Professor James McDonald BSc, PhD, PGCertHE, FHEA

Professor James McDonald

School of Biosciences
Professor of Microbial Ecology

Contact details

Email
j.e.mcdonald@bham.ac.uk
Twitter
Address
N107, School of Biosciences

Professor McDonald and his research team apply a combination of cultivation-based and molecular approaches to characterise and engineer both host-associated and environmental microbiomes, to understand their role in host health status, biogeochemical cycling and ecosystem function. Current research focusses on microbiome engineering approaches to address key global challenges such as waste management and sustainable fuel production (using microbiomes to produce biofuels and biogas), and in combating tree disease (engineering microbial communities for disease suppression and health promotion). Prof. McDonald is also interested in integrating knowledge on microbiome engineering and microbiome science across diverse systems (e.g. plants, humans, industrial systems) to identify key scientific principles that underpin microbiome assembly and function.

Qualifications

  • PostGraduate Certificate in Higher Education (2013), Bangor University.
  • Ph.D. in Environmental Microbiology (2008), University of Liverpool. Thesis; Molecular ecology of anaerobic cellulose-degrading microorganisms in landfill sites.
  • B.Sc. (Hons), University of Manchester (2004). Microbiology with Industrial Experience. Industrial Experience with the Forensic Science Service.

Biography

Professor McDonald joined the School of Biosciences in 2022 to work with colleagues across the Institute of Microbiology and Infection, the Birmingham Institute of Forest Research (BIFor) and the College of Life and Environmental Sciences.

He completed a BSc in Microbiology with Industrial Experience at The University of Manchester (2004), followed by a PhD in Environmental Microbiology at the University of Liverpool (2008) under the supervision of Prof. Alan McCarthy and Dr. Heather Allison. This was followed by three short research contracts focused on bacteriophage ecology, the canine oral microbiota, and developing methods for SNP profiling in canine genomes.  In 2010 he was appointed as Research Lecturer at Bangor University, North Wales, where he established research programmes on the microbiology of anaerobic waste degradation, the role of polymicrobial communities in tree disease, and collaborations with Dr. Shelagh Malham, Prof. Davey Jones, and others, on bacterial and viral pathogen ecology in the environment. He was promoted to permanent Lecturer in 2013, Senior Lecturer in 2015 and full Professor in 2019. During this time, he held various roles including module and degree programme coordinator, Director of Postgraduate Research, and sat on School and College Management Boards.

Postgraduate supervision

Prof. McDonald currently supervises 6 PhD researchers and 2 Master’s candidates. He welcomes enquiries about potential Master’s and PhD projects on research themes within his group. Please contact him by email: j.e.mcdonald@bham.ac.uk

Research

Research in Prof. McDonald’s group focusses on the following broad themes:

  • Investigating the role of the oak microbiome in health and disease, characterising microbial disease suppression, engineering the oak microbiome to future-proof tree health and combat tree disease.
  • Characterising the microbial processes of waste biomass conversion to biogas in landfill sites and anaerobic digestion plants to develop engineered microbiomes for enhanced waste conversion to biogas.
  • Integrating knowledge on microbiome engineering and microbiome science across diverse systems (e.g. plants, humans, industrial systems) to identify key scientific principles that underpin microbiome assembly and function.

Other activities

  • Associate editor for Proceedings of the Royal Society B (2019-present)
  • UK ambassador for the International Society for Microbial Ecology (ISME) (2014-present)
  • Prokaryote Division committee member for the Microbiology Society (2019-2022)
  • Guest editor for Proceedings of the Royal Society B (2020)
  • Fellow of the Higher Education Academy (2014).

