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 Research Associate in the Molecular Genetics and Genomics Group, in the Genomic Medicine Section of the National Heart and Lung Institute.  I'm a microbial ecologist by training, originally working on the functional ecology of marine microorganisms using mainly molecular techniques.

Joining the group in 2010 I was initially funded as a Centre for Respiratory Infection Basic Science Fellow, and am now supported by Professor Miriam Moffatt and Professor Bill Cookson's Wellcome Trust Joint Senior Investigator Award.  

Currently, I am using high throughput sequencing 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 a acute infection such as cases of H1N1 pandemic flu and other viral infections.  

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.  I am also interested methodologies and in improving techniques.

I am an editor at FEMS Microbiology Letters, particularly handling microbiome related submissions and have reviewed manuscripts for a wide range of journals and grants for the MRC, South African MRC and Danish Council for Independent Research.

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



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

Cox MJ, Turek EM, Hennessy C, et al., 2017, Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients, Plos One, Vol:12, ISSN:1932-6203

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-+

Dickson RP, Cox MJ, 2017, Gut microbiota and protection from pneumococcal pneumonia, Gut, Vol:66, ISSN:0017-5749

Molyneaux PL, Cox MJ, Wells AU, et al., 2017, Changes in the respiratory microbiome during acute exacerbations of idiopathic pulmonary fibrosis, Respiratory Research, Vol:18, ISSN:1465-993X

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