How the gut, liver and microbiota interact in health and disease
Oesophageal High Resolution Manometry-idiopathic pulmonary fibrosis (IPF)
C. difficile encased in a multispecies biofilm
How the gut, liver and microbiota interact in health and disease
- Faculty of Medicine and Health
- School of Medicine
- Groups and institutes
- Leeds Institute of Medical Research
- Division of Gastroenterology Hepatology and Antimicrobial Resistance
LIMR Division of Gastroenterology, Hepatology and Antimicrobial Resistance
Welcome to the Division of Gastroenterology, Hepatology and Antimicrobial Resistance (GHAM)
Head of Division: Dr Ian Rowe
Deputy Head of division: Dr Caroline Chilton
The Gastroenterology, Hepatology and Antimicrobial Resistance (GHAM) division brings together complementary strengths in gastrointestinal, liver, and antimicrobial research to address pressing clinical challenges and improve patient outcomes. Supported by NIHR infrastructure awards, including the Biomedical Research Centre and HealthTech Research Centre, GHAM provides a platform for cutting-edge science, fostering innovation, collaboration and the development of future academic leaders.
Our research spans fundamental biology, translational studies, and patient-centred clinical investigations. By integrating expertise across gastroenterology, hepatology, and antimicrobial resistance, we explore how the gut, liver and microbiota interact to influence health, resilience and treatment strategies, aiming to understand disease mechanisms, develop innovative diagnostics and therapies, and evaluate interventions at both individual and population levels to improve patient outcomes.
Key Focus Areas:
- Gastroenterology: Advancing early detection and prevention of gastrointestinal disease, including colorectal cancer; improving understanding of gut-brain interactions and gastrointestinal symptom management; exploring microbiome-diet interactions; and developing targeted therapies for conditions such as IBS.
- Hepatology: Addressing patient-relevant liver disease challenges, including non-alcoholic fatty liver disease (NAFLD) and cirrhosis, with a focus on early diagnosis, risk stratification, and prevention of complications.
- Antimicrobial Resistance (AMR): Evaluating new treatments and diagnostics for healthcare-associated infections; conducting large-scale surveillance of resistance patterns; and investigating the interplay between gut microbiota, nutrients, and antimicrobials to identify biomarkers and therapeutic strategies.
Across all areas, GHAM researchers collaborate closely with Leeds Teaching Hospitals NHS Trust, the University of Leeds, and patient and public engagement groups. This integrated approach ensures our research is translational, patient-focused, and positioned to influence clinical practice, public health, and policy.
The Intelligence Layer: Who Drives the Science
Our work is powered by a diverse and interconnected network of researchers, analysts, and clinicians. Across disciplines and career stages, each contributes unique expertise to generate, interpret, and translate data into insight on antimicrobial resistance.
Prof. Mark Wilcox
Prof Wilcox (Leeds, NHS) leads national AMR efforts. His research covers C. difficile, diagnostics, antibiotic resistance, gut microbiome, and antimicrobial development.
More on Prof. Mark WilcoxProf. Mark Hull
Prof Hull is a clinician scientist focused on colorectal cancer prevention, integrating molecular biology, nutrition, and clinical trials to develop chemoprevention and risk-reduction strategies.
More on Prof. Mark HullProf. Lesley Houghton
Prof Houghton focuses on gut–brain disorders like IBS and connections between gastrointestinal dysfunction and diseases such as respiratory conditions.
More on Prof. Lesley HoughtonProf. Alex Ford
Prof. Ford studies the epidemiology and treatment of disorders of gut-brain interaction, such as irritable bowel syndrome and functional dyspepsia, using randomised trials and meta-analysis.
More on Prof. Alex FordDr Jonathan Sandoe
Dr Sandoe focuses on antimicrobial stewardship and prescribing, with expertise in infective endocarditis, healthcare-associated infections, and antimicrobial resistance.
