment of diseases. My interests are focused on identifying the genetic basis of antibiotic resistance in bacteria, and understanding how this resistance is acquired and maintained in bacteria. Many antibiotic resistance genes are carried on mobile genetic elements, such as plasmids, conjugative transposons and integrative genetic elements, which are able to transfer between different bacteria further disseminating resistance. My investigations include looking at antibiotic resistance in bacteria from both clinical and environmental area which can contribute to hospital-acquired and community-acquired infections, and looking at diversity in the resistance mechanisms and their associated genetic elements.

I lead the Plantimicrobials project that is investigating plants for sources of novel antimicrobials to help combat antibiotic resistance, in collaboration with the Lost Gardens of Heligan and Cornish Essential Oils. I also collaborate with Dr Raul Bescos Garcia looking at the effects of propolis on oral bacteria. 

Bacterial Diversity

Bacteria often live in complex communities that can comprise several hundred different species. Many of these communities are poorly investigated, with limited knowledge on their composition and diversity. My research looks at bacteria community diversity, understanding what bacteria are present and potentially investigating them for novel compounds and enzymes. 

I currently have a number of collaborate partners and interested parties which include the Animal and Plant Health Agency (part of DEFRA), Anglia Ruskin University, Philip Parker Associates Environmental Consultancy, the Church of England and the National Trust, along with other charities and organisations.

I always welcome prospective PhD students which have an interest in these related areas. Please contact me in the first instance.

Research degrees awarded to supervised students

I have supervised over 10 MSc and 70 undergraduate project students in areas covering antibiotic resistance in clinical and environmental bacteria, molecular analysis of resistance mechanisms, novel antimicrobial therapies and bacterial pathogens. 

Current PhD students

  • Madeleine Steer (PhD candidate – co-supervisor with Professor Richard Thompson). Quantifying the influence of waste water treatment on the release of microplastics to the environment, 2018-present (Funding: NERC Industrial CASE with UKWIR).

  • Darshana Srivastava (PhD candidate - Director of Studies, with co-supervisors Professor Mathew Upton and Dr Lee Hutt). Plantimicrobials: Botanical epiphytic bacteria as a source of novel bioactive compounds for the treatment of pathogenic infections. 2023-present.


Completed PhD students

Current Group Members

  • Thomas Garry (UG year-long placement student 2022-23)

Recent Group Members

  • Ioanna Giannakidou (UG summer placement student 2022)
  • Stephanie MacLean (UG year-long placement student 2021-22)
  • Ellie Rowlands (UG summer placement student 2021)
  • Rachael Burton (UG summer placement student 2020)
  • Benedict Paulukiewicz (UG summer placement student 2019)
  • Agnes George (UG year-long placement student 2017-18)


