Imperial College London


Faculty of MedicineDepartment of Metabolism, Digestion and Reproduction

Professor of Chemical Biology



+44 (0)20 7594 3220elaine.holmes




661Sir Alexander Fleming BuildingSouth Kensington Campus





Head of division of Computational and Systems Medicine

Research Interests:

Prof. Holmes is the Head of the Division of Computational and Systems Medicine and a Professor of Chemical Biology in the Department of Surgery and Cancer at Imperial College, in London, UK.  She has over 20 years experience in metabonomic technology and its applications.  Her focus is on the discovery and development of metabolic biomarkers of disease in personalised healthcare and population studies with significant contributions to cardiovascular, neuroscience and infectious disease research.  Recently Prof. Holmes has driven large-scale profiling efforts defining the concept of the metabolome-wide association study (MWAS) in molecular epidemiology, specifically exploring the link between hypertension, diet and metabolic profiles.  She has also developed methods for characterizing gut microbiome host metabolic interactions and has applied these to the study of gastrointestinal related diseases including colorectal cancer, obesity and IBD. She also has an established track record in the development of chemometric and statistical methods for analysis of Omics data. Specific research focus areas:

  • Application of metabolic profiling technologies to systems biology and translational medicine problems
  • Development of statistical spectroscopy and other data processing methods for discovery and development of metabolic biomarkers for disease
  • Development and application of data integration strategies for co-analysis of complex multidimensional datasets
  • Development of methods for characterizing metabolic interactions between the gut microbiome and host, with application to assessing the role of microbiome in health and disease.
  • Metabolome-wide association studies (MWAS) in molecular epidemiology, specifically exploring the link between hypertension, diet and metabolic profiles.

Honors and Memberships:

  • Visiting Professor, Purdue University, West Lafayette Inidiana
  • 2012 – Visiting Professor of CEU University San Pablo (Madrid)
  • 2007 – William Glasser Visiting Professor, University of the Sciences, Philadelphia
  • 2006 – Visiting Professor, Wuhan Institute of Physics and Mathematics, Chinese Academy of Science, People’s Republic of China
  • 2011 – Fellow, Society of Biology
  • 2006 – 2010 Editorial Board, Chemical Research in Toxicology
  • 2010 – Member of the MRC-HPA Centre for Environmental Health Executive Committee
  • 2007 – Editorial Board, Biomarkers in Medicine
  • 2010 – Fellow, Royal Society of Chemistry
  • 2009 – Member of the British Toxicology Society
  • 2012 – Editorial board of Toxicology Research
  • 2009 – Editorial Board, Analytical Biochemistry
  • 2014 - Editorial Board, Journal of Biological Chemistry

Spin off Company:

Key Publications in systems biology and gut microbial impact on health and disease

  • 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 J, Knights D, Ursell LK, Knight R, Gordon JI. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science. 2013 Feb 1;339(6119):548-54. doi: 10.1126/science.1229000. Epub 2013 Jan 30. PubMed PMID: 23363771.
  • Holmes E, Li JV, Marchesi JR, Nicholson JK. Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk. Cell Metab. 2012;16(5):559-64. doi: 10.1016/j.cmet.2012.10.007. PubMed PMID: 23140640.
  • Holmes E, Kinross J, Gibson GR, Burcelin R, Jia W, Pettersson S, Nicholson JK. Therapeutic modulation of microbiota-host metabolic interactions. Sci Transl Med. 2012;4(137):137rv6. doi: 10.1126/scitranslmed.3004244. Review. PubMed PMID: 22674556.
  • Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S.  Host-gut microbiota metabolic interactions. Science. 2012; 336(6086):1262-7. doi: 10.1126/science.1223813. PubMed PMID: 22674330.
  • Thomas EL, Parkinson JR, Hyde MJ, Yap IK, Holmes E, Doré CJ, Bell JD, Modi N. Aberrant adiposity and ectopic lipid deposition characterize the adult phenotype of the preterm infant. Pediatr Res. 2011 Nov;70(5):507-12. doi: 10.1038/pr.2011.732. PubMed PMID: 21772225.

Key Publications in Epidemiology

  • Holmes E, Loo RL, Stamler J, Bictash M, Yap IK, Chan Q, Ebbels T, De Iorio M, Brown IJ, Veselkov KA, Daviglus ML, Kesteloot H, Ueshima H, Zhao L, Nicholson JK, Elliott P. Human metabolic phenotype diversity and its association with diet and  blood pressure. Nature. 2008; 453(7193):396-400. doi: 10.1038/nature06882. PubMed PMID: 18425110.
  • Hankinson AL, Daviglus ML, Van Horn L, Chan Q, Brown I, Holmes E, Elliott P, Stamler J. Diet composition and activity level of at risk and metabolically healthy obese American adults. Obesity (Silver Spring). 2012 Apr 19. doi: 10.1038/oby.2012.98. [Epub ahead of print] PubMed PMID: 22513488; PubMed Central  PMCID: PMC3416914.
  • Loo RL, Chan Q, Brown IJ, Robertson CE, Stamler J, Nicholson JK, Holmes E, Elliott P; INTERMAP Research Group. A comparison of self-reported analgesic use and detection of urinary ibuprofen and acetaminophen metabolites by means of metabonomics: the INTERMAP Study. Am J Epidemiol. 2012 Feb 15;175(4):348-58. doi:10.1093/aje/kwr292. PubMed PMID: 22223708; PubMed Central PMCID:PMC3271812.

Selected Publications

Journal Articles

Chambers E, Byrne C, Morrison D, et al., 2019, Dietary supplementation with inulin-propionate ester or inulin improves insulin sensitivity in adults with overweight and obesity with distinct effects on the gut microbiota, plasma metabolome and systemic inflammatory responses: a randomised cross-over trial, Gut, Vol:68, ISSN:0017-5749, Pages:1430-1438

Garcia Perez I, Posma JM, Gibson R, et al., 2017, Objective assessment of dietary patterns using metabolic phenotyping: a randomized, controlled, crossover trial, The Lancet Diabetes & Endocrinology, Vol:5, ISSN:2213-8587, Pages:184-195

Andreas NJ, Al-Khalidi A, Jaiteh M, et al., 2016, Role of human milk oligosaccharides in Group B Streptococcus colonisation, Clinical and Translational Immunology, Vol:5, ISSN:2050-0068

McPhail MJW, Shawcross D, Lewis MR, et al., 2016, Mutlivariate metabotyping of plasma accurately predicts survival in decompensated cirrhosis, Journal of Hepatology, Vol:64, ISSN:1600-0641, Pages:1058-1067

Dona AC, Jimenez B, Schaefer H, et al., 2014, Precision High-Throughput Proton NMR Spectroscopy of Human Urine, Serum, and Plasma for Large-Scale Metabolic Phenotyping, Analytical Chemistry, Vol:86, ISSN:0003-2700, Pages:9887-9894

Nicholson JK, Holmes E, Kinross J, et al., 2012, Host-gut microbiota metabolic interactions., Science, Vol:336, Pages:1262-1267

Holmes E, Kinross J, Gibson GR, et al., 2012, Therapeutic Modulation of Microbiota-Host Metabolic Interactions, Science Translational Medicine, Vol:4, ISSN:1946-6234, Pages:137rv6-137rv6

Li JV, Ashrafian H, Bueter M, et al., 2012, Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk, Gut, Vol:60, Pages:1214-1223

More Publications