More on Dr Jonathan SandoeDr Andrew Kirby
Dr Kirby focuses on complex intra-abdominal infections, surgical antibiotic prophylaxis, and healthcare-associated infections, integrating antibiotic pharmacology with narrative-based approaches.
More on Dr Andrew KirbyDr Ian Rowe
Dr Rowe is a clinical hepatologist focusing on liver disease outcomes, risk stratification, and early detection of complications, integrating epidemiology and clinical trials to improve patient care.
More on Dr Ian RoweDr Caroline Chilton
Dr Chilton is specialising in healthcare-associated infections, antimicrobial resistance, and gut microbiota, using in vitro models to study antibiotic–microbiome interactions and C. difficile.
More on Dr Caroline ChiltonDr Jane Freeman
Dr Freeman is a Clinical microbiologist specialising in Clostridioides difficile, antimicrobial-mediated dysbiosis, AMR, and diagnostics; established the human gut model of CDI at Leeds.
More on Dr Jane FreemanDr Suparna Mitra
Dr Mitra integrates microbiome, dietary, and environmental datasets to uncover how antimicrobial resistance (AMR) emerges across systems, focusing on global health and underrepresented populations.
More on Dr Suparna MitraDr Ines Moura
Dr Moura decodes gut microbiome dynamics and antimicrobial resistance using advanced in vitro models to understand pathogen behaviour, antibiotic impact, and therapeutic interventions.
More on Dr Ines MouraDr Christopher Rooney
Dr Rooney is a Clinical microbiologist bridging microbiome research and patient care, focusing on AMR, autoimmunity, and translating multi-omics insights into diagnostics and practice.
More on Dr Christopher Rooney
Indoor Microbiomes and Healthy Buildings Workshop Invitation
One-day interdisciplinary workshop on “Indoor Microbiomes and Healthy Buildings” at the University of Leeds (19 May 2026, Nexus Building, 09:30–16:00), funded through a grant secured by Dr Suparna Mitra from the Healthy Buildings Network.
The event explores how building design and operation shape indoor microbial communities and their links to health, sustainability, and resilience, bringing together researchers from engineering, microbiology, architecture, public health, environmental science, and data science.
It includes a call for ECR poster abstracts (250 words max) due by 10 May 2026, and is free to attend with registration open online.
Indoor Microbiomes & Healthy Buildings: Rethinking the Future of Indoor Health
GHAM News Updates
GermBugs: Resource for clinical education
GermBugs is a resource developed at Leeds Institute of Medical Research to facilitate teaching healthcare staff clinical microbiology. The use of stories and images helps students learn difficult concepts and makes the subject memorable.
Using in vitro systems to model gut microbiota communities
Dr Chilton aims to understand the complex interplay between the normal gut microbiota, therapeutic agents, and opportunistic infections, with a particular focus on how antimicrobial resistance reshapes these interactions. His research uses in vitro gut microbiota models derived from stool samples to simulate community-level changes following different treatments, with the goal of improving patient outcomes after therapy.
Field-Based AMR Surveillance in LMIC Communities
Dr Mitra focuses on antimicrobial resistance, with particular attention to how diet, environment, and microbial ecology interact across human and environmental systems. Antimicrobial resistance in low- and middle-income countries is strongly shaped by unrestricted antibiotic use and complex community-level health behaviours. Through field-based studies in Bangladesh and India, this work examines how these practices influence resistance dynamics, generating insights across human and environmental interfaces. This community-centred approach offers a transferable model for AMR surveillance and intervention across similar global settings.
Honorary Fellowships by the Academy for Healthcare Science.
We are proud to announce that two senior leaders from the NIHR (National Institute for Health and Care Research) Leeds Biomedical Research Centre have been awarded Honorary Fellowships by the Academy for Healthcare Science.