Grants & contracts

  • Society for Applied Microbiology Summer Studentship - PI; £2485. Evaluating the Antimicrobial Activity of a Propolis-based Mouthwash on Oral Bacteria, with Ms Rachael Burton. 2021
  • Higher Education Innovation Fund (University of Plymouth) - Co-I with Professor Mat Upton; £9000. The Antibiotic Accelerator Network, ABX - engaging with industry to remove bottlenecks in antibiotic discovery. 2021
  • Seale-Hayne Educational Trust - PI; £5109. Microbial migrants: Microplastics as a vector in the spread of antibiotic resistant bacteria. 2020
  • Society for Applied Microbiology Summer Studentship - PI; £2489. Investigating bacteria associated with microplastics leaving wastewater treatment, with Mr Benedict Paulukiewicz. 2019
  • NERC Industrial CASE Studentship - Co-I with Professor Richard Thompson; £89,114. Quantifying the influence of waste water treatment on the release of microplastics to the environment, with Ms Madeline Steer. Commenced October 2018. 
  • Society for Applied Microbiology PhD Studentship - Co-I with Dr. Mat Upton, Dr Kerry Howell and Dr Alistair Bishop; £69,459). Deep Sea Discovery - Investigating deep sea sponges for novel bacteriocins, with Mr Matthew Koch. Commenced October 2017.
  • Plymouth University PhD Studentship - Co-I with Dr Kerry Howell, Dr Mat Upton and Dr Alistair Bishop; ~£61,000. The microbial ecology of deep sea sponges and mining for novel biologics, with Ms Poppy Hesketh-Best. Commenced September 2017.
  • Harry Smith Vacation Studentship, Microbiology Society - PI; £1845. Determining antibiotic resistance in bacteria from treated waste water, with Ms Melissa Temlett. 2017. 
  • Anglia Ruskin University Postgraduate Studentship (tuition fee only) - Co-PI with Dr. Benjamin Evans; ~£19,000). Investigating antibiotic resistance in aquatic sources, with Mr David Doherty. 2015.
  • Microbiology Society Harry Smith Vacation Studentship - PI; £1865. Investigating the molecular mechanisms of carbapenem resistance; with Mr Elliot Harper. 2015.
  • Deputy Vice Chancellor Extra-curricular Award, Anglia Ruskin University. Collaboration with Dr. Richard Jones; £1500. 2015.
  • Anglia Ruskin University, Postdoctoral Award. Co-I with Dr. Benjamin Evans; ~£48,000. Determining the mechanisms of carbapenem resistance in Acinetobacter baumanii; with Yuiko Takebayashi. Commenced November 2014. 
  • Enterprising Academics Award. Anglia Ruskin University. PI; £5000. Investigating pathogens and antibiotic resistance in UK farms. 2014. 
  • Anglia Ruskin University Graduate Summer Studentship. PI; £2000. Investigating bacterial diversity in faecal samples; with Mr Harry Tracey. 2014. 
  • Anglia Ruskin University Graduate Summer Studentship. PI; £2000. Investigating antibiotic resistance in clinical Enterococcus; with Ms Charlotte Bygraves. 2013
  • Anglia Ruskin University Postgraduate Studentship. (Co-PI with Dr. Benjamin Evans; ~£60,000. Investigating the mechanisms of antimicrobial resistance in oral bacteria; with Mr Simon Whelan. Commenced March 2013.




Publications

Publications

Key publications

Key publications are highlighted

Journals
Articles
Hesketh-Best PJ, January GG, Koch MJ, Warburton PJ, Howell KL & Upton M (2023) 'Whole genomes of deep-sea sponge-associated bacteria exhibit high novel natural product potential' FEMS Microbes , DOI Open access
Takebayashi Y, Henderson SR, Chirgadze DY, Warburton PJ & Evans BA (2022) 'OXA-66 structure and oligomerisation of OXAAb enzymes' Access Microbiology 4, (10) , DOI Open access
Koch MJ, Hesketh-Best PJ, Smerdon G, Warburton PJ, Howell K & Upton M (2021) 'Impact of growth media and pressure on the diversity and antimicrobial activity of isolates from two species of hexactinellid sponge' Microbiology 167, (12) , DOI Open access
Takebayashi Y, Findlay J, Heesom KJ, Warburton PJ, Avison MB & Evans BA (2021) 'Variability in carbapenemase activity of intrinsic OxaAb (OXA-51-like) β-lactamase enzymes in Acinetobacter baumannii' J Antimicrob Chemother 76, (3) 587-595 Author Site , DOI Open access
Warburton PJ & Roberts AP (2016) 'Comment on: Resistance gene naming and numbering: is it a new gene or not?' Journal of Antimicrobial Chemotherapy dkw407-dkw407 , DOI Open access
Warburton PJ, Amodeo N & Roberts AP (2016) 'Mosaic tetracycline resistance genes encoding ribosomal protection proteins' Journal of Antimicrobial Chemotherapy dkw304-dkw304 , DOI Open access
Arivaradarajan P, Warburton PJ, Paramasamy G, Nair SP, Allan E & Mullany P (2016) 'Identification of an antibacterial protein by functional screening of a human oral metagenomic library' FEMS Microbiology Letters 363, (1) fnv200-fnv200 , DOI Open access
Arivaradarajan P, Paramasamy G, Nair SP, Allan E & Mullany P (2015) 'Identification of an antibacterial protein by functional screening of a human oral metagenomic library' FEMS Microbiology Letters 362, (18) fnv142-fnv142 , DOI Open access
Card RM, Warburton PJ, MacLaren N, Mullany P, Allan E & Anjum MF (2014) 'Application of Microarray and Functional-Based Screening Methods for the Detection of Antimicrobial Resistance Genes in the Microbiomes of Healthy Humans' PLoS ONE 9, (1) 0-0 , DOI Open access
Warburton PJ, Ciric L, Lerner A, Seville LA, Roberts AP, Mullany P & Allan E (2012) 'TetAB(46), a predicted heterodimeric ABC transporter conferring tetracycline resistance in Streptococcus australis isolated from the oral cavity' Journal of Antimicrobial Chemotherapy 68, (1) 17-22 , DOI Open access
Mullany P, Allan E & Warburton PJ (2012) 'Tetracycline resistance genes and mobile genetic elements from the oral metagenome' Clinical Microbiology and Infection 18, 58-61 , DOI
Brouwer MSM, Warburton PJ, Roberts AP, Mullany P & Allan E (2011) 'Genetic Organisation, Mobility and Predicted Functions of Genes on Integrated, Mobile Genetic Elements in Sequenced Strains of Clostridium difficile' PLoS ONE 6, (8) e23014-e23014 , DOI Open access
Warburton PJ, Allan E, Hunter S, Ward J, Booth V, Wade WG & Mullany P (2011) 'Isolation of bacterial extrachromosomal DNA from human dental plaque associated with periodontal disease, using transposon-aided capture (TRACA)' FEMS Microbiology Ecology 78, (2) 349-354 , DOI Open access
Warburton P, Roberts AP, Allan E, Seville L, Lancaster H & Mullany P (2009) 'Characterization of <i>tet</i> (32) Genes from the Oral Metagenome' Antimicrobial Agents and Chemotherapy 53, (1) 273-276 , DOI
Warburton PJ, Palmer RM, Munson MA & Wade WG (2007) 'Demonstration of in vivo transfer of doxycycline resistance mediated by a novel transposon' Journal of Antimicrobial Chemotherapy 60, (5) 973-980 , DOI Open access
Chapters
Mullany P, Allan E & Warburton PJ (2011) 'Chapter 9: The Human Oral Metagenome' Metagenomics of the Human Body Springer New York 165-173 , DOI
Mullany P, Warburton P & Allan E (2010) 'The Human Oral Metagenome' Metagenomics of the Human Body Springer New York 165-173 , DOI
Presentations and posters
Hesketh Best P, Howell K, Upton M, Bishop A, Warburton P, Foster N & Koch M Hesketh Best P, Howell K, Upton M, Bishop A, Warburton P, Foster N & Koch M 'Assessing and optimising culturing methods for the associated-bacteria of two species of deep-sea sponges (class Hexactinellida) for antimicrobial bioprospecting' , DOI
Koch M, Best P, Farnham G, Kiernan M, Bishop A, Warburton P, Howell K & Upton M Koch M, Best P, Farnham G, Kiernan M, Bishop A, Warburton P, Howell K & Upton M 'Characterisation of the microbiome for two hexactinellid sponges and purification of associated antimicrobial agents from their resident microbes' , DOI
Personal

Personal

Other academic activities

Grant reviewer:
  • Biotechnology and Biological Sciences Research Council, UK
  • Health Research Board, Ireland.
Manuscript reviewer:
  • Environmental Pollution
  • Journal of Antimicrobial Chemotherapy
  • Frontiers in Microbiology
  • Environmental Microbiology
  • FEMS Microbiology Ecology
  • Microbiology Journal
  • Journal of Medical Microbiology