Publications

  •                                                                                                                   Luke S. Hillary, Evelien M. Adriaenssens, David L. Jones, James E. McDonald. (2022) ISME Communications. 2, Article number: 34
  • Jessica L. Kevill, Cameron Pellett, Kata Farkas, Mathew R. Brown, Irene Bassanoce, Hubert Denise, James E. McDonald, Shelagh K. Malham, Jonathan Porter, Jonathan Warren, Nicholas P. Evens, Steve Paterson, Andrew C. Singer, Davey L. Jones. (2022) Science of The Total Environment. 808, 151916.
  •               
    Pettifor, B. & McDonald, J., Aug 2021, Forest Microbiology: Tree Microbiome: Phyllosphere, Endosphere and Rhizosphere. Asiegbu, F. O. & Kovalchuk, A. (eds.). 1 ed. Academic Press, Elsevier, Vol. 1. p. 161 - 173 12 p.
  •       
    Farkas, K., Hillary, L., Thorpe, J., Walker, D., Lowther, J. A., McDonald, J., Malham, S. & Jones, D. L., 23 Feb 2021, Methods and Protocols. 4, 1, 10 p., 17.

  • Alexander, J., Malham, S., Smyth, D., Webb, J., Fidler, D., Bayford, P., McDonald, J. & Le Vay, L., 15 Feb 2021, Aquaculture. 532, 736003.
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    Hillary, L. S., Farkas, K., Maher, K. H., Lucaci, A., Thorpe, J., Distaso, M. A., Gaze, W. H., Paterson, S., Burke, T., Connor, T. R., McDonald, J. E., Malham, S. K. & Jones, D. L., 15 Jul 2021, In : Water Research. 200, p. 117214 1 p.

  • George, P. B. L., Fidler, D. B., Van Nostrand, J. D., Atkinson, J. A., Mooney, S. J., Creer, S., Griffiths, R. I., McDonald, J. E., Robinson, D. A. & Jones, D. L., 14 Sep 2021, In : Frontiers in Microbiology. 12, 735022.

  • Adriaenssens, E. M., Farkas, K., McDonald, J. E., Jones, D. L., Allison, H. E. & McCarthy, A. J., 15 Sep 2021, In : Water Research. 203
  •              
    Crampton, B. G., Plummer, S., Kaczmarek, M., McDonald, J. & Denman, S., Sep 2020, In : Plant Pathology. 69, 7, p. 1301-1310 10 p.

  • McDonald, J., Marchesi, J. R. & Koskella, B., 23 Dec 2020, In : Proceedings of the Royal Society B: Biological Sciences. 287, 1941, 20202886.
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    Doonan, J., Broberg, M., Denman, S. & McDonald, J., 26 Aug 2020, In : Proceedings of the Royal Society B: Biological Sciences. 287, 1933, 20200956.
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    Bashawri, Y. M. A., Robins, P., Jones, D. L., McDonald, J., Cooper, D. & Williams, P., 19 Oct 2020, In : International Journal of Environmental Research and Public Health. 17, 20, 15 p., 7608.
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    Jones, D. L., Baluja, M. Q., Graham, D. W., Corbishley, A., McDonald, J. E., Malham, S. K., Hillary, L. S., Connor, T. R., Gaze, W. H., Moura, I. B., Wilcox, M. H. & Farkas, K., 20 Dec 2020, In : Science of the Total Environment. 749, 141364.
  •  Farkas, K. & McDonald, J. E., 2020, In : Journal of Microbiology and Biology Education. Vol 21, no. 2
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    Pettifor, B. J., Doonan, J., Denman, S. & McDonald, J., Mar 2020, In : Systematic and Applied Microbiology. 43, 2
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    Farkas, K., Walker, D., Adriaenssens, E., McDonald, J., Hillary, L., Malham, S. & Jones, D. L., 15 Aug 2020, In : Water Research. 181, 115926.
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    Farkas, K., Hillary, L., Malham, S., McDonald, J. & Jones, D. L., Oct 2020, In : Current Opinion in Environmental Science & Health. 17, p. 14-20 7 p.
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    Farkas, K., Adriaenssens, E. M., Walker, D. I., McDonald, J., Malham, S. & Jones, D. L., 1 Jun 2019, In : Food and Environmental Virology. 11, 2, p. 113-119
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    Broberg, M. & McDonald, J., 5 Feb 2019, In : Methods and Protocols. 2, 1, 15.
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    Doonan, J., Denman, S., Pachebat, J. A. & McDonald, J., 8 Jan 2019, In : Microbial Genomics. 5, 1, 15 p.
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    Broberg, M., Doonan, J., Mundt, F. & McDonald, J., 30 Jan 2018, In : Microbiome. 6, 21.
  •         
    Denman, S., Doonan, J., Ransom-Jones, E., Broberg, M., Plummer, S., Kirk, S. A., Scarlett, K., Griffiths, A., Kaczmarek, M., Foster, J., Peace, A., Golyshin, P., Hassard, F., Brown, N., Kenny, J. G. & McDonald, J., 2018, In : The ISME Journal. 12, p. 386-399
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    Farkas, K., Marshall, M., Cooper, D., McDonald, J. E., Malham, S. K., Peters, D. E., Maloney, J. D. & Jones, D. L., Nov 2018, In : Environmental Science and Pollution Research. 25, 33, p. 33391-33401

