In this section

Host-Microbes-Diet Interactomics

Contact

Jia.li@imperial.ac.uk

10th Floor, Commonwealth Building, Hammersmith Campus.

020 7594 3230

What we do

We are a dynamic, multidisciplinary research group exploring the chemical complexity of the human gut. Our work focuses on how diet, gut microbiota, and host biology interact to shape health outcomes. We investigate how microbial and host-derived metabolites influence gut physiology and disease risk, including colorectal cancer and obesity. We also investigate how obesity treatment -whether surgical, pharmacological, or dietary - can reshape the gut microbiome and influence cardiometabolic health across generations.

Our team uses cutting-edge techniques—metabolic phenotyping, transcriptomics, immunofluorescence, immunohistochemistry, and flow cytometry—across a range of models, from cellular systems and rodent models to human cohorts. This integrated approach allows us to uncover the molecular mechanisms driving host-microbe-diet interactions.

Why it is important

The gut is more than a digestive organ—it's a biochemical hub where microbes and dietary components influence intestinal epithelial function, immunity, metabolism, and disease. Disruptions in this system are linked to major global health challenges, including cancer and metabolic disorders. By decoding the chemical dialogue between the host, microbes, and diet, we aim to identify new biomarkers, therapeutic targets, and dietary strategies that can transform how we prevent and treat disease.

How it can benefit patients

Our research aims to translate complex biochemical insights into tangible health benefits. By understanding how diet, microbial communities, and host responses interact, we can:

Identify early biomarkers of gut-related diseases, enabling earlier diagnosis and more targeted prevention.

Develop disease risk stratification strategies that support disease prevention and early diagnosis and intervention.

Inform clinical interventions—including surgery, medication, and nutrition—for obesity, with a focus on how these treatments affect long-term and even intergenerational cardiometabolic health.

Ultimately, our work bridges fundamental science and clinical application, helping to shape the future of precision nutrition and gut-targeted therapies.

Theme 1 – Diet, Microbiome & Gut Health

We investigate how diet shapes the gut microbiome and influences disease risk. Our studies in African populations show that high-fat, low-fibre diets increase colorectal cancer (CRC) risk, while fibre-rich diets are protective. In malnourished Malawian twins, we revealed how diet and microbiota co-regulate host physiology. We’re now uncovering mechanisms through which the gut microbiome (microbiota and their metabolites, such as indole-3-aldehyde) influence the intestinal mucosal health and CRC risk.

Theme 2 – Bariatric Surgery, Gut Microbiome & Colorectal Cancer

Bariatric surgery is an effective treatment for obesity and Type 2 Diabetes—but how does it affect long-term gut health? We study how Roux-en-Y Gastric Bypass (RYGB) reshapes the microbiome and alters host metabolism, with a focus on its potential impact on CRC risk. This work bridges metabolic surgery and cancer prevention through a microbiome lens. Here is an example of tyramine which is produced by gastric bypass-associated gut bacteria and increases colorectal cancer risk, and a short video.

Theme 3 – Obesity Treatment & Intergenerational Health

With nearly half of UK women of reproductive age overweight or obese, we explore how obesity treatments—like bariatric surgery and GLP-1 receptor agonists —affect not just maternal health, but also the cardiometabolic risk of their children. Our research addresses a critical knowledge gap in the transgenerational effects of modern obesity therapies.

Theme 4 – Bariatric Surgery & Polycystic Ovary Syndrome

Polycystic Ovary Syndrome (PCOS) affects up to 1 in 10 women of reproductive age and is closely linked to obesity and metabolic dysfunction. Bariatric surgery has been shown to improve spontaneous ovulation. We investigate how bariatric surgery alters metabolic pathways in women with PCOS. Our goal is to understand how these changes are associated with improved ovulation.

