Professor Hoyles focuses on microbiome research. She combines microbiology and bioinformatics approaches in vitro and in vivo to understand how members of the gut microbiota function and influence human health and disease. She has specific expertise in anaerobic microbiology, and the processing and analyses of various types of omics data (microbiomic, transcriptomic, metabolomic, genomic). Using integrated systems-level approaches, Professor Hoyles has defined the contribution of the microbiome and its metabolites to non-alcoholic fatty liver disease, metabolic retroconversion and integrity of the blood–brain barrier.
August 2020 – present: Professor of Microbiome and Systems Biology, Nottingham Trent University, UK.
March 2021 – present: Visiting Professor (Dept of Surgery and Cancer), Imperial College London, UK.
August 2018 – July 2020: Associate Professor (Reader) in Microbiology, Nottingham Trent University, UK.
August 2018 – February 2021: Visiting Reader (School of Public Health), Imperial College London, UK.
March 2016 – July 2018: MRC Intermediate Research Fellow in Data Science (UK Med-Bio), Imperial College London, UK.
November 2014 – February 2016: Lecturer in Microbiology, University of Westminster, UK.
October 2012 – November 2014: Postdoctoral Research Associate in Bioinformatics and Translational Systems Biology, Imperial College London, UK.
October 2011 – September 2012: Advanced MRC scholar, MSc (DIC) Bioinformatics and Theoretical Systems Biology, Imperial College London, UK.
October 2009 – September 2011: Government of Ireland Postdoctoral Fellow in Science, Engineering and Technology (IRCSET scheme), University College Cork, Ireland.
Professor Hoyles started her career at the Institute of Food Research, Reading as a taxonomist, characterizing novel fastidious Gram-positive anaerobes isolated from clinical and veterinary sources. Her GlaxoSmithKline-funded PhD, at the University of Reading in the Food Microbial Sciences Unit headed by Professor Glenn Gibson, focused on using in vitro fermentation systems to understand the effect of an anti-obesity therapy on the human gut microbiota and its lipolytic activity. She then secured an Irish Government Fellowship at University College Cork to work in the bacteriophage research group of Professor Douwe van Sinderen, developing methods to improve recovery and characterization of bacteriophage populations within the human gut.
Since training as a computational biologist, Professor Hoyles has worked extensively in the field of systems biology. Most recently, she has worked on numerous animal and human studies integrating microbiomic, metabolomic and transcriptomic data to better understand how the microbiome and its metabolites influence intestinal and systemic health.
Professor Hoyles is Research Lead for the Antimicrobial Resistance, Omics and Microbiota research theme, situated within the Centre for Health, Ageing and Understanding Disease (CHAUD) and affiliated with the Department of Biosciences.
Her research interests are wide-ranging, covering:
- Coriobacteriia, Klebsiella and Sutterella spp. associated with the gut microbiota
- Microbial lipid metabolism
- Shotgun metagenomics (microbiome and virome)
- Transcriptomics (eukaryote and prokaryote)
- Effect of gut-derived microbial metabolites on mammalian health
- Dietary interventions to manipulate the gut microbiome to improve health outcomes
- Microbiota of the small intestine
- Use of in vitro systems to study diet–microbiome interactions
- Klebsiella oxytoca-related bacteria, their metabolic end-products and their bacteriophages
Available self-funded/sponsor-funded projects
Opportunities arise to carry out postgraduate research towards an MPhil/PhD in the areas identified above. Further information may be obtained on the NTU Research Degrees' website. Those interested in undertaking self-funded/sponsor-funded PhD studies under Professor Hoyles's supervision should refer to the projects listed below; they are currently being offered by Professor Hoyles and align with her research interests and expertise.
A range of projects investigating the contribution of gut-associated Klebsiella spp. to the microbiome are available under Professor Hoyles's supervision. Contact her directly if you are interested in these projects.
Fully funded PhD studentship available to develop novel therapeutics derived from Klebsiella spp. and their bacteriophages.
- Isolation and characterization of bacteriophages against Klebsiella pneumoniae and Klebsiella oxytoca.
- Pangenome analysis of Fusobacterium necrophorum subsp. funduliforme. Collaboration with University of Westminster.
- Genomic diversity of the Klebsiella oxytoca complex.
- Genomic diversity of Collinsella aerofaciens and other Coriobacteriia.
- Diversity of Bacteroides fragilis, focusing on its antimicrobial resistance genes and virulence factors. Collaboration with Queen's University Belfast.
- Influence of dietary methylamines on growth and metabolism of members of the human gut microbiota.