  • Malham, S., Farkas, K., McDonald, J., Jones, D. L., Cooper, D. & de Rougemont, A., 1 Sep 2018, In : Science of the Total Environment. 634, p. 1174 1183 p.
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    Farkas, K., McDonald, J., Malham, S. & Jones, D. L., 10 Sep 2018, In : Methods and Protocols. 1, 3, 35.
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    Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vazquez-Baeza, Y., Gonzalez, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., Haroon, M. F., Kanbar, J., Zhu, Q., Song, S. J., Kosciolek, T., Bokulich, N. A., Lefler, J., Brislawn, C. J., Humphrey, G., Owens, S. M., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J. A., Clauset, A., Stevens, R. L., Shade, A., Pollard, K. S., Goodwin, K. D., Jansson, J. K., Gilbert, J. A., Knight, R., Agosto Rivera, J. L., Al-Moosawi, L., Alverdy, J., Amato, K. R., Andras, J., Angenent, L. T., Antonopoulos, D. A., Apprill, A., Armitage, D., Ballantine, K., Bárta, J., Baum, J. K., Berry, A., Bhatnagar, A., Bhatnagar, M., Biddle, J. F., Bittner, L., Boldgiv, B., Bottos, E., Boyer, D. M., Braun, J., Brazelton, W., Brearley, F. Q., Campbell, A. H., Caporaso, J. G., Cardona, C., Carroll, J., Cary, S. C., Casper, B. B., Charles, T. C., Chu, H., Claar, D. C., Clark, R. G., Clayton, J. B., Clemente, J. C., Cochran, A., Coleman, M. L., Collins, G., Colwel, R. R., Contreras, M., Crary, B. B., Creer, S., Cristol, D. A., Crump, B. C., Cui, D., Daly, S. E., Davalos, L., Dawson, R. D., Defazio, J., Delsuc, F., Dionisi, H. M., Dominguez-Bello, M. G., Dowell, R., Dubinsky, E. A., Dunn, P. O., Ercolini, D., Espinoza, R. E., Ezenwa, V., Fenner, N., Findlay, H. S., Fleming, I. D., Fogliano, V., Forsman, A., Freeman, C., Friedman, E. S., Galindo, G., Garcia, L., Garcia-Amado, M. A., Garshelis, D., Gasser, R. B., Gerdts, G., Gibson, M. K., Gifford, I., Gill, R. T., Giray, T., Gittel, A., Golyshin, P., Gong, D., Grossart, H-P., Guyton, K., Haig, S-J., Hale, V., Hall, R. S., Hallam, S. J., Handley, K. M., Hasan, N. A., Haydon, S. R., Hickman, J. E., Hidalgo, G., Hofmockel, K. S., Hooker, J., Hulth, S., Hultman, J., Hyde, E., Ibáñez-Álamo, J. D., Jastrow, J. D., Jex, A. R., Johnson, L. S., Johnston, E. R., Joseph, S., Jurburg, S. D., Jurelevicius, D., Karlsson, A., Karlsson, R., Kauppinen, S., Kellogg, C. T. E., Kennedy, S. J., Kerkhof, L. J., King, G. M., Kling, G. W., Koehler, A. V., Krezalek, M., Kueneman, J., Lamendella, R., Landon, E. M., Lane-deGraaf, K., LaRoche, J., Larsen, P., Laverock, B., Lax, S., Lentino, M., Levin, I. I., Liancourt, P., Liang, W., Linz, A. M., Lipson, D. A., Liu, Y., Lladser, M. E., Lozada, M., Spirito, C. M., MacCormack, W. P., MacRae-Crerar, A., Magris, M., Martín-Platero, A. M., Martín-Vivaldi, M., Martínez, L. M., Martínez-Bueno, M., Marzinelli, E. M., Mason, O. U., Mayer, G. D., McDevitt-Irwin, J. M., McDonald, J., McGuire, K. L., McMahon, K. D., McMinds, R., Medina, M., Mendelson, J. R., Metcalf, J. L., Meyer, F., Michelangeli, F., Miller, K., Mills, D. A., Minich, J., Mocali, S., Moitinho-Silva, L., Moore, A., Morgan-Kiss, R. M., Munroe, P., Myrold, D., Neufeld, J. D., Ni, Y., Nicol, G. W., Nielsen, S., Nissimov, J. I., Niu, K., Nolan, M. J., Noyce, K., O’Brien, S. L., Okamoto, N., Orlando, L., Ortiz