Dr Michael J Cox

Michael Cox

Institute of Microbiology and Infection
Lecturer in Microbial Ecology and the Respiratory Microbiome

Contact details

Institute of Microbiology and Infection
Biosciences Building
University of Birmingham
B15 2TT

Dr Cox is a microbial ecologist who studies the bacteria that reside in the respiratory tract in the context of respiratory diseases. These can be chronic diseases such as Chronic Obstructive Pulmonary Disease or Cystic Fibrosis, or acute infections such as following a viral infection. He is interested in the function of the respiratory microbiota and how it interacts with the human respiratory tract, using techniques such DNA sequencing and culture to investigate this.


  • PhD in Marine Microbial Ecology, University of Warwick and Plymouth Marine Laboratory, 2005
  • BSc (Hons) Microbiology with Intercalated Year, University of Warwick, 2001


Mike began his scientific career in marine microbial ecology, working on the relationship between microbial communities in seawater and trace atmospheric gases during his PhD at the University of Warwick and Plymouth Marine Laboratory.  This was followed by postdoctoral work at the University of Liverpool on polysaccharide degrading marine bacteria.In 2008 he took the opportunity to change direction with a visiting fellowship at the University of California San Francisco, applying microbial ecology techniques to a polymicrobial infection in the lungs of people with Cystic Fibrosis.  In 2010 he moved to the National Heart and Lung Institute at Imperial College London, expanding to a wider range of lung diseases with Professor Miriam Moffatt and Professor Bill Cookson.He joined the Institute of Microbiology and Infection in 2019 to establish his own group on respiratory microbial ecology.


Dr Cox supports teaching in the Institute through lectures, small group teaching, and practical sessions on courses including:

Postgraduate supervision

Mike is always interested in hearing from potential PhD students who want to explore the respiratory microbiome and its impact on disease.  You can contact Mike by email.


Mike’s research focuses on:

  • Using microbial ecology to understand the function of the respiratory microbiome
  • Translating microbiome research for clinical benefit in respiratory diseases
  • Expanding our understanding of the respiratory microbiome beyond bacteria to other groups of microorganisms

I collaborate with the Birmingham Acute Care Research Group.

Other activities


  • Editor FEMS Microbiology Letters from 2015
  • Member of the Scientific Advisory Committee for the NIHR/Wellcome Clinical Research Facility for Birmingham Health Partners from 2019

Membership of Scientific Societies:

  • Society for Applied Microbiology (SfAM)
  • European Society for Clinical Microbiology and Infectious Diseases (ESCMID)
  • European Respiratory Society (ERS)
  • British Association of Lung Research (BALR)


Recent publications


Cox, M, Ege, MJ & von Mutius, E (eds) 2019, The lung microbiome. European Respiratory Society. https://doi.org/10.1183/2312508X.erm8319


Cox, MJ, Loman, N, Bogaert, D & O'Grady, J 2020, 'Co-infections: potentially lethal and unexplored in COVID-19', The Lancet. Microbe, vol. 1, no. 1, pp. e11. https://doi.org/10.1016/S2666-5247(20)30009-4

Gregorova, M, Morse, D, Brignoli, T, Steventon, J, Hamilton, F, Albur, M, Arnold, D, Thomas, M, Halliday, A, Baum, H, Rice, C, Avison, MB, Davidson, AD, Santopaolo, M, Oliver, E, Goenka, A, Finn, A, Wooldridge, L, Amulic, B, Boyton, RJ, Altmann, DM, Butler, DK, McMurray, C, Stockton, J, Nicholls, S, Cooper, C, Loman, N, Cox, MJ, Rivino, L & Massey, RC 2020, 'Post-acute COVID-19 associated with evidence of bystander t-cell activation and a recurring antibiotic-resistant bacterial pneumonia', eLife, vol. 9, e63430, pp. 1-13. https://doi.org/10.7554/eLife.63430