Dr Kerrie Davies MBE and Dr Jane Freeman have each received the title of Honorary Fellow of the Academy for Healthcare Science, the highest honour awarded by the Academy, in recognition of their outstanding contributions to healthcare science, research leadership and patient care. As Co-Deputy Theme Leads for AMR and Infection at the NIHR Leeds BRC, Kerrie and Jane play a central role in translating cutting-edge research into improved patient outcomes. Both are also dedicated mentors and champions for Healthcare Scientists in research careers. Congratulations on this outstanding achievement.
Building Global AMR Partnerships: Network meeting in India
In January 2026, Dr Suparna Mitra convened an Academy of Medical Sciences–funded network meeting at SRM Institute, India, co-led with Prof. Jayaseelan Murugaiyan, bringing together over 20 collaborators to advance interdisciplinary antimicrobial resistance (AMR) research. The meeting strengthened international partnerships, enabled data sharing, and fostered new collaborations across clinical, microbiome, and data science. It also supports cross-sectional data collection across three Indian cities, including faecal samples, dietary (FFQ), behavioural, and anthropometric data, enabling integrated analysis of AMR across community settings.
ECR research culture grant
Dr Ines Moura is co-leading a research culture grant to fund training opportunities to ECRs/PDRAs across the FMH, FBS and FEPS, to promote closer links ahead of the faculties alignment.
As part of this grant, we will be funding a limited number of places to the PRINCE2 project management course, to support career development.
On the 20th May we will also be hosting an event on Career pathways for ECRs - Building the Career you want. This session will bring together experts from RIS and OD&PL to share their insight on funding opportunities and how to showcase your skills to look for job opportunities within, and outside, academia.
Future events include an interdisciplinary sandpit for ECRs on the 25th June that will be hosted with the support of the Horizons team and a social event (details to be confirmed) in July.
The artist and the scientist
In April Dr Jane Freeman was invited speaker at the National Centre for Academic and Cultural Exchange (NCACE) Festival Week: The artist and the scientist: knowledge generation from lab to the public featuring work from longstanding collaboration with international bioartist, Anna Dumitriu
Events organised by Empower Leeds Women (ELW) Network
Dr Jane Freeman and Dr Kerrie Davis hosted the Empower Leeds Women (ELW) “Woman of the North” event in Jan. This featured Keynote Speaker Fatima Khan Shah, West Yorkshire Inclusivity Champion at the WY Mayors Office.
They also hosted three webinars in the “Empowering Women through movement” series co-host by The ELW and the University of Leeds Inter Active Network
Latest Conference News Updates from GHAM
Dr Jane Freeman was Invited speaker at ESCMID Global 2026 on Adoption and implementation: the long and winding road in the Value of Diagnostics session ESCMID: Munich 2026
Dr Jon Sandoe is part of the European Society of Clinical Microbiology and Infectious Diseases guideline development group that has recently published European guidelines on the evaluation and management of antibiotic allergies.
Dr Ines Moura delivered invited talk at Bionow BioInfect 2026 Conference in Manchester on ‘MiGut – a laboratory model to study the gut microbiome and GI infections’.
Dr Ines Moura delivered a talk on ‘Recapturing individual inflammatory responses in IBD microbiomes using an in vitro colonic model (MiGut)’ at ESCMID 2026 in Munich.
GHAM Publications (2026)
Design of Treatment Trials for Disorders of Gut-Brain Interaction. Sayuk GS, Brenner DM, Carbone F, Knowles SR, Lacy BE, Staudacher HM, Ford AC.Gastroenterology. 2026 May;170(6):1388-1407. doi: 10.1053/j.gastro.2025.12.040.
Safety and efficacy of CRS3123 in adults with a primary episode or first recurrence of Clostridioides difficile infection: a phase 2, randomised, double-blind, multicentre, vancomycin-controlled study. Louie T, Ribble W, Boccumini L, Johnson K, De Groote MA, Day J, Mason C, Sun X, Freeman J, Gu K, Tillotson G, Wilcox MH, Janjic N, Jarvis TC, Nayak SU, Ochsner UA, Bruss JB.Lancet Infect Dis. 2026 May;26(5):535-548. doi: 10.1016/S1473-3099(25)00721-2.