Castellano, Y., Osuolale, O., Oswald, W., Parnell, J., Peralta-Sánchez, J. M., Petraitis, P., Pfister, C., Pilon-Smits, E., Piombino, P., Pointing, S. B., Pollock, F. J., Potter, C., Prithiviraj, B., Quince, C., Rani, A., Ranjan, R., Rao, S., Rees, A. P., Richardson, M., Riebesell, U., Robinson, C., Rockne, K. J., Rodriguezl, S. M., Rohwer, F., Roundstone, W., Safran, R. J., Sangwan, N., Sanz, V., Schrenk, M., Schrenzel, M. D., Scott, N. M., Seger, R. L., Seguin-Orlando, A., Seldin, L., Seyler, L. M., Shakhsheer, B., Sheets, G. M., Shen, C., Shi, Y., Shin, H., Shogan, B. D., Shutler, D., Siegel, J., Simmons, S., Sjöling, S., Smith, D. P., Soler, J. J., Sperling, M., Steinberg, P. D., Stephens, B., Stevens, M. A., Taghavi, S., Tai, V., Tait, K., Tan, C. L., Tas, N., Taylor, D. L., Thomas, T., Timling, I., Turner, B. L., Urich, T., Ursell, L. K., van der Lelie, D., Van Treuren, W., van Zwieten, L., Vargas-Robles, D., Vega Thurber, R., Vitaglione, P., Walker, D. A., Walters, W. A., Wang, S., Wang, T., Weave, T., Webster, N. S., Wehrle, B., Weisenhorn, P., Weiss, S., Werner, J. J., West, K., Whitehead, A., Whitehead, S. R., Whittingham, L. A., Willerslev, E., Williams, A. E., Wood, S. A., Woodhams, D. C., Yang, Y., Zaneveld, J., Zarraonaindia, I., Zhang, Q. & Zhao, H., 23 Nov 2017, In : Nature. 551, 7681, p. 457-+ *provided environmental samples from an ongoing project to the consortium
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    Hassard, F., Sharp, J., Taft, H., Le Vay, L., Harris, J., McDonald, J., Tuson, K., Wilson, J., Jones, D. & Malham, S., Jun 2017, In : Food and Environmental Virology. 9, 2, p. 123-141
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    Farkas, K., Hassard, F., McDonald, J., Malham, S. & Jones, D., 24 Jan 2017, In : Frontiers in Microbiology. 6, p. 1-12 53.
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    Farkas, K., Peters, D. E., McDonald, J., de Rougemont, A., Malham, S. & Jones, D., Sep 2017, In : Food and Environmental Virology. 9, 3, p. 342-349
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    Antwis, R. E., Griffiths, S. M., Harrison, X. A., Aranega-Bou, P., Arce, A., Bettridge, A. S., Brailsford, F., de Menezes, A., Devaynes, A., Forbes, K. M., Fry, E. L., Goodhead, I., Haskell, E., Heys, C., James, C., Johnston, S. R., Lewis, G. R., Lewis, Z., Macey, M. C., McCarthy, A., McDonald, J., Mejia-Florez, N. L., O'Brien, D., Orland, C., Pautasso, M., Reid, W. D. K., Robinson, H. A., Wilson, K. & Sutherland, W. J., May 2017, In : Fems Microbiology Ecology. 93, 5, fix044.
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    Denman, S., Barrett, G., Kirk, S. A., McDonald, J. & Coetzee, M. P. A., 7 Jan 2017, In : Forestry. 90, 1, p. 148-161
  • Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass- Degrading Diversity                
    Ransom-Jones, E., McCarthy, AJ., Haldenby, S., Doonan, J. & McDonald, JE., Aug 2017, In : mSphere. 2, 4, e00300.
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    Kaczmarek, M., Mullett, M. S., McDonald, J. & Denman, S., 1 Jun 2017, In : PLoS ONE. 12, 6, e0178390.
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    Hassard, F., Andrews, A., Jones, D. L., Parsons, L., Jones, V., Cox, B. A., Daldorph, P., Brett, H., McDonald, J. & Malham, S., Oct 2017, In : Frontiers in Microbiology. 8, 1996.
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    Potter, C., Freeman, C., Golyshin, P., Ackerman, G., Fenner, N., McDonald, J., Ehbair, A., Jones, T., Murphy, L. & Creer, S., Sep 2017, In : Scientific Reports. 7, 11314.
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    Brady, C., Arnold, D., McDonald, J. & Denman, S., Jul 2017, In : World Journal of Microbiology and Biotechnology. 33, 7, p. 143