- Integrated systems biology approaches to understand how the gut microbiome influences NAFLD (Guts UK, Diabetes UK). Collaboration with Imperial College London.
- Direct manipulation of the small-intestinal microbiota to improve post-operative outcomes. Collaboration with Imperial College London.
- Metagenomics and culturomics applied to the microbiota of the human small intestine. Collaboration with Imperial College London.
- The influence and manipulation of the gut microbiota in chronic kidney disease. Collaboration with The William Harvey Research Institute.
- Microbiome-associated metabolites and the gut–brain axis (Alzheimer's Research UK). Collaboration with Queen Mary University of London.
- Microbiome work associated with ATHLETE – Advancing tools for human early lifecourse exposome research and translation (EU Horizon 2020).
Postgraduate research student supervision
Mr Mohamed Eladawy. Bacteria associated with catheter infections in an Egyptian hospital, and their exploitation for novel antimicrobials. PhD, Nottingham Trent University. October 2021–present. Sponsored by the Egyptian Government – Ministry of Higher Education/Egyptian Cultural and Education Bureau.
Miss Onnicha Leelastwattanagul. Characterization of Collinsella aerofaciens associated with the human gut microbiota. PhD, Nottingham Trent University. October 2021–present.
Mr Samuel Dawson. Understanding metabolism of dietary methylamines by the human gut microbiota. PhD, Nottingham Trent University. October 2019–present.
Dr Preetha Shibu. Investigations of carbapenem-resistant Klebsiella species and associated clinical considerations. Professional Doctorate, University of Westminster. Completed 2019. Paper 1 | Paper 2 | Paper 3
Dr Thanikan Thorasin. Investigation and characterization of the ‘Atopobium cluster’ of the human faecal microbiota. PhD, University of Reading. Completed 2015. Paper 1
Co-supervise one PhD student at NTU. Co-supervise two Clinical Research Fellows at Imperial College London.
Hamied Foundation UK–India Antimicrobial Resistance (AMR) Visiting Professor 2019–2020 (extended to 2022 due to COVID-19)
Fellow of the Royal Society of Biology
Contributed to a POSTnote on The Microbiome and Human Health delivered to Members of Parliament in May 2018 by the Houses of Parliament Parliamentary Office of Science & Technology
Member of the Executive Committe of the ESCMID Study Group for Host And Microbiota Interaction – ESGHAMI
Co-vice Chair of the Research Committee of the Healthcare Infection Society
ILSI Europe Expert Group/Organizing Committee on ‘Mechanistic Insights into the Gut–Brain Axis'
Member of the Microbiology Society
Member of the Healthcare Infection Society
Member of the Society for Applied Microbiology
Member of the British Society for Antimicrobial Chemotherapy
Refer to Professor Hoyles’s publons record for details of some of the journals she has reviewed manuscripts for. She was a Handling Editor for FEMS Microbiology Letters (2019–2022), an Associate Editor for BMC Microbiology (2020–2021), an Academic Editor for PeerJ (2017–2020) and a Review Editor on the Editorial Board of Nutrition and Metabolism, part of the journal Frontiers in Nutrition (2019–2020).
Professor Hoyles regularly reviews grants for the BBSRC, MRC and Wellcome Trust. She has also acted as a peer-reviewer for applications to The Netherlands Organisation for Health Research and Development (ZonMw), the Government of Ireland Postdoctoral Fellowship scheme, the Government of Ireland Postgraduate Scholarship scheme, the Newton Bhabha Fund, the Estonian Research Council and the Lister Institute Research Prize.
Member of the advisory cluster (8) Committee 2021: NWO Open Competition ENW-XL.
Review panel member 2021: UiO:Life Science convergence environments.