Fundamentals of Neurogastroenterology: Physiological Aspects and Clinical Implications. De Giorgio R, Boeckxstaens GE, Cryan JF, D'Amato M, Dinning PG, Hasler WL, Vanuytsel T, Houghton LA.Gastroenterology. 2026 May;170(6):1114-1132. doi: 10.1053/j.gastro.2026.02.004.
ESCMID clinical guidelines on the evaluation and management of a reported antibiotic allergy. Joean O, Sermet K, Ashkenazi-Hoffnung L, Kiymaz YC, Blumenthal K, Bonazzetti C, Chiriac AM, Gomez-Zorrilla S, Karakike E, Khatamzas E, Powell N, Trubiano JA, Wijnakker R, Sandoe J, Nagavci B, De Boer MGJ.Clin Microbiol Infect. 2026 May;32(5):767-787. doi: 10.1016/j.cmi.2026.02.011.
What are patients' and healthcare professionals' views on managing penicillin allergy? A qualitative evidence synthesis. Kildonaviciute K, Wanat M, Roberts NW, Sandoe J, Tonkin-Crine S.JAC Antimicrob Resist. 2026 Apr 20;8(2):dlag049. doi: 10.1093/jacamr/dlag049.
Letter: The Persistence of Anxiety and Depression in Inflammatory Bowel Disease-A Core Phenotype Beyond Inflammatory Activity. Authors' Reply. Riggott C, Fairbrass KM, Guthrie EA, Black CJ, Selinger CP, Ford AC, Gracie DJ.Aliment Pharmacol Ther. 2026 Apr 17. doi: 10.1111/apt.70673.
Natural History of Psychological Symptoms in Individuals With Rome IV Irritable Bowel Syndrome and Association With Gastrointestinal Symptom Severity. Khasawneh M, Goodoory VC, Ford AC, Black CJ.Neurogastroenterol Motil. 2026 Apr;38(4):e70301. doi: 10.1111/nmo.70301.
Stability of Classification Systems for Irritable Bowel Syndrome. Khasawneh M, Goodoory VC, Ng CE, Ford AC, Black CJ.Aliment Pharmacol Ther. 2026 Apr;63(8):1132-1139.
Blood Culture Pathways in UK Hospitals: An Exploratory Survey. Drury K, Anton-Vazquez V, Sellers P, Lant S, Kirby A, Walsh C, de Sario V, Lambourne J, Khan D, Holmes C, Dall'Antonia M, Bamford KB, Twagira MFN, Barton E, Nageshwaran V, Jeffery K, Parker A, Subbaraj KP, Sabtu N, Patel T, Deas G, Pichierri G, Palmer R, McKerr E, Hamson C, White L, Senior E, Prescott D, Gupta I, Planche T.J Hosp Infect. 2026 Apr 8:S0195-6701(26)00117-9. doi: 10.1016/j.jhin.2026.03.027.
Unravelling the Links Between Gastroesophageal Reflux and Lung Disease: New Insights. Bradley JA, Koop A, Lee AS, Beirne P, Johnson MM, DeVault KR, Houghton LA. Dig Dis Sci. 2026 Apr 15. doi: 10.1007/s10620-026-09894-7.
Clostridioides difficile pathogenesis and control. Chilton CH, Viprey V, Normington C, Moura IB, Buckley AM, Freeman J, Davies K, Wilcox MH.Nat Rev Microbiol. 2026 Mar;24(3):215-232. doi: 10.1038/s41579-025-01242-2.
Predicting the Risk of Decompensation in Patients with Cirrhosis - a Validated Machine Learning Approach. Johnson PJ, Kalyuzhnyy A, Grauslys A, Toyoda H, Villa E, Elshaarawy O, Stewart S, Rowe IA, Shearer J, Guha IN.Am J Gastroenterol. 2026 Mar 25. doi: 10.14309/ajg.0000000000004004.
