Imperial College London


Faculty of MedicineNational Heart & Lung Institute

Research Associate



+44 (0)20 7594 7974michael.cox1 Website




413Guy Scadding BuildingRoyal Brompton Campus





I am a Microbial Ecologist in the Genomic Medicine Section of the National Heart and Lung Institute. 

Currently, I am using high throughput sequencing and bacterial culture techniques in order to identify changes in microbial assemblages in the respiratory tract in a wide range of diseases.  These include chronic diseases such as cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma, as well as acute infections such as acquired pneumonias, cases of H1N1 pandemic flu and other viral infections.  

Originally I trained as a marine microbial ecologist at the University of Warwick and Plymouth Marine Laboratory and at the University of Liverpool, switching focus to respiratory tract microbial ecology with a Visiting Fellowship at the University of California San Francisco in 2008.  

My interests lie in the interactions of the human microbiome with itself and the human host, the phylogeny and function of microbial communities, and in translational applications of microbial ecology in states of health and disease.  Selection pressures are strong in the respiratory tract, particularly given the unique group of organisms associated with each respiratory disease and identifying these pressures will lead to greater understanding of disease pathogenesis and potential therapies. 

Methodologies and introducing and improving techniques in human microbiome research has been an important part of my research. Through collaboration with the Wellcome Trust Sanger Institute and the University of Birmingham we identified contamination in DNA extraction kits as being a significant and ongoing methodological problem in all microbiome studies.

I have been active in public engagement contributing to everything from installation art pieces at the Imperial Festival, to radio programs for children's digital radio. Most recently with The Curious Act and The Royal Brompton Hospital I have been planning and delivering Exhale & Exchange, a series of events that involve patients, clinicians, researchers and the public in exploring breath and breathing. These are based at the Wellcome Reading Room as part of their Open Platform series and we are using them to pilot the use of different media in public engagement. 

I am an editor at FEMS Microbiology Letters, handling microbiome related submissions and have reviewed manuscripts for a wide range of journals and grants for the Wellcome Trust, Royal Society, MRC, South African MRC and Danish Council for Independent Research. I am currently working on a monograph on the Lung Microbiome for the European Respiratory Society and on the Host-associated Microbiome for the British Ecological Society. I am a member of the Society for Applied Microbiology and the Microbiology Society.  

Equality and Diversity in science is of particular interest to me, and I am a member of the Athena Swan Self-Assessment Team for the department, contributing to our most recent submission. I have also contributed talks to events by Pride in STEM.  

Teaching mostly at the MSc level, I contribute to the MSc courses in Genomic Medicine; Genes, Drugs and Stem Cells; Immunology; MRes Respiratory and Cardiovascular Stream, and in Cancer Biology. I lecture on the microbiome, public engagement and bioinformatics. I have designed and run courses on bioinformatic analysis of human microbiome data using R and Linux.  

My Google Scholar page is available here, ORCID here and I am active on Twitter and can be contacted here



Groves HT, Cuthbertson L, James P, et al., 2018, Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota, Frontiers in Immunology, Vol:9, ISSN:1664-3224

Cookson WOCM, Cox MJ, Moffatt MF, 2018, New opportunities for managing acute and chronic lung infections, Nature Reviews Microbiology, Vol:16, ISSN:1740-1526, Pages:111-120

Cox MJ, 2017, Ventilator-associated pneumonia: when is a pathogen not a pathogen?, Thorax, Vol:72, ISSN:0040-6376, Pages:774-775

Molyneaux PL, Willis-Owen SAG, Cox MJ, et al., 2017, Host-Microbial Interactions in Idiopathic Pulmonary Fibrosis, American Journal of Respiratory and Critical Care Medicine, Vol:195, ISSN:1073-449X, Pages:1640-1650

Depner M, Ege MJ, Cox MJ, et al., 2017, Bacterial microbiota of the upper respiratory tract and childhood asthma, Journal of Allergy and Clinical Immunology, Vol:139, ISSN:0091-6749, Pages:826-+

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