Theme 5 – Antibiotics, Microbiome & Diarrhoea

Intake of antibiotics profoundly disturb the gut microbiota composition and metabolism. We examine how different antibiotics and combinations disrupt the gut microbiome and contribute to antibiotic-associated diarrhoea. Our goal is to identify microbial signatures and interventions that can mitigate these side effects.

Theme 6 – Analytical Innovation in Metabolic Phenotyping

We develop and refine cutting-edge tools for metabolic phenotyping, including NMR spectroscopy for spatial tissue metabolite mapping and optimised protocols for biological sample handling, such as faecal sample metabolite extraction, short-chain fatty acid quantification and etc. Our methodological advances support high-resolution insights into host-microbe metabolic interactions.

Funders, related centres

Funders

Related centres

Industry

Lab4 Proboltics

Related education courses

Group alumni

Staff:

PhDs:

Assistant Professor Jutarop Phetcharaburanin
Dr Aruchuna Ruban
Dr Natalie McLymont
Dr Elisabeth Vonhof
Dr Grace Barker
Dr Qiling Chen
Dr Nikita Gandhi
Dr Aminah Alotaibi
Dr Cong Hu
Dr Shiva Thambiah Radhakrishnan
Dr Kate Gallagher
Dr Mu Wang
Dr Renata Oliveira de Vasconcelos
Dr Yang Bi

External PhD students:

Dominic Ritler (University of Bern)
Ornuma Haonon (Khon Kaen University)
Sureerat Padthaisong (Khon Kaen University)

Masters’ students

Selected Publications

Glymenaki M, Curio S, Shrestha S, Zhong Q, Rushton L, Barry R, El-Bahrawy M, Marchesi JR, Wang Y, Gooderham NJ, Guerra N, Li JV. Roux-en-Y gastric bypass-associated fecal tyramine promotes colon cancer risk via increased DNA damage, cell proliferation, and inflammation. Microbiome. 2025. 13, 60.
Ramaboli MC, Ocvirk S, Khan Mirzaei M, Eberhart BL, Valdivia-Garcia M, Metwaly A, Neuhaus K, Barker G, Ru J, Nesengani LT, Mahdi-Joest D, Wilson AS, Joni SK, Layman DC, Zheng J, Mandal R, Chen Q, Perez MR, Fortuin S, Gaunt B, Wishart D, Methé B, Haller D, Li JV, Deng L, Swart R, O'Keefe SJD. Diet Changes due to Urbanization in South Africa are Linked to Microbiome and Metabolome Signatures of Westernization and Colorectal Cancer. Nat Commun. 2024. 15:3379.
Wang M, Guo J, Hart AL, Li JV. Indole-3-Aldehyde Reduces Inflammatory Responses and Restores Intestinal Epithelial Barrier Function Partially via Aryl Hydrocarbon Receptor (AhR) in Experimental Colitis Models. J Inflamm Res. 2023. 16:5845-5864.
Jones B, Sands C, Alexiadou K, Minnion J, Tharakan G, Behary P, Ahmed A, Purkayastha S, Lewis M, Bloom S, Li JV, Tan T. The metabolomic effects of tripeptide gut hormone infusion compared to Roux-en-Y gastric bypass and caloric restriction. J Clin Endocrinol Metab 2022. 107(2):e767-e782.
Seyfried F, Phetcharaburanin J, Glymenaki M, Nordbeck A, Hankir M, Nicholson JK, Holmes E, Marchesi JR, Li JV. Roux-en-Y gastric bypass surgery in Zucker rats induces bacterial and systemic metabolic changes independent of caloric restriction-induced weight loss. Gut Microbes. 2021.13(1):1-20.
Li JV, Ashrafian H, Sarafian M, Homola D, Rushton L, Barker G, Cabrera PM, Lewis MR, Darzi A, Lin E, Gletsu Miller NA, Atkin SL, Sathyapalan T, Gooderham NJ, Nicholson JK, Marchesi JR, Athanasiou T, Holmes E. Roux-en-Y Gastric bypass-induced bacterial perturbation contributes to altered host-bacterial co-metabolic phenotype. Microbiome 2021; 9:139.
West KA, Kanu C, Maric T, McDonald JAK, Nicholson JK, Li JV, Johnson MR, Holmes E, Savvidou MD. Longitudinal metabolic and gut bacterial profiling of pregnant women with previous bariatric surgery. Gut. 2020; 69(8):1452.
O’Keefe SJD, Li JV, Lahti L, Ou J, Carbonero F, Mohammed K, Posma JM, Kinross J, Wahl E, Ruder E, Vipperla K, Naidoo V, Mtshali L, Tims S, Puylaert PGB, DeLany J, Krasinskas A, Benefiel AC, Kaseb HO, Newton K, Nicholson JK, de Vos WM, Gaskins HR, Zoetendal EG. Fat, fibre and cancer risk in African Americans and rural Africans. Nat Commun 2015; 6:6342
Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, Liu J, Houpt E, Li JV, Holmes E, Nicholson JK, Knights D, Ursell LK, Knight R, Gordon JI. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 2013; 339:548-554
Li JV*, Ashrafian H*, Bueter M, Kinross J, Sands C, le Roux CW, Bloom SR, Darzi A, Athanasiou T, Marchesi JR, Nicholson JK, Holmes E. Metabolic surgery profoundly influences gut microbial-host metabolic crosstalk. Gut 2011; 60:1214-1223