  • Hassard, F., Gwyther, C. L., Farkas, K., Andrews, A., Jones, V., Cox, B., Brett, H., Jones, D., McDonald, J. & Malham, S., 1 Nov 2016, In : Frontiers in Microbiology.

  • McDonald, J., Larsen, N., Pennington, A., Connolly, J., Wallis, C., Rooks, D. J., Hall, N., McCarthy, A. J. & Allison, H. E., 8 Jun 2016, In : PLoS ONE. 11, 6, e0157046.
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    Perkins, T. L., Perrow, K. A., Rajko-Nenow, P., Jago, C. F., Jones, D. L., Malham, S. K. & McDonald, J. E., 1 Dec 2016, In : Science of the Total Environment. 572, p. 1645-1652
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    Ransom-Jones, E. & McDonald, J., 22 Sep 2016, In : Genome Announcements. 4, 5, e0098516.
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    Denman, S., Plummer, S., Peace, A. & McDonald, J., 1 Oct 2016, In : Systematic and Applied Microbiology. 39, 7, p. 484-490

  • Doonan, J., Denman, S., McDonald, J. & Golyshin, P., 30 Nov 2016, Metagenomics. Streit, W. R. & Daniel, R. (eds.). Springer New York, Vol. 1539. p. 85-97 (Methods in Molecular Biology; vol. 1539).
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    Emmett, B., Cooper, D., Smart, S., Jackson, B., Thomas, A., Cosby, B., Evans, C., Glanville, H., McDonald, J., Malham, S., Marshall, M., Jarvis, S., Rajko-Nenow, P., Webb, G. P., Ward, S., Rowe, E., Jones, L., Vanbergen, E. J., Keith, A., Carter, H., Pereira, M. G., Hughes, S., Lebron, I., Wade, A. & Jones, D., 1 Dec 2016, In : Science of the Total Environment. 572, p. 1586-1600

  • Winterbourn, J., Clements, K., Lowther, J. A., Malham, S., McDonald, J. & Jones, D., 15 Nov 2016, In : Water Research. 105, November, p. 241-250
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    Robins, P. E., Skov, M. W., Lewis, M. J., Gimenez, L., Davies, A. G., Malham, S. K., Neill, S. P., McDonald, J. E., Whitton, T. A., Jackson, S. E. & Jago, C. F., 17 Dec 2015, In : Estuarine, Coastal and Shelf Science. 169, p. 119-135
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    Doonan, J., Denman, S., Gertler, C., Pachebat, J. A., Golyshin, P. N. & McDonald, J. E., 1 Jan 2015, In : Journal of Applied Microbiology. 118, 1, p. 193-201 9 p.
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    Rhymes, J. M., Rhymes, J., Jones, L., Lapworth, D. J., White, D., Fenner, N., McDonald, J. E. & Perkins, T. L., 20 Jan 2015, In : Science of the Total Environment. 511, p. 703-710

