Dr Michael J Cox

Michael Cox

Institute of Microbiology and Infection
Assistant Professor 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.

 Dr Cox is currently PGR Lead for the Institute of Microbiology and Infection.


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


Dr Cox joined the Institute of Microbiology and Infection in 2019 and established the Respiratory Microbiome Group to study the interactions between bacterial communities in the respiratory tract and respiratory disease.

He 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 Dr Cox 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.


Dr Cox supports teaching in the Institute through lectures, small group teaching, and practical sessions

  • Module Organiser – MSc Genomic Medicine - Applied Genomics and Infectious Disease
  • Module Organiser – MSc Microbiology and Infection – Core Concepts and Skills in Microbiology
  • Biomedical Sciences – Immunity and Infection
  • Biomedical Sciences – Bacterial Threats and Defence

Dr Cox hosts project and dissertation students from various undergraduate and postgraduate taught programmes and these can be wet lab or bioinformatics based projects.

Postgraduate supervision

Dr Cox currently supervises or co-supervises a number of students with respiratory microbiome components to their projects. He has supervised 6 PhD students to completion, including both fundamental science based and clinical based projects. He 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.


Dr Cox'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

Dr Cox collaborates with the Birmingham Acute Care Research Group and with clinical researchers in the University Hospitals Birmingham NHS Foundation Trust and the Birmingham Women and Children’s NHS Foundation Trust.

Other activities


  • Editor Microbial Genomics from 2020
  • Editor FEMS Microbiology Letters from 2015-2020
  • 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


Cuthbertson, L, Löber, U, Ish-Horowicz, JS, McBrien, CN, Churchward, C, Parker, JC, Olanipekun, MT, Burke, C, McGowan, A, Davies, GA, Lewis, KE, Hopkin, JM, Chung, KF, O’Carroll, O, Faul, J, Creaser-Thomas, J, Andrews, M, Ghosal, R, Piatek, S, Willis-Owen, SAG, Bartolomaeus, TUP, Birkner, T, Dwyer, S, Kumar, N, Turek, EM, William Musk, A, Hui, J, Hunter, M, James, A, Dumas, M-E, Filippi, S, Cox, MJ, Lawley, TD, Forslund, SK, Moffatt, MF & Cookson, WOC 2024, 'Genomic attributes of airway commensal bacteria and mucosa', Communications Biology, vol. 7, no. 1, 171. https://doi.org/10.1038/s42003-024-05840-3

Quarton, S, McGee, K, Cumley, N, Behruznia, M, Jeff, C, Belchamber, K, Cox, M, Thickett, D, Scott, A, Parekh, D, McNally, A & Sapey, E 2024, 'Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol', PLoS ONE, vol. 19, no. 3, e0298425. https://doi.org/10.1371/journal.pone.0298425

Cardenas, PA, Cox, M, Willis-Owen, SAG, Moffatt, MF, Cookson, WOC & Cooper, P 2023, 'Delayed acquisition of airway commensals in antibiotic naive children and its relationship with wheezing in rural Ecuador', Frontiers in Allergy, vol. 4, 1214951. https://doi.org/10.3389/falgy.2023.1214951

Njovu, IK, Nalumaga, PP, Ampaire, L, Nuwagira, E, Mwesigye, J, Musinguzi, B, Kassaza, K, Taseera, K, Kiguli Mukasa, J, Bazira, J, Iramiot, JS, Baguma, A, Bongomin, F, Kwizera, R, Achan, B, Cox, MJ, King, JS, May, R, Ballou, ER & Itabangi, H 2023, 'Investigating Metabolic and Molecular Ecological Evolution of Opportunistic Pulmonary Fungal Coinfections: Protocol for a Laboratory-Based Cross-Sectional Study', JMIR Research Protocols, vol. 12, e48014. https://doi.org/10.2196/48014

Watson, R, Oldfield, M, Bryant, JA, Riordan, L, Hill, HJ, Watts, JA, Alexander, MR, Cox, MJ, Stamataki, Z, Scurr, DJ & de Cogan, F 2022, 'Efficacy of antimicrobial and anti-viral coated air filters to prevent the spread of airborne pathogens', Scientific Reports, vol. 12, no. 1, 2803. https://doi.org/10.1038/s41598-022-06579-9

Chotirmall, SH, Bogaert, D, Chalmers, JD, Cox, MJ, Hansbro, PM, Huang, YJ, Molyneaux, PL, O'Dwyer, DN, Pragman, AA, Rogers, GB, Segal, LN & Dickson, RP 2022, 'Therapeutic targeting of the respiratory microbiome', American Journal of Respiratory and Critical Care Medicine, vol. 206, no. 5, pp. 535-544. https://doi.org/10.1164/rccm.202112-2704PP

Turek, EM, Cox, MJ, Hunter, M, Hui, J, James, P, Willis-Owen, SAG, Cuthbertson, L, James, A, Musk, AW, Moffatt, MF & Cookson, WOCM 2021, 'Airway microbial communities, smoking and asthma in a general population sample', EBioMedicine, vol. 71, 103538. https://doi.org/10.1016/j.ebiom.2021.103538

Ahmed, B, Cox, MJ, Cuthbertson, L, James, P, Gardner, L, Cookson, W, Davies, J, Moffatt, M & Bush, A 2021, 'Comparison of the airway microbiota in children with chronic suppurative lung disease', BMJ Open Respiratory Research, vol. 8, no. 1, e001106. https://doi.org/10.1136/bmjresp-2021-001106

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

Other contribution

Cuthbertson, L, Cox, M, provided, PNPJN, Churchward, CP, Cookson, B & Moffatt, M 2020, CTAB extraction of DNA and RNA of respiratory samples for microbial work v1.. https://doi.org/10.17504/protocols.io.bf28jqhw


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

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