News

Chinese Life Scientists Society in the UK – 30th Annual Conference at CRUK, Cambridge, 11-12 September 2025

Jia, as the Chair of the Chinese Life Scientists Society in the UK, organised the 30th Annual Conference in Cambridge, along with the Cambridge Life Science Network and Cambridge Chem & Bio Seminar.

Dr Jiao Xiao, a visiting researcher supported by CSC scholarship in our lab, presented her work on the alkaloid-mediated modulation of neuroinflammation and gut microbiota attenuates depression-like behaviour in mice.

Workshop on Phenomic Medicine – Bangkok, Thailand 3-5th September 2025

Dr Caroline Clarke, Professors Julien Wist, Elaine Holmes and Jeremy Nicolson, Dr Jutarop Phetcharaburanin and Dr Jia Li have successfully delivered a 3-day workshop on phenomics medicine, attended by 50 researchers and policy makers.

Harnessing Phenomic Medicine and Personal Health AI for Smarter Health Solutions Conference - Bangkok, Thailand, 1st September 2025

Together with Asst. Prof. Jutarop Phetcharaburanin from Khon Kaen University, we are excited to kick off an initiative with the launch of our conference on “Harnessing Phenomic Medicine and Personal Health AI for Smarter Health Solutions.” Our goal is to catalyse the integration of phenomics and AI into health monitoring systems to advance disease prevention and personalised care. This initiative was financially supported by the British Council.

Kaoutar Abaakil and Jia Present at Metabolomics Annual Conference 2025

Thoroughly enjoyed the Metabolomics Society annual conference 2025 in beautiful Prague. Jia presented the research on post-bariatric pregnancies and their impact on neonatal outcomes, and Kaoutar Abaakil presented her PhD research on the sex-dependent effects of the diets and relation to colon cancer.

Summer picnic in the Wormwood Scrubs

Kaoutar Abaakil and Xuan Yang Present at Digestive Disease Week 2025

Miss Kaoutar Abaakil and Miss Xuan Yang attended the prestigious Digestive Disease Week 2025 conference, held in San Diego from May 3–6.

Kaoutar presented a poster titled “Distinct transcriptional and metabolic adaptations in the jejunum from mice fed with a Western or a Mediterranean diet.”

Xuan delivered a talk on “Impact of dietary heme on circulating, hepatic and gut microbial metabolism in germ-free mice colonized with a defined microbial community.”

Their contributions highlighted cutting-edge research in diet-microbiome interactions and metabolic health.