Sponsors and collaborators
Current and former collaborators
Dr Alan Walker, University of Aberdeen, UK
Dr Anne McCartney, University of Reading, UK
Dr David Randall, The William Harvey Research Institute, UK
Dr David Vauzour, Norwich Medical School, UK
Dr Geoffrey Foster, SRUC Scotland's Rural College, UK
Dr James Abbott, University of Dundee, UK
Dr Linda Stewart, Queen's University Belfast, UK
Dr Michael Cox, University of Birmingham, UK
Dr Pamela Greenwell, University of Westminster, UK
Dr Sarah Butcher, EMBL-EBI, UK
Dr Simon McArthur, Blizard Institute, UK
Dr Thomas Hitch, University Hospital RWTH Aachen, Germany
Dr Yogesh Shouche, National Centre for Microbial Resource at the National Centre for Cell Science, Pune, India
Professor Edward Moore, Culture Collection University of Gothenburg, Sweden
Professor George Hanna, Imperial College London, UK
Professor Glenn Gibson, University of Reading, UK
Professor John Wallace, University of Aberdeen, UK
Professor Jon Swann, University of Southampton, UK
Professor José-Manuel Fernández-Real, Hospital of Girona "Dr Josep Trueta", Spain
Professor Lindsay Hall, Quadram Institute, UK and Technical University of Munich, Germany
Professor Marc-Emmanuel Dumas, Imperial College London, UK
Professor Massimo Federici, University of Rome Tor Vergata, Italy
Professor Rémy Burcelin, Institut National de la Santé et de la Recherche Médicale (INSERM), France
Professor Sheila Patrick, Queen's University Belfast, UK
Professor Simon Carding, Quadram Institute, UK
Professor Stella Knight, Imperial College London, UK
Funders past and present
Cancer Research UK
Healthcare Infection Society
Royal Society (Yusuf and Farida Hamied Foundation International Exchange Award)
The Academy of Medical Sciences (Hamied Foundation UK–India Antimicrobial Resistance Visiting Professorship)
Institute for Translational Medicine and Therapeutics
Medical Research Council
Alzheimer’s Research UK
British Society for Antimicrobial Chemotherapy
Irish Research Council for Science, Engineering and Technology
Selected peer-reviewed research
Smith-Zaitlik T, Shibu P, McCartney AL, Foster G, Hoyles L, Negus D. Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes. Microbiology (Reading). 2022 Sep;168(9). doi: 10.1099/mic.0.001247. PMID: 36156193.
Stachulski AV, Knausenberger TB, Shah SN, Hoyles L, McArthur S. A host-gut microbial amino acid co-metabolite, p-cresol glucuronide, promotes blood-brain barrier integrity in vivo. Tissue Barriers. 2022 May 20:2073175. doi: 10.1080/21688370.2022.2073175. PMID: 35596559.
Fromentin S, Forslund SK, Chechi K, Aron-Wisnewsky J, Chakaroun R, Nielsen T, Tremaroli V, Ji B, Prifti E, Myridakis A, Chilloux J, Andrikopoulos P, Fan Y, Olanipekun MT, Alves R, Adiouch S, Bar N, Talmor-Barkan Y, Belda E, Caesar R, Coelho LP, Falony G, Fellahi S, Galan P, Galleron N, Helft G, Hoyles L, Isnard R, Le Chatelier E, Julienne H, Olsson L, Pedersen HK, Pons N, Quinquis B, Rouault C, Roume H, Salem JE, Schmidt TSB, Vieira-Silva S, Li P, Zimmermann-Kogadeeva M, Lewinter C, Søndertoft NB, Hansen TH, Gauguier D, Gøtze JP, Køber L, Kornowski R, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Letunic I, Bäckhed F, Oppert JM, Nielsen J, Raes J, Bork P, Stumvoll M, Segal E, Clément K, Dumas ME, Ehrlich SD, Pedersen O. Microbiome and metabolome features of the cardiometabolic disease spectrum. Nat Med. 2022 Feb;28(2):303-314. doi:10.1038/s41591-022-01688-4.
Menghini R*, Hoyles L*, Cardellini M*, Casagrande V, Marino A, Gentileschi P, Davato F, Mavilio M, Arisi I, Mauriello A, Montanaro M, Scimeca M, Barton RH, Rappa F, Cappello F, Vinciguerra M, Moreno-Navarrete JM, Ricart W, Porzio O, Fernández-Real JM, Burcelin R, Dumas ME, Federici M M. ITCH E3 ubiquitin ligase downregulation compromises hepatic degradation of branched-chain amino acids. Mol Metab. 2022 Feb 9:101454. doi:10.1016/j.molmet.2022.101454. *Shared first authorship.
Hoyles L, Pontifex MG, Rodriguez-Ramiro I, Anis-Alavi MA, Jelane KS, Snelling T, Solito E, Fonseca S, Carvalho AL, Carding SR, Müller M, Glen RC, Vauzour D, McArthur S. Regulation of blood-brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide. Microbiome. 2021 Nov 27;9(1):235. doi:10.1186/s40168-021-01181-z.
Shibu P, McCuaig F, McCartney AL, Kujawska M, Hall LJ, Hoyles L. Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster. Microb Genom. 2021 June 18. doi:10.1099/mgen.0.000592.