Parental awareness and management of antibiotic side effects and allergies in children and young people: a UK survey. Clayton L, Demirjian A, Sandoe JAT, Lecky DM.JAC Antimicrob Resist. 2026 Mar 24;8(2):dlag040. doi: 10.1093/jacamr/dlag040.
Gut microbiome signatures in colorectal neoplasia: a cross-sectional study across neoplasia stages and subtypes. Louca P, Manning S, Hackney E, Sharp L, Hull MA, Koo S, Young GR, Taylor GS, Dunneram Y, Mitra S, Hampton JS, Dobson C, Neilson LJ, Addison C, El-Omar EM; COLO-COHORT research team; Stewart CJ, Rees CJ.Gut. 2026 Mar 6:gutjnl-2025-337478. doi: 10.1136/gutjnl-2025-337478.
Current challenges in real-world management of Clostridioides difficile infection. Granata G, Davies K, Guery B, Freeman J, Heritage J, Lillis CJ, Pipitone G; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridioides difficile.Clin Microbiol Infect. 2026 Mar;32(3):347-349. doi: 10.1016/j.cmi.2025.12.012.
Omega-3 polyunsaturated fatty acids and gut microbiota. Hull MA, Sun H.Curr Opin Clin Nutr Metab Care. 2026 Mar 1;29(2):123-130. doi: 10.1097/MCO.0000000000001176.
Prevalence of disability in inflammatory bowel disease: a systematic review and meta-analysis. Nardone OM, Calabrese G, Ford AC, Castiglione F, Savarino EV, Jairath V, Yuan Y, Danese S, Parigi TL, Barberio B.Inflamm Bowel Dis. 2026 Mar 5:izag022. doi: 10.1093/ibd/izag022.
Dietary Patterns Are Associated With Variations in the Global Prevalence and Severity of Rome IV Irritable Bowel Syndrome. Jaafari H, Houghton LA, West RM, Shuweihdi F, Staudacher H, Nikolova S, Ford AC, Whorwell PJ, Bangdiwala SI, Palsson OS, Sperber AD, Vasant DH.Clin Gastroenterol Hepatol. 2026 Mar;24(3):814-823.e3. doi: 10.1016/j.cgh.2025.06.004.
Operationalising Genomic Surveillance for Antimicrobial Resistance in Low- and Middle-Income Countries: A One Health Perspective from Bangladesh. Singh K, Mitra S.Microorganisms. 2026 Feb 25;14(3):527. doi: 10.3390/microorganisms14030527.
Novel Symptom Subgroups in Patients With Irritable Bowel Syndrome Are Associated With Healthcare Utilisation in Secondary and Tertiary Care. Goodoory VC, Khasawneh M, Riggott C, Vasant DH, Eugenicos M, Aziz I, Corsetti M, Paine PA, Danvers R, McKinnie K, Bush D, Black CJ, Ford AC. Aliment Pharmacol Ther. 2026 Feb 19. doi: 10.1111/apt.70583.
Capnocytophaga canimorsus endocarditis following a dog lick - a case report. Garr W, Verga M, O'Neill J, Sandoe J, Javangula K.Access Microbiol. 2026 Jan 28;8(1):001113.v3. doi: 10.1099/acmi.0.001113.v3.
The effect of omega-3 polyunsaturated fatty acids on short-chain fatty acid production and the gut microbiome in an in vitro colonic fermentation model. Aldoori J, Mitra S, Davie A, Toogood GJ, Edwards C, Hull MA.Gut Microbiome (Camb). 2026 Jan 6;7:e1. doi: 10.1017/gmb.2025.10016.
All in my head or all in my gut? An update on irritable bowel syndrome. Woods AT, Ford AC, Black CJ.Curr Opin Gastroenterol. 2026 Jan 1;42(1):52-58. doi: 10.1097/MOG.0000000000001141.