Groves, HT, Higham, SL, Moffatt, MF, Cox, M & Tregoning, JS 2020, 'Respiratory viral infection alters the gut microbiota by inducing inappetence', mBio, vol. 11, no. 1, e03236-19. https://doi.org/10.1128/mBio.03236-19

Cuthbertson, L, Felton, I, James, P, Cox, MJ, Bilton, D, Schelenz, S, Loebinger, MR, Cookson, WOC, Simmonds, NJ & Moffatt, MF 2020, 'The fungal airway microbiome in cystic fibrosis and non-cystic fibrosis bronchiectasis', Journal of Cystic Fibrosis. https://doi.org/10.1016/j.jcf.2020.05.013

Wootton, DG, Cox, MJ, Gloor, GB, Litt, D, Hoschler, K, German, E, Court, J, Eneje, O, Keogan, L, Macfarlane, L, Wilks, S, Diggle, PJ, Woodhead, M, Moffatt, MF, Cookson, WOC & Gordon, SB 2019, 'A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease', Scientific Reports, vol. 9, 2388 . https://doi.org/10.1038/s41598-018-38090-5

Ahmed, B, Cox, MJ, Cuthbertson, L, James, P, Cookson, WOC, Davies, JC, Moffatt, MF & Bush, A 2019, 'Longitudinal development of the airway microbiota in infants with cystic fibrosis', Scientific Reports, vol. 9, 5143 . https://doi.org/10.1038/s41598-019-41597-0

Cuthbertson, L, Oo, SWC & Cox, M 2019, 'Viral respiratory infections and the oropharyngeal bacterial microbiota in acutely wheezing children.', PLoS ONE, vol. 14, no. 10, e0223990. https://doi.org/10.1371/journal.pone.0223990

Ahmed, B, Cox, MJ, Cuthbertson, L, James, PL, Cookson, WOC, Davies, JC, Moffatt, MF & Bush, A 2018, 'Comparison of the upper and lower airway microbiota in children with chronic lung diseases', PLoS ONE, vol. 13, no. 8, e0201156, pp. 1-15. https://doi.org/10.1371/journal.pone.0201156

Chapter (peer-reviewed)

Dickson, RP & Cox, M 2019, Sampling the lung microbiome. in M Cox, MJ Ege & E von Mutius (eds), The lung microbiome. European Respiratory Society, pp. 1-17. https://doi.org/10.1183/2312508X.10015418


Ahmed, B, Cox, MJ & Cuthbertson, L 2019, 'Growing up with your airway microbiota: a risky business', Thorax, vol. 74, no. 6, pp. 525-526. https://doi.org/10.1136/thoraxjnl-2019-213162

Other contribution

Cox, M 2020, Post-acute COVID-19 associated with evidence of bystander T-cell activation and a recurring antibiotic-resistant bacterial pneumonia.. https://doi.org/10.1101/2020.09.17.20190033

Turek, EM, Cox, MJ, Hunter, M, Hui, J, James, P, Willis-Owen, SAG, Cuthbertson, L, James, A, Musk, AW, Moffatt, MF & Cookson, WOCM 2019, Distinctive airway microbial ecology of smokers and asthmatics.. https://doi.org/10.1101/583559

Brill, SE, James, PL, Cuthbertson, L, Zhu, A, Lawley, T, Cookson, WOCM, Cox, MJ, Wedzicha, JA & Moffatt, MF 2018, Haemophilus, Antibiotic Therapy and the Airway Microbiome in Chronic Obstructive Pulmonarydisease.. https://doi.org/10.1101/419127

Review article

Carney, SM, Clemente, JC, Cox, MJ, Dickson, RP, Huang, YJ, Kitsios, GD, Kloepfer, KM, Leung, JM, LeVan, TD, Molyneaux, PL, Moore, BB, O'Dwyer, DN, Segal, LN & Garantziotis, S 2020, 'Methods in lung microbiome research', American Journal of Respiratory Cell and Molecular Biology, vol. 62, no. 3, pp. 283-299. https://doi.org/10.1165/rcmb.2019-0273TR

View all publications in research portal