Mayneris-Perxachs J, Cardellini M, Hoyles L, Latorre J, Davato F, Moreno-Navarrete JM, Arnoriaga-Rodríguez M, Serino M, Abbott J, Barton RH, Puig J, Fernández-Real X, Ricart W, Tomlinson C, Woodbridge M, Gentileschi P, Butcher SA, Holmes E, Nicholson JK, Pérez-Brocal V, Moya A, Clain DM, Burcelin R, Dumas ME, Federici M, Fernández-Real JM. Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome. Microbiome. 2021 May 7;9(1):104. doi:10.1186/s40168-021-01052-7.
D'Amato A, Di Cesare Mannelli L, Lucarini E, Man AL, Le Gall G, Branca JJV, Ghelardini C, Amedei A, Bertelli E, Regoli M, Pacini A, Luciani G, Gallina P, Altera A, Narbad A, Gulisano M, Hoyles L, Vauzour D, Nicoletti C. Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients. Microbiome. 2020 Oct 1;8(1):140. doi:10.1186/s40168-020-00914-w.
Kujawska M, La Rosa SL, Roger LC, Pope PB, Hoyles L, McCartney AL, Hall LJ. Succession of Bifidobacterium longum strains in response to a changing early life nutritional environment reveals dietary substrate adaptations. iScience. 2020 Aug 21;23(8):101368. doi:10.1016/j.isci.2020.101368.
Chen Y, Brook TC, Soe CZ, O'Neill I, Alcon-Giner C, Leelastwattanagul O, Phillips S, Caim S, Clarke P, Hall LJ, Hoyles L. Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors. Microb Genom. 2020 Jun;6(6):e000377. doi:10.1099/mgen.0.000377.
Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, Kujawska M, Martin S, Peel N, Acford-Palmer H, Hoyles L, Clarke P, Hall LJ, Clark MD. Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens. Nat Microbiol. 2020 Mar;5(3):430-442. doi:10.1038/s41564-019-0626-z.
Hoyles L, Fernández-Real JM, Federici M, Serino M, Abbott J, Charpentier J, Heymes C, Luque JL, Anthony E, Barton RH, Chilloux J, Myridakis A, Martinez-Gili L, Moreno-Navarrete JM, Benhamed F, Azalbert V, Blasco-Baque V, Puig J, Xifra G, Ricart W, Tomlinson C, Woodbridge M, Cardellini M, Davato F, Cardolini I, Porzio O, Gentileschi P, Lopez F, Foufelle F, Butcher SA, Holmes E, Nicholson JK, Postic C, Burcelin R, Dumas ME. Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women. Nat Med. 2018 Jul;24(7):1070-1080. doi:10.1038/s41591-018-0061-3.
Hoyles L, Jiménez-Pranteda ML, Chilloux J, Brial F, Myridakis A, Aranias T, Magnan C, Gibson GR, Sanderson JD, Nicholson JK, Gauguier D, McCartney AL, Dumas ME. Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota. Microbiome. 2018 Apr 20;6(1):73. doi:10.1186/s40168-018-0461-0.
Hoyles L, Snelling T, Umlai UK, Nicholson JK, Carding SR, Glen RC, McArthur S. Microbiome-host systems interactions: protective effects of propionate upon the blood-brain barrier. Microbiome. 2018 Mar 21;6(1):55. doi:10.1186/s40168-018-0439-y.
Herridge WP, Shibu P, O'Shea J, Brook TC, Hoyles L. Bacteriophages of Klebsiella spp., their diversity and potential therapeutic uses. J Med Microbiol. 2020 Feb;69(2):176-194. doi:10.1099/jmm.0.001141.
Carding SR, Davis N, Hoyles L. Review article: the human intestinal virome in health and disease. Aliment Pharmacol Ther. 2017 Nov;46(9):800-815. doi:10.1111/apt.14280.
Hoyles L, Wallace RJ. Gastrointestinal tract: fat metabolism in the colon. Editor: H Goldfine; Health Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids. Handbook of Hydrocarbon and Lipid Microbiology. Springer, 2020, https://doi.org/10.1007/978-3-030-15147-8_30.
Hoyles L, Wallace RJ. Gastrointestinal tract: intestinal fatty acid metabolism and implications for health. Editor: H Goldfine; Health Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids. Handbook of Hydrocarbon and Lipid Microbiology. Springer, 2020, https://doi.org/10.1007/978-3-030-15147-8_31.
Hoyles L, Swann J. Chapter 18 - Influence of the human gut microbiome on the metabolic phenotype, Editors: JC Lindon, JK Nicholson, E Holmes; The Handbook of Metabolic Phenotyping, Elsevier, 2019, pages 535-560, https://doi.org/10.1016/B978-0-12-812293-8.00018-9.
Gut microbiome, gut microbiota, translational systems biology.