  • Robinson, R. L. & McDonald, J. E., 1 Jul 2014, In : Bioscience Education. 22, 1, p. 42-53
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    Ransom-Jones, E., Jones, D. L., Edwards, A. & McDonald, J. E., 17 Jul 2014, In : Systematic and Applied Microbiology. 37, 7, p. 502-509

  • McDonald, J. E. & Robinson, R. L., 1 Jul 2014, In : Bioscience Education. 22, 1, p. 54-69
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    Perkins, T. L., Clements, K., Baas, J. H., Jago, C. F., Jones, D. L., Malham, S. K. & McDonald, J. E., 14 Nov 2014, In : PLoS ONE. 9, 11
  •          
    Malham, S. K., Rajko-Nenow, P., Howlett, E., Tuson, K. E., Perkins, T. L., Pallett, D. W., Wang, H., Jago, C. F., Jones, D. L. & McDonald, J. E., 7 Jul 2014, In : Environmental Science: Processes and Impacts. 16, p. 2145-2155
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    Golyshin, P., Gwyther, C. L., Jones, D. L., Golyshin, P. N., Edwards-Jones, G., McKillen, J., McNair, I., McDonald, J. E. & Williams, A. P., 21 May 2013, In : Environmental Science and Technology. 47, 10, p. 5267–5275
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    Winterbourn, J. B., Clements, K., Malham, S., McDonald, J. & Jones, D. L., Jan 2013, 92 McLeod et al (eds.). Proc. 9th Int. Conf. Molluscan Shellfish Safety . p. 89-92
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    de Menezes, A. B., McDonald, J. E., Allison, H. E. & McCarthy, A. J., May 2012, In : Applied and Environmental Microbiology. 78, 9, p. 3495-9 5 p.
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    Rooks, D. J., McDonald, J. E. & McCarthy, A. J., 2012, In : Methods in Enzymology. 510, p. 375-94 20 p.
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    McDonald, J. E., Rooks, D. J. & McCarthy, A. J., 2012, In : Methods in Enzymology. 510, p. 349-74 26 p.
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    Ransom-Jones, E., Jones, D., McCarthy, A. J. & McDonald, J. E., Feb 2012, In : Microbial Ecology. 63, 2, p. 267-281
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    McDonald, J. E., Houghton, J. N., Rooks, D. J., Allison, H. E. & McCarthy, A. J., 1 Apr 2012, In : Environmental Microbiology. 14, 4, p. 1077-1087
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    Rooks, D. J., Smith, D. L., McDonald, J. E., Woodward, M. J., McCarthy, A. J. & Allison, H. E., 21 Jul 2010, In : Genes. 1, 2, p. 210-26 17 p.
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    McDonald, J. E., Allison, H. E. & McCarthy, A. J., 1 Feb 2010, In : Applied and Environmental Microbiology. 76, 4, p. 1301-1306
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    Rooks, D. J., Yan, Y., McDonald, J. E., Woodward, M. J., McCarthy, A. J. & Allison, H. E., 1 May 2010, In : Environmental Microbiology. 12, 5, p. 1194-1204
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    McDonald, J. E., Smith, D. L., Fogg, P. C., McCarthy, A. J. & Allison, H. E., 1 Apr 2010, In : Applied and Environmental Microbiology. 76, 7, p. 2360-2365
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    Edwards, J. L., Smith, D. L., Connolly, J., McDonald, J. E., Cox, M. J., Joint, I., Edwards, C. & McCarthy, A. J., 26 Oct 2010, In : Genes. 1, 3, p. 371-84 14 p.

  • McDonald, J. E., De Menezes, A. B., Allison, H. E. & McCarthy, A. J., 1 Aug 2009, In : Applied and Environmental Microbiology. 75, 15, p. 5148-5152
          
McDonald, J. E., Lockhart, R. J., Cox, M. J., Allison, H. E. & McCarthy, A. J., 1 May 2008, In : Environmental Microbiology. 10, 5, p